James Adams is an Emerging Technologies Librarian at the University of Oklahoma in Norman, Oklahoma. His work at OU includes exploring new tools and teaching them to faculty, staff, and students in order to further research and instruction at the university.
Joshua Adelman is a computational biophysicist who uses modeling and simulation to understand how proteins move small molecules across the cell membrane. He is one of the core developers of the open source, Weighted Ensemble Simulation Toolkit (WESTPA) and spends most of his days building computational tools and crunching data for the good of science using python. He received his Ph.D. in Biophysics at the University of California, Berkeley and is currently a Research Assistant Professor in the Department of Biological Sciences at the University of Pittsburgh.
Aron Ahmadia works at the intersection of applied mathematics, software engineering, and application domains as diverse as adaptive optics, semiconductor lithography, and ice-sheet modeling. His focus is in the collaborative development of robust, reproducible, and scalable software tools for computational science.
Arfan Ahmed worked as a software developer for a number of years before completing a PhD in Medical Imaging writing software chemotherapy response prediction in breast cancer patients at the University of Hull, UK. As a postdoc he took on the post of Research Fellow automating disease detection in retinal images at the University of Aberdeen, Scotland. Currently he holds the post of Research Software engineer with the National Phenome Centre at Imperial College London.
Matthew Aiello-Lammens is an ecologists currently working as a postdoc at the University of Connecticut. His research interests include conservation biology, invasion biology, community ecology, and quantitative ecology. When not doing research, he spends time with his wife and daughter, preferably out in the woods.
Joshua Ainsley is a Data Scientist at Fino Consulting in NYC, where he applies statistical and machine learning approaches to projects in the education and energy sectors. Previously, he was a postdoc at Tufts University where he performed neuroscience research aimed at better understanding learning and memory using high throughput RNA sequencing. As someone who had to slowly gain programming skills to understand the large biological data sets generated by his research, he is excited to make the process a bit easier for others.
Inigo Aldazabal holds a PhD on Materials Physics and works in the San Sebastian Materials Physics Center – CFM(CSIC-UPV/EHU) as CIO and scientific computing specialist. There he tries to fill the gap between physicists and computer science, while managing a couple of HPC Clusters and parallelizing some codes in between.
Harriet Alexander is a PhD student in the MIT/Woods Hole Oceanographic Institution Joint Program in Biological Oceanography. Her work focuses on using high-throughput sequence data to better understanding the nutritional physiology and biogeochemical role of marine phytoplankton.
Russell Alleen-Willems holds an MA in applied archaeology and specializes in archiving and disseminating digital archaeological data and information. He is interested in helping people learn about archaeology, as well as how to use software, including databases, analytical programs, and games, to better analyze, present, share, and interpret archaeology in academia, cultural resource management, and public education.
James Allen holds a PhD in theoretical physics from Durham University where he modelled the dynamics of solitons on 4 dimension membranes in string theory. He is currently working as the co-founder of ShareLaTeX, which is an online collaborative LaTeX editor for scientists. He is interested in how technology can make scientists more efficient, and more productive.
Pete Alonzi is a native of Chicago, but now resident in Virginia. He was always interested in science so he wound up becoming a full time researcher in particle physics, and has recently transitioned to the field of data science.
Areej Alsheikh-Hussain is a PhD student at the University of Queensland working on vaccine target identification from the genomes of Streptococcal fish pathogens. Coming from two backgrounds, computer science and marine biology, she's interested in helping biologists utilize computing power to facilitate their research.
Carlos Anderson is a software developer at the University of Michigan Health System, where he collaborates with researchers in radiation therapy in order to improve cancer treatments. He obtained a Ph.D. in Evolutionary Biology (Michigan State University), an M.S. in Biology, and a B.S. in Computer Science (University of Central Florida).
Carrie Andrew was first an ecologist wandering midwestern US forests in search of fungi and plants. Following this she instructed at two universities in Chicago, Illinois. An ecological research postdoc at the University of Oslo in Norway further shifted her path, so that now Carrie spends her days working in R (still with fungal data).
Catalina Anghel is a postdoctoral fellow at the Ontario Institute for Cancer Research, working on computational deconvolution of tumour gene expression profiles. She received her Ph.D. in mathematics from the University of Toronto.
Markus Ankenbrand is a PhD student at the University of Würzburg. His main focus is the development of bioinformatical tools to facilitate ecological data analysis. He is enthusiastic about disseminating computational skills.
Mario Antonioletti works on optimising and parallelising codes for high performance computing systems. He has become involved in Software Carpentry through the UK's Software Sustainability Institute.
Jorge Aranda obtained his Ph.D. in Computer Science at the University of Toronto. He is now a postdoctoral researcher at the University of Victoria, where he studies coordination and communication in software teams.
Dhavide Aruliah is an associate professor at the University of Ontario Institute of Technology in Oshawa, Ontario. His research interests are in scientific computing, specifically in computational inverse problems, numerical linear algebra, and the numerical solution of PDEs.
Jaime Ashander is a population biologist who develops theory on the consequences of trait change for population dynamics, and methods to infer population processes from genomic and phenotypic time series. Currently a post-doc at UCLA, Jaime received his Ph.D. from the University of California - Davis in 2016.
is a PhD candidate and NSF Graduate Research Fellow in the Physics
Department at Yale University. She uses numerical simulations to
study clusters of galaxies. In particular, she is interested in
using simulations to interpret observations and to model
astrophysical processes. Camille is also active in a number of
outreach activities and is committed to promoting diversity in
STEM fields. She's been an instructor with Software Carpentry
since 2013, and is excited to share programming skills with an
increasingly wider audience.
Liaison: Diversity Initiatives
Jon Badalamenti is a postdoctoral microbiologist at the University of Minnesota. Jon’s research uses genomics and bioinformatics approaches to study how microbes respire metals deep within the earth.
Sung Eun Bae works at New Zealand eScience Infrastructure (NeSI) as a supercomputing consultant, supporting NZ researchers to utilize HPC resources to challenge bigger science. He also serves as NeSI's education and training coordinator organizing/delivering scientific programming workshops across NZ. He received his Ph.D in algorithm and data structure at the University of Canterbury. He is a real "carpenter" busy with his woodwork projects during the weekends.
Christie Bahlai is a Research Associate in the Department of Entomology at Michigan State University in East Lansing, Michigan, where she studies long term and broad scale population and community ecology of insects. She's interested in collaboratively generated data and reproducible research and maintains a blog called Practical Data Management for Bug Counters. She obtained her PhD in Environmental Biology from the University of Guelph.
Alex Bajcz is a PhD candidate at the University of Maine, where he studies reproductive trade-offs in plants. His research interests include plant ecology and evolutionary biology, applied statistics, and simulation modeling, but he is looking to expand into science education research and the synthesis of ecological theory as well. He is also moonlights as a crossword constructor, among other things; he has had puzzles published by the New York Times and Los Angeles Times.
Thomas Ballinger worked for several years at medical imaging lab at Brigham and Women's Hospital, then left to work as a facilitator at the Recurse Center, a programming workshop for experienced programmers. After four years of helping participants become better programmers (and produce a lot of BitTorrent clients as a side effect) he's now prototyping live coding environments in the browser and learning about programming pedagogy.
Asher Baltzell is a graduate student at the University of Arizona interested in the intersection of science, data, and computers. He works with a number of other scientists in diverse fields ranging from genomics to astronomy. Asher is particularly interested in interactive data visualization, distributed computing, and web-based scientific analysis platforms.
Piotr Banaszkiewicz studies automatics control and robotics at AGH-UST in Kraków, Poland. Student by day, programmer by night, he loves Python. Even though half of his curriculum is Matlab-based.
Pauline Barmby is an associate professor in the Department of Physics & Astronomy at Western University in London, Canada. She studies star formation and star clusters in nearby galaxies with as many telescopes as she can get her hands on, and teaches introductory electromagnetism, data analysis, and even astrophysics.
Diego Barneche is a Postdoctoral Research Fellow at Monash University who is passionate about global patterns of diversity, macroevolution, and statistical and mathematical modelling. He loves learning and teaching programming skills for science.
Ewan Barr is a postdoctoral researcher at Swinburne University of Technology in Melbourne. His research revolve around radio astronomy, pulsar science, and high-performance supercomputing, with a focus on adapting complex radio astronomy algorithms to run on graphics processors. This has led him to become heavily involved in the design and development of the next-generation Square Kilometre Array (SKA) radio telescope.
Christian Barra is a student of Statistics and BigData in the University of Padua. He is interested in Python, Statistics, Machine Learning, Education and IoT devices. He is a member of of the EuroPython Society Board and Python Italia APS, since 2015 he co-organizes EuroPython.
Radovan Bast is a senior engineer at the High Performance Computing Group at UiT The Arctic University of Norway. His work evolves around developing and supporting quantum chemistry software and software for the simulation of marine ecosystem components. He is interested in using, sharing, and teaching modern collaborative development tools and work-flows.
Berenice Batut is a post-doctoral researcher in bioinformatics. She is currently working on analyses of gut microbiota data in Clermont-Ferrand, France. During her PhD in computational biology and bioinformatics, she studied reductive genome evolution using in silico experimental evolution and comparative genomics.
Dana Bauer is a developer and open source community advocate at Rackspace. Her team sponsors OSS projects and open communities, teaches workshops and gives talks to a wide range of technical audiences, and builds tools to help developers use the open cloud. Dana is also an organizer with the Philadelphia Python User Group, an instructor with Girl Develop It, and a passionate supporter of diverse technical communities. She has a background in geography, science (chemistry and math), and science writing.
Philipp Bayer is a PhD student at the School of Agriculture and Food Sciences, University of Queensland. He's working on the improvement of plant genomes and is interested in open code and open science. He is one of the co-founders of openSNP.org.
Rob Beagrie is a PhD student at Imperial College in London. He works on regulatory DNA (e.g. enhancers) in mammalian genomes, and is particularly interested in how the physical contacts they make with distant genomic regions may regulate the expression of genes.
Erin Becker studied microbial genomics at UC Davis where she also did a postdoc in Biology Education Research. She has experience developing and implementing practice-based instructional training programs as well as building community for supporting instructional innovation.
David Beitey works closely with researchers and research groups in improving their digital skill and abilities. He is extremely passionate about open source technologies, and is a maintainer of and an active contributor to many projects, such as the eSpaces platform for cross-instituional collaboration. His current role is part of the eResearch Centre at James Cook University, Australia.
Mahdi Belcaid obtained his undergraduate degree from the University of Quebec at Montreal and his Ph.D in Computer Science from the University of Hawaii At Manoa. He currently works as a Bioinformatics Core leader and an assistant research professor at the Hawaii Institute of Marine Biology. He teaches computational skills and bioinformatics to graduate students and his research focuses on algorithms for analyzing high-throughput biological data in various subfields of biology.
Evgenij Belikov is a PhD student in Computing Science at Heriot-Watt University in Edinburgh, working in the area of Parallel Functional Programming. In particular, he investigates the effectiveness and scalability of adaptive run-time system policies such as load balancing, scheduling and granularity control to achieve performance portability across diverse parallel architectures.
Jason Bell is the Senior Research Technologies Officer at CQUniversity Australia and eResearch Analyst for the Queensland Cyber Infrastructure Foundation (QCIF), where his primary focus is to assist CQUniversity researchers achieve better research outcomes through the use of technology. Jason holds a Bachelor of Information Technology (with honours) from CQUniversity Australia.
Nichole Bennett is a Ph.D. candidate in Ecology, Evolution, and Behavior at The University of Texas at Austin, where she is studying climate change impacts by investigating local adaptation and thermal biology in a butterfly-plant system. During fall semesters, she organizes a weekly informal Introduction to Biological Statistics Course. She also hosts a weekly science radio show They Blinded Me With Science on 91.7FM KVRX Austin and coordinates Science Under the Stars, a free, outdoor lecture series that helps graduate students communicate their research to the public.
Jared Berghold works for Intersect Australia, a not-for-profit organisation helping researchers at Australian universities achieve research impact through technology. Previously, Jared spent four years at the UNSW research centre, iCinema, developing software for large-scale immersive and interactive art installations.
Casey Bergman is an evolutionary informatician at the University of Georgia, where he is an associate professor in the Institute of Bioinformatics and Department of Genetics. His research uses diverse computational methods to better understand the structure, function, and evolution of genomes. An ex-expat, he spent over ten years in the UK before returning to the US in 2016 to dehumidify.
Joey Bernard works with ACENET-Compute Canada, helping research groups with their computational needs. He also writes a monthly column in Linux Journal on scientific software and a monthly column in Linux User and Developer on writing Python programs on the Raspberry Pi. He recently finished writing the book Python Recipes for the publisher APress.
Michelle Berry is a researcher at University of Michigan utilizing genomics data to study the microbial ecology of harmful algal blooms on Lake Erie. She loves using R to tackle microbiome datasets and is passionate about sharing her code and creating reproducible research. She has a B.A. in Human Biology and an M.S. in Earth Systems from Stanford University.
Marius Bjørnstad is an engineer at the Norweigan Sequencing Centre in Oslo, which does DNA sequencing for researchers in Norway. He deals with system administration, a lot of programming, and some data analysis. Marius has previously studied high energy physics, and worked on data analysis at the LHCb experiment at CERN.
Lukas Blakk is a tech generalist with a degree in Software Development from Seneca College in Toronto. She's the founder of the Ascend Project which aims to help marginalized adults gain access to tech skills through a barrier-removing accelerator program in open source contribution. Lukas has big plans for creating software companies that are worker cooperatives and designed from the start with diversity and inclusiveness in their DNA.
John Blischak is a graduate student at the University of Chicago. His research focuses on the transcriptional response of human macrophages to infection by Mycobacterium tuberculosis. He greatly benefited from attending a Software Carpentry bootcamp and enjoys passing along these useful skills to other scientists.
Maxime Boissonneault earned his Ph. D. in Quantum Physics at Université of Sherbrooke and has been working as a high performance computing specialist for Calcul Québec at Université Laval since 2013. While he has no academic background in computing, he has learned numerous programming languages ever since he was 12, going from Java to C++ through Python and C#. When he is not talking science, computers or social issues, he enjoys playing World of Warcraft and going on cruises around the world.
Steve Bond is a postdoctoral fellow at the National Human Genome Research Institute. In his previous life he was an old-school bench biologist, slinging liquid by the microliter, but these days he bangs on a keyboard hoping some biology will fall out. Steve's primary research focus is the molecular evolution of gene families, and he is also the lead developer of BuddySuite, a command-line toolkit for manipulating biological data files.
Jessica Bonnie is a Data Specialist at the University of Virginia Center for Public Health Genomics where she works with large-scale genomic data primarily focused in autoimmune disease research. She is fascinated by automation and enjoys finding ways to make things work.
Madeleine Bonsma is a graduate student in the Department of Physics at the University of Toronto, where she studies bacteria-virus interactions and a bacterial adaptive immune system called CRISPR. She loves peer-led learning, teaching programming and undergraduates, and Python. When not frowning at her computer screen, she enjoys running, novels, and the great outdoors.
James Boocock is a Masters candidate in Genetics at the University of Otago. He investigates genetic variation, in particular deletions and insertions, focusing on questions of relevance to the medical and agricultural sectors. Having begun his studies with BSc in computer science, most of his research involves programming. He hopes Software Carpentry will enable him to share his passion and programming skills with a wide audience.
Azalee Bostroem is pursing a PhD in Physics at UC Davis. When she is not in class or doing homework, she studies supernovae and massive stars. Before returning to school, Azalee was a Senior Research and Instrument Analyst at the Space Telescope Science Institute, where she supervised the development of the calibration pipelines of the two spectrographs on the Hubble Space Telescope (the Cosmic Origins Spectrograph and Space Telescope Imaging Spectrograph).
earned his Ph.D. in Chemistry from the University of Michigan in
2011. From running simulations and writing software to automate
data collection and analysis, he has since contributed to a range
of projects in image processing, machine learning, and the DARPA
AVM program. He is passionate about open science, open data, and
reproducible research, as well as good software design and
Daina Bouquin is the Assistant Head Librarian of the Harvard-Smithsonian Center for Astrophysics. At the CfA, Daina works to foster open science, professional development, and technical innovation to support the astronomy and astrophysics communities. She is committed to lowering social and technical barriers that impact people's ability create and share new knowledge.
Ross Bowman is a Computer Specialist for the Oklahoma State University Library and is responsible for research and development within the Systems department. He is also pursuing a Masters of Library and Information Studies from the University of Oklahoma. Ross' interests and work exists at the crossroads of libraries and technology.
Amy Boyle is a software developer at Washington State University Vancouver, where she writes code for auditory neuroscience research. She designs and implements programs for data acquisition, analysis and visualization. She is also an organizer for the Portland Pyladies chapter.
Erik Bray is a research engineer at Laboratoire de Recherche en Informatique
where he works on the OpenDreamKit project, and was formerly a
software engineer at Space Telescope Science Institute. His software experience ranges from web
development to kernel hacking, and in his "free" time he studies particle physics.
Maintainer: Windows Installer
Lisa Breckels is a computational biologist at the University of Cambridge, UK. Her work focuses on the development of bioinformatics and statistical tools, that utilise pattern recognition and machine learning methods to enable robust analysis of high-throughput quantitative proteomics data. She is a contributor to the Bioconductor project through several R packages. Lisa has a PhD is Computational Chemistry/Biology and BSc in Mathematics.
Lindsay Brin is an ecosystem ecologist who uses biogeochemical and microbial ecological tools to understand the effects of environmental change, and is currently working as a postdoc at the University of New Brunswick. She loves playing with data and teaching the skills necessary to do so more efficiently and effectively. When she's not in the field or immersed in analysis, she can be found trail running, doing yoga, and playing drums in a rock band.
Karl Broman is Professor in the Department of Biostatistics and Medical Informatics at the University of Wisconsin-Madison. An applied statistician focusing on problems in genetics and genomics, he enjoys programmming in R, Ruby, C/C++, and CoffeeScript, and is an enthusiastic advocate for open and reproducible science as well as GNU Make.
Amy Brown is a freelance science editor and self-publishing consultant, raises two girls, and sings as often as possible.
Kyler Brown is a PhD student at the University of Chicago. He studies how the brains of songbirds control vocal muscles and how vocal muscles produce song. Kyler was a student in a Software Carpentry Workshop in 2012, and now uses Python, Git and the Unix shell to run experiments and analyze data.
Dana Brunson is assistant vice president of research cyberinfrastructure and director of the high performance computing center at Oklahoma State University. She is an passionate advocate for training researchers in diverse disciplines to use computational tools in their work.
Jennifer Bryan is an Associate Professor in the Statistics Department and the Michael Smith Laboratories at the University of British Columbia in Vancouver. She's a biostatistician specialized in genomics and takes a special interest and delight in data analysis and statistical computing. Jenny is a former member of the Software Carpentry Foundation's Steering Committee.
Jarek Bryk is a lecturer in molecular biology at the University of Huddersfield in the north of England, where he is trying to get his head around analysing DNA to learn about evolutionary processes in natural populations of small furry animals. As a beginner in bioinformatics he often finds himself learning and teaching it at the same time...
Zachary Brym is a curriculum developer and website designer for the Data Carpentry for Biologists semester-long course. He earned his PhD in ecology in the Department of Biology at Utah State University where he studied tree fruit physiology and orchard management using data-driven models of tree growth and fruit production.
William Reinar is a PhD student at Centre for Ecological and Evolutionary Synthesis (CEES) in the Institute of Biosciences, University of Oslo. He currently works within evolutionary genomics. His focus is the genomic basis of adaptation, which requires combining high-throughput sequencing data with environmental data.
Abigail Cabunoc Mayes is the lead developer
for the Mozilla Science
Lab, an open science initiative of the Mozilla Foundation.
Prior to joining Mozilla, Abby worked as a software developer at
the Ontario Institute for Cancer Research where she was the
technical lead on the WormBase website.
Maintainer: Using Databases and SQL
Patrick Calhoun is a System Developer and Administrator for the OU Supercomputing Center for Education and Research. He received his Bachelor of Science degree in Computer Engineering from the University of Oklahoma in 2006. Patrick's interests include automating system administration tasks, developing open-source software, and gardening.
Jared Camins-Esakov is a programmer and bibliographer, coding catalogues and occasionally cataloguing source code. He currently works as a front-end developer in the healthcare sector; when not programming, he spends his time baking and ballroom dancing.
After 13 years of slogging in the software industry trenches, Rosangela Canino-Koning returned to university to pursue a PhD in Computer Science and Evolutionary Biology at Michigan State University. In her copious spare time, she reads, hikes, travels, and hacks on open source software.
Chris Cannam is a software developer with the Sound Software project at Queen Mary, University of London. He has had extensive experience as a commercial software developer and on numerous open source applications, particularly in the music and audio fields.
Gerard Capes was a researcher in
Atmospheric Science, and learnt to program through analysis of
field data and simulations of laboratory experiments. Now a
Research Software Engineer, he provides technical support to other
researchers at the University Of Manchester.
Maintainer: Automation and Make
Greg Caporaso is an assistant professor of Biologial Sciences at Northern Arizona University, and an open source bioinformatics software developer. Greg leads development of the scikit-bio and QIIME bioinformatics software packages, and is the primary author of An Introduction to Applied Bioinformatics, an open source, interactive bioinformatics text. For more details, see the Caporaso Lab website.
Daren Card is a PhD student in Quantitative Biology at the University of Texas at Arlington. His work focuses on using large genomic datasets to understand vertebrate population biology, genetics, and evolution.
Lindsay Carr received a BS in Biological Systems Engineering from Virginia Tech in May 2015. She now works as a Data Scientist at the US Geological Survey (USGS) Office of Water Information. Her primary role is to create tools in R for accessing and using USGS water data in reproducible workflows, and introducing USGS scientists to R and the tools.
Ian Carroll is a Data Scientist at the National Socio-Environmental Synthesis Center (SESYNC) in Annapolis, where he supports science teams doing computational synthesis of socio-environmental data and teaches introductory data skills workshops. He is a theoretical ecologist by training and has enjoyed doing research at the University of California Santa Barbara, the Woods Hole Oceanographic Institute, and Georgetown University.
Reed Cartwright is a geneticist who develops computational and statistical methodologies to explore evolutionary questions. Much of his research focuses on mutation — the raw material of evolution — and its impact on biological systems.
Tim Cerino is the founder of Avery Analytics, a consulting firm focused on data science applications and education for economics, financial institutions, and enterprise risk management. He has worked in the capital markets industry and as an economic researcher. He has an MBA in Finance and an MA in Statistics and Data Science from Columbia University.
Cliburn Chan is a computational immunologist at Duke University whose research interests center around statistical analysis of immunological data and building dynamical systems models of the immune response. Originally trained as a medical doctor, he caught the math bug and eventually completed a PhD in nonlinear dynamics at University College London. He teaches how to integrate biomedical knowledge with the statistical perspective in the Masters program in Biostatistics and is currently developing a new graduate course in computational statistics that will be introduced in Spring 2015.
Amanda Charbonneau is a Genetics grad student at Michigan State University. Her PhD project uses genomics to look for genetic differences between weedy plants and their presumed ancestors, to see what genes are important in becoming invasive. When she isn't working, you can find her teaching high school students science or wrangling birds of prey, generally not at the same time.
John Chase is a research software engineer at Northern Arizona University. John's research is focused on microbial ecology and the human microbiome. He is also a contributor to scikit-bio, an open source bioinformatics software package, and to An Introduction to Bioinformatics, an open source bioinformatics textbook.
Kyriakos Chatzidimitriou is a post-doctoral research associate at the Aristotle University of Thessaloniki (AUTH) working on EU research and innovation projects. His research interests are in the areas of machine learning for and with software engineering, digital analytics and building autonomous agents for real world domains as for example for trading environments and for the semantic web. He is also an adjunct instructor in the Interdepartmental and Interdisciplinary Postgraduate Programme on Advanced Computer and Communication Systems at AUTH.
Daniel Chen (@chendaniely)
is a doctoral student in Genetics, Bioinformatics, and Computational Biology
and works in the
Social and Decision Analytics Laboratory
under the Biocomplexity Institute of Virginia Tech.
He received his MPH at the
Mailman School of Public Health in Epidemiology and
is interested in integrating hospital data in order to perform predictive health analytics
and build clinical support tools for clinicians.
Maintainer: Programming with R
Marco Chiapello obtained a PhD in Biotechnology working on fungal-metal interaction using a proteomics approach. He now works as a Data Research Technician at the University of Cambridge Center for Proteomics, where he focuses on proteomics data analysis using R.
Chelsea Chisholm is a Ph.D. student with the Center for Macroecology, Evolution and Climate in Copenhagen, Denmark. Her research focuses on understanding the assembly of ecological communities, mainly forests, from local to macro scales. On top of teaching introductory R workshops and statistics for biologists, she is an active supporter of open science and diversity in STEM.
Jinlung Choi is a postdoctoral research associate at Iowa Sate University. His research involved building database of reference soil, bacterial community change in the soil with and without fertilizer, and also bacterial community change in the fresh water in the lake to determine possible agal bloom contributor.
Shreyas Cholia is the deputy group leader of the Data and Analytics Services Group at the
NERSC facility of Lawrence Berkeley National Laboratory.
He leads the science gateway, web and workflow related efforts at NERSC,
and is particularly interested in how web APIs and tools can facilitate data-centric computing.
He studied Computer Science and Cognitive Sciences at Rice University.
Erica Christensen is a PhD student in Wildlife Ecology and Conservation at the University of Florida, with an MS in Environmental Science and a BA in Mathematics. Her current work involves describing long-term dynamics in ecological time series, particularly dynamics related to extreme events and/or rapid regime shifts.
Garret Christensen is an economist with the Berkeley Initiative for Transparency in the Social Sciences and the Berkeley Institute for Data Science. He has conducted public health research in Kenya for Emory University and taught economics at Swarthmore College. He has also run more than 50 ultramarathons and walked from border to border across the entire United States four complete times.
Adina Chuang Howe is an assistant professor in the Department of Agricultural and Biosystems Engineering at Iowa State University, where she uses skills learned from Software Carpentry to train students and study microbial communities in the environment. Adina is a former member of the Steering Committee.
Chue Hong is Director of
the Software Sustainability
Institute, and is based at the University of Edinburgh. His
research interests are in community engagement and development,
software sustainability, and the integration and analysis of
Kally Chung is a graduate student at State University of Campinas (Brazil) working with Integer Programming in the Supply Chain field. She loves to learn and to share what she learns, specially subjects related to Math and Programming.
Kathy Chung is a generalist with a background in civil engineering, English, and drama. She received her PhD on the drama of Canadian playwright Sharon Pollock from the University of Toronto. She has worked as a water resource engineer (briefly, long ago), learning skills counsellor, writing instructor, and stage manager. She is interested in bringing useful computing tools to more people in the social sciences and humanities.
Richard Clare is a senior lecturer in the Department of Electrical and Computer Engineering at the University of Canterbury, New Zealand. He has worked in scientific programming for the fields of adaptive optics, biomedical imaging and earthquake engineering, in New Zealand, Germany and the United States.
Sarah Clayton is a Digital Scholarship Specialist at the University of Oklahoma Libraries, where she helps faculty and students explore tools to perform and showcase their research more effectively. She is especially interested in incorporating digital scholarship techniques into humanities and social science courses.
Sophie Clayton is an oceanographer at the University of Washington who explores the ways in which ocean physics shape plankton communities. She received her PhD in Oceanography from the MIT/WHOI Joint Program, and wishes that she had taken a Software Carpentry workshop before accumulating endless folders of creatively-titled MATLAB scripts.
Marek Cmero is a PhD student at the University of Melbourne working on prostate cancer research for the Department of Surgery. His background is in Computer Science and Bioinformatics, and currently he is working on developing novel algorithms and analysing cancer data sets using python and R. His research interests include tumour heterogeneity/evolution and genomic rearrangements.
Warren Code is Associate Director of the Science Centre for Learning and Teaching in the Faculty of Science at the University of British Columbia, with a key responsibility being coordination and leadership of the Carl Wieman Science Education Initiative, whose mission is to improve science education at UBC and disseminating results for others. He has built on his PhD in Mathematics and the teaching from that time to pursue undergraduate math and science education research and its implications for teaching and learning.
Luis Pedro Coelho is a postdoc in computational biology at the European Molecular Biology Laboratory (EMBL). He is working on understanding microbial communities using metagenomics and bioimage analysis. Luis divides his time between Heidelberg and Luxembourg.
Ruth Collings is a MLIS graduate interested in web design, digital privacy and security issues, and accessibility and universal design in libraries.
Arliss Collins is the training coordinator for the Mozilla Science Lab, an open science initiative of the Mozilla Foundation. She was educated as a geophysical engineer, re-trained as a business/systems analyst, and now works on educational activities and trainings for Mozilla. She is a Canadian mother of two with a long-standing passion for curling.
Matthew J. Collins is a senior systems programmer with the Advanced Computing and Information Systems lab at the University of Florida. His main project is managing the hardware infrastructure and developer outreach for iDigBio, a national effort to digitize natural history collections in the US. In his spare time he advises the Data Science and Informatics student organization.
Vincenza Colonna works in human evolutionary genomics and her main research interests are natural selection and consanguineous populations. Her research focuses on causes and consequences of genetic diversity and natural selection. She is group leader at the National Research Council in Napoli, Italy where she is also leading a local project for training in Bioinformatics. She graduated from University of Napoli Federico II (Italy) and did postdoctoral work at University of Ferrara (Italy) and at the Wellcome Trust Sanger Institute (UK). She was lectures in Genetics and Bioinformatics at the University of Ferrara (Italy).
Michael Connell, Ed.D., holds a Master's degree in Computer Science from the Massachusetts Institute of Technology and a Doctorate in Education from Harvard University. His research has centered mostly on applied cognitive science and evidence-based educational technology design, and for over a decade he has consulted to startups, non-profits, for-profit corporations, and governmental organizations in the areas of instructional design, assessment design, educational technology design, and data science. He is currently Vice President of Training at Enthought, Inc.
Lindsay Coome is a PhD student in the Department of Psychology at the University of Toronto where she studies the evolutionary and biological basis of human sexual orientation. She received her BA from Western University and her MA from the University of Toronto. She enjoys teaching R and statistics, and in her spare time she can be found enjoying music and nature.
Victor Cordero is a full-time performance test engineer on the iPlant Collaborative Quality Assurance team. His background ranges from Assembly language coding to Python, telecommunications, networking and Project Management.
John Corless is an industrial physicist and engineering manager who works on the development of optical systems. He has a PhD in Optics from the University of Rochester and an MBA from the University of San Francisco.
Thomas Coudrat is a PhD candidate at the Monash Institute of Pharmaceutical Sciences in Melbourne, Australia. He is involved in drug discovery programs where he applies molecular modeling simulations to predict protein structure, dynamics and interaction with potential drugs. His time is split between method development, method application and research community engagement.
Grace Cox is a postdoc at the University of Liverpool and visiting researcher at the University of Leeds. She is a geophysicist by training, and is interested in geomagnetism and the dynamics of Earth's outer core. Her research focusses on how fluid motions in the core manifest in ground-based and satellite-based observations of Earth's magnetic field.
Logan Cox is a software developer for Repository Services at the University of Oklahoma Libraries. His professional focus is building tools for wrangling content, and he loves working at the intersection between books and the modern web.
Stefano Cozzini, based in Trieste, is a development scientist who coordinates HPC/Cloud activities of the CNR/IOM Democritos research Center. He is now also coordinator of the Master's in High Performance Computing, and is working hard on his small start-up company, where he tries to promote HPC to an industrial audience. He enjoy teaching IT and HPC topics all around the world.
Karen Cranston is the Training Coordinator and Informatics Project Manager at the National Evolutionary Synthesis Center (NESCent). She is an evolutionary biologist interested in phylogenetic methods, phyloinformatics and an evangelist for data sharing and data interoperability in biology. Karen is the lead PI of Open Tree of Life, an NSF-funded project to synthesize published evolutionary trees.
Nic Crouch is a consultant with Deloitte Enterprise Information Management in Melbourne. He works on business intelligence and big data analysis for his clients. In his spare time and at work, he is a Python programmer and he's previously presented about graph databases at PyCon Australia.
Crouch is a software architect at
the Software Sustainability
Institute, and is based at
the University of
Southampton. He assists researchers and their communities by
consulting on software that is integral to their research.
Remi Daigle is a marine ecologist interested in larval ecology, ocean health, and the design of marine protected areas. He is currently a postdoc at the University of Toronto and McGill focusing on the optimization of networks of marine protected areas for sea cucumbers on Canada's west coast using biophysical larval dispersal modelling and MARXAN. He is also involved in developing the Ocean Health Index in Canada.
Ryan Dale was trained as a marine benthic ecologist (MS and PhD), but is now a bioinformatician at NIH. He writes code and develops tools to study how cells turn genes on and off by manipulating the three-dimensional structure of DNA and chromatin.
is a bioinformatician and PhD candidate at the University of
Melbourne and the Murdoch Children's Research Institute. Harriet
has a BA (Psychology), a BSc (Genetics and Biochemistry) and an
MSc (Bioinformatics) from the University of Melbourne. Harriet is
committed to serving the bioinformatics community through
organisations such as COMBINE. She has substantial experience in
teaching both the undergraduate and graduate level with a
particular focus on skills workshops in such areas as genomics,
Python, R, Unix and Git version control.
Maintainer: Programming with R
Emily Davenport is a postdoc in the department of Molecular Biology and Genetics at Cornell University. Her research interests took her from a purely wet-lab biology background to dry-lab, computational territory while studying the human microbiome and genomics.
Rob Davey is a group leader at the Genome Analysis Centre (TGAC) in Norwich, UK. He has a BSc in Microbiology and a PhD in Bioinformatics, and enjoys the challenges of solving problems through programming and algorithms. He is a firm open source, open data and open science advocate, with a deep desire to help train researchers in best practice for bioinformatics and software development.
Matt Davis is a scientific software engineer at Autodesk. His interests include scientific Python, web applications, computing education, diversity in tech, and exploring beautiful California. Matt is a former Vice-Chair of the Software Carpentry Foundation's Steering Committee.
is the Training Coordinator for Computational Science and Engineering
at the University of Illinois at Urbana-Champaign,
where he conducts training across a range of traditional engineering software programs and packages.
His professional interests include engineering pedagogy,
the foundations of computing,
and the history of science.
Christof De Bo works at the BioInformatics Training and Services (BITS) facility of VIB, a biotechnology research institute in Flanders, Belgium. There he holds the position of ELN Application Scientist and Research Informatics Scientist. He obtained his Bachelor degree in Bioinformatics at the University College West Flanders and performed his internship at the University College Cork, Ireland. In his spare time he plays badminton and enjoys cycling.
Lachlan Deer is a PhD Candidate in Economics at the University of Zurich. His research focuses on consumer decision making and firm's strategic interactions, and is currently studying the impact of social media platforms influences consumer purchasing patterns and firm's advertising strategies. He is interested in scientific computing and is a co-developer of a course on scientific computing for researchers in economics and finance; and is passionate about improving the uptake of reproducible research practices among business, economics and finance academics and professionals.
Raffaella Demichelis is a chemist working in computational materials science and geochemistry. Her research is focused on developing models able to describe and predict the atomic structure, the physical properties, and the surface chemistry of minerals, biominerals, and other materials. She joined the Software Carpentry team to help people acquire basic computing skills that will make their work easier, more accessible, less lonely, and, why not, that will eventually make them having more fun in doing it.
Tim Dennis is the Data Librarian at the UCSD Library where he provides data services, including instruction, one-on-one consulting, and community building. He is a regular user of R, Python, SQL and command-line tools and has extensive experience helping researchers and students with these tools.
James Derrick is a 2nd year PhD student in the Earth Science and Engineering department at Imperial studying the shock physics of granular materials using mesoscale modelling techniques. He is one of the developers of the shock physics code iSALE and predominantly codes in Fortran or Python.
James Desjardins is a high performance computing analyst for SHARCNet (of Compute Ontario & Compute Canada). With an MA in Behavioral Neuroscience he worked for over a decade as the electophysiolography technologist at the Brock University Lifespan Development Research Centre. Although most of his early career was spent developing neuroscience analyses in Matlab/Octave, his academic trajectory began as a painter with a BA in Visual Arts.
is a Research Computing Engineer at McGill University in
the Computational BRain Anatomy
Laboratory. He develops software for analyzing MRI data and
teaches open science to researchers and graduate students.
Maintainer: The Unix Shell
Upendra Kumar Devisetty is a Science Informatician working at CyVerse, with a Ph.D. in Plant Molecular Biology and Biotechnology. He has broad bioinformatics experience with particular expertise in Next Generation Sequencing and RNA Sequencing. At CyVerse he focuses on building tools and apps, providing Extended Collaborative Support (ECS), and helping teach new users how to use components of the CyVerse infrastructure.
Catherine Devlin After a misspent youth studying chemical engineering, Catherine accidentally became a database administrator in 1999 and a Python programmer in 2004. She is the founding chair of PyOhio and president of Dayton's Dyanamic Languages group. She enjoys human languages, history, horses, working at 18F, and amateur forestry.
Andrés Díaz-Gil has a PhD in theoretical physics specialized in lattice gauge theories, and is currently dedicated to scientific computing. He is nowadays the CIO of the Institute for Theoretical Physics of the Spanish Research Council in Madrid. His interests include high performance computing, the application of big data to theoretical physics and software tools for better research.
Matt Dickenson is interested in bringing contemporary best practices and tools from software engineering to researchers in a variety of fields. He has taught programming courses at his alma mater, Duke University, as well as the University of Houston and Washington University. His work focuses on machine learning and computer vision.
Ross Dickson has a Ph.D. in computational chemistry, and has been back and forth between academia and the software development industry a few times over the years. Now he helps profs, post-docs, and students in Atlantic Canada solve research problems involving high-performance computers.
John Didion studies the epigenomics of type 2 diabetes as a postdoctoral fellow in the laboratory of Dr. Francis Collins at the National Human Genome Research Institute.
Joanna Diong is a physiotherapist by training who learned programming initially for statistics, then to handle electromyography and joint motion data in human movement research. She uses Python and Git, and is passionate about using scientific computing in research as part of good science. She co-authors the blog Scientifically Sound to help others do the same.
Phillip Doehle is a mathematics graduate student at Oklahoma State University. He is interested in numerical analysis and the development of algorithms for high performance computing, and is also an open-source software enthusiast.
Emily Dolson is a PhD student at Michigan State University, where she studies a combination of computer science, evolutionary biology, and ecology. Having been lured over to computer science from pure biology, she feels strongly about the importance of making training in computational skills more accessible to scientists.
David Dotson specializes in molecular dynamics simulation of biomolecules, which allow us to probe the mechanisms of protein function in atomic detail. He is a Python enthusiast, Linux nerd, and an advocate for the use of open source software in science. He is currently a Ph.D. student in the Center for Biological Physics at Arizona State University.
Kim Doyle is an early career research at the University of Melbourne in Media and Communication where she is completing her PhD on Data Journalism. Her interests include data mining and social media. She participated in THATcamp2014 and was a helper for the nltk steam at the first Research Bazar conference in 2015. She is also the graduate student representative for the Digital Humanities Incubator at Melbourne University.
Alastair Droop is a bioinformatician and computational biologist working at the University of Leeds. His research involves the analysis of large next-generation datasets for cancer research. He works for the Leeds MRC Medical Bioinformatics Centre, and has expertise in large data analysis, R and Python.
Laurent Duchesne is a software developer at Calcul Québec, Université Laval. He earned a B.Sc. in Computer Science in 2004 and has worked for a variety of software-related companies using Java, C, C++ and Python. He has been in high performance computing since 2010, training researchers and helping them write and maintain optimal code. This involves reviewing and implementing algorithms for parallelization in a wide-range of domains such as biology and geographic information science (GIS).
is the Executive Director of the Software Carpentry Foundation. He has had various career trajectories including, long-term strategic planning, landscape ecology research, monitoring of global agricultural production and collaborating on the computational workflows of scientists. Now he helps scientists to more effective in their data-driven analysis by spreading the practices of Software Carpentry to organizations around the world.
Meghan Duffy is an ecologist at the University of Michigan, where she is an Associate Professor in the Department of Ecology and Evolutionary Biology. Her research focuses on disease ecology and aquatic ecology. She also writes for the Dynamic Ecology blog.
Susan Duncan is a PhD student in Cognitive Neuroscience at UC Irvine and an NYC expat. Her research interests include figuring out how the brain does language and recovers from stroke. She wishes she had found Software Carpentry earlier in her research career and is glad to have the opportunity to ease the way for others.
Stevan Earl is the Information Manager for the Central–Arizona Phoenix Long-Term Ecological Research project and the Julie Ann Wrigley Global Institute of Sustainability at Arizona State University. He has a background in ecosystem ecology, but now focuses primarily on information management. In addition to managing research data, Stevan works with students and investigators to promote sound data management.
Dirk Eddelbuettel has been contributing to Debian as a developer / maintainer since 1995. Most of his open source focus centers around R to which he has been contributing since the late 1990s. He works in Chicago as a senior quantitative analyst, and holds a PhD in Mathematical Economics from EHESS.
Justin Ely is a Senior Research and Instrument Analyst at the Space Telescope Science Institute. His main activity there is to support the science operations of the Hubble Space Telescope by leading the calibration pipeline efforts for the Cosmic Origins Spectrograph and the Space Telescope Imaging Spectrograph. Day-to-day you'll find him coding Python, C++, and SQL to improve the performance of HST instruments or to study Active Galactic Nuclei and time-varability in UV spectra.
is an associate professor at Saint Étienne University
(France), working in the Machine Learning group of laboratoire
Hubert Curien. His research currently focuses on probabilistic
modeling and machine learning, but he has interests in various
other fields including computer vision, software architecture,
neuro-sciences, epidemiology and artificial intelligence. After
spending some time individually promoting best practices and Git,
mainly to his colleagues, he finally decided to join the Software
Aaron Erlich is a Ph.D. candidate in Political Science at the University of Washington. He studies how individuals in developing countries understand political uncertainty. Not coming from a programing background, he works to understand the challenges those in the (social) sciences have in learning to program. He has taught courses in both R and Python.
Oier Echaniz Beneitez is a PhD student doing software engineering and data analysis in the Computational Intelligent Group of the University of the Basque Country (UPV/EHU), Spain, where he develops tools for abdomo-pelvic CT & MR image processing and diagnosis. He is a co-founder and the actual chair of ACPySS, a local Basque non-profit free software organization. He has been on the board of the EuroPython Society since 2015 and co-organized EuroPython 2015 and EuroPython 2016.
Andy Evans is a lecturer at the University of Leeds, UK. He works in a variety of fields from Folklore to Glaciology, but most of his programming is in agent based modelling of socio-economics, along with Geographical Information Systems. He started coding back when programs came on paper tape and games were played a printout at a time.
David Eyers is a faculty member of the University of Otago in New Zealand. He has broad interests that span cloud computing, distributed systems and high performance computing, middleware, security, and energy efficiency.
Varda Faghir Hagh is a PhD student in Computational Condensed Matter Physics at Arizona State University and she studies the critical behavior of physical systems as they go through a phase transition. Varda is originally from Iran and would like to help Software Carpentry expand their workshops to more developing countries and encourage women and researchers from any underrepresented groups to learn and use programming.
Daniel Falster is a post-doc at Macquarie University in Sydney, Australia. He uses a combination of math, computer models, and large data sets to test fundamental ideas about the processes shaping terrestrial vegetation and plant diversity. He is passionate about science, open data, reproducible research, and teaching biologists to code.
Emmanouil Farsarakis is head of all Software Carpentry training provided by ARCHER, the UK National Supercomputing Service. He is an Applications Developer at EPCC and the University of Edinburgh, where his work focuses mostly on the optimisation and parallelisation of scientific codes. He also has many years' experience in education of multiple disciplines.
Bennet Fauber got a degree in history, and fell into computing by way of computerized typesetting and statistics. He has been providing statistical and computing support since 1986, primarily at the University of Michigan.
Xu Fei took a detour to work for the UN in New York after completing his MS in neuroscience at McGill University in Canada. There he became fascinated by how adults learn new skills. He finally went for the SWC instructor training in 2014 and immediately regretted not doing it sooner. Currently he is running a startup to test the hypothesis that good data skills would make nonprofit organizations more efficient.
Angus Ferguson is a masters student in History at the University Of Melbourne. His current research is on tertiary education policy and its effects on university teaching and research. He also has an interest in finding ways to apply computational approaches to historical questions.
Filipe Fernandes works for the Southeast Coastal Ocean Observing Regional Association. His activities involves building skill score assessment of numerical oceans models. Located at Salvador (Brazil) he is an oceanographer interested in regional numerical models.
Selene Fernandez-Valverde is a genomicist and bioinformatician working as a Research Fellow at the National Laboratory for Genomic Biodiversity in Mexico (LANGEBIO). She is a founder of the civil organisation Más Ciencia por Mexico (More Science For Mexico), aimed at promoting science and technology in her home country. She is an advocate of good practice in science and informatics and have a keen interest in all things related to gene regulation and RNA.
Felipe Ferreira Bocca is a Ph.D. Candidate at the School of Agricultural Engineering at the University of Campinas, where he is trying to quantify how much sugarcane production can be affected by the use of Machine Learning to recommend how to use Nitrogen fertilizers. This involves modeling sugarcane yield and its response to fertilizer, developing a recommendation algorithm and performing simulations for different weather scenarios.
Luis Figueira is a software developer with significant experience working in research environments. He graduated as an electrotechnical engineer, specialising in speech processing. For the past 3 years he's been working in the SoundSoftware project, based in the Centre for Digital Music, Queen Mary University of London, helping researchers from the audio and music fields to build more robust and reusable research software.
Dmytro Fishman received a Bachelor's degree from the National University of Ukraine (KPI), and Master's degree from the University of Tartu (Estonia). He is now a PhD student at the University of Tartu, working in the field of bioinformatics, and has taught data mining, machine learning, bioinformatics, and text algorithms courses. He Has been a program committee member in the Summer School AACIMP in Kyiv, Ukraine, and is currently a member of UPEER, an organisation that aims to contribute to development of scientific societies in Ukraine. He is also an active participant in Kaggle competitions.
Rich FitzJohn is a postdoc at Macquarie University (Sydney, Australia). His research focusses on species traits and diversity, understanding how diversity in both species and their traits is generated. As a theoretical biologist, he uses a number of computational and statistical approaches, especially in R.
Abraham Flaxman is an Assistant Professor at the Institute for Health Metrics and Evaluation at the University of Washington. His research applies mathematical models and numerical methods to challenges in global health metrics. He loves it when scientists use revision control for their computational research code.
Chris Fonnesbeck is an Assistant Professor in the Department of Biostatistics at the Vanderbilt University School of Medicine in Nashville. He specializes in computational statistics, Bayesian methods, meta-analysis, epidemiology, and applied decision analysis. He hails from Vancouver, B.C. and received his Ph.D. from the University of Georgia.
Hugues Fontenelle is a biomedical engineer turned bioinformatician. He's working with Clinical Diagnostics at the Oslo University Hospital in Norway. Thanks to High Throughput Sequencing, he's turning patient's DNA into bits and bytes, which helps finding the cause of their genetic and rare disease.
Jes Ford is a Data Science postdoc at the University of Washington eScience Institute. She taught herself to program while doing astrophysics research in graduate school, and unfortunately reinvented a lot of wheels in the process. Now she enjoys helping other scientists adopt the best practices she has learned, so that research can be done more efficiently.
Talitha Ford is a neuroscience PhD student at Swinburne University of Technology, Melbourne. She uses Python and R regularly in her research, and loves sharing the skills she has learned with colleagues and those eager to learn. Talitha also participates in the NeuralCode group at Swinburne, which was set up to help scientists learn Python, R and a bit of SQL.
Konrad Förstner holds a PhD in bioinformatics and is working at the Core Unit Systems Medicine of the University of Würzburg, Germany where he is mainly dealing with high-throughput sequencing data. Besides his research activities he tries to make the world a better place by spreading the idea of openness in science.
Auriel Fournier is a wildlife ecologist currently pursuing her PhD in Biology in the Arkansas Cooperative Fish and Wildlife Research Unit at the University of Arkansas. Her work focuses on the migration ecology and habitat use of migrating rails during fall migration and evaluating the tradeoffs of wetland management for rails and waterfowl. She is interested in collaborative and reproducible ecological research (typically with a bird focus) and trying to rescue all the data hidden away in filing cabinets.
Philip Fowler uses computer simulation to understand how the proteins that sit in the membranes around cells in your body work. He enjoys teaching, especially trying out new ways of engaging students. By training he is a physicist but his interests have led him to the Department of Biochemistry at the University of Oxford, where he is currently a postdoc, via a PhD in Chemistry.
Andrew Fraser is a scientist in the Computational Physics Division of Los Alamos National Laboratory. He has a PhD in Physics from UT Austin. In 2008 when his book Hidden Markov Models and Dynaimcal Systems was published, one could build it from source that he distributed with a single "make" invocation.
Bob Freeman is Director of Research Technology Operations at Harvard Business School, where he works to spread the good word about best scripting practices and data hygiene to Biz and Econ folks. With a PhD in Virology from Harvard University, he was worked on numerous -omics projects as both a test-tube nerd and informatics geek. In addition, he has hopped out of research at various times to enhance research practices and high-performance computing workflows for scientists across different disciplines.
Chris Friedline is an NSF Postdoctoral Research Fellow at Virginia Commonwealth University working on uncovering the genetic architecture of a fire-adapted phenotype in four Pine species. He has a background in Information Technology, a masters in Bioinformatics, a Ph.D. in Integrative Life Sciences, and a passion for studying molecular evolution at multiple time scales.
Zhuo (April) Fu is a Postdoctoral Scholar at University of Virginia, where she studies diabetes and obesity at physiological and cellular level. She is passionate for optimizing and popularizing computing techniques that can facilitate data summarization and promote communication between scientists and the general public, especially in data visualization.
Geoffrey Fucile holds a PhD from the University of Toronto (Cell and Systems Biology, Collaborative Graduate Program in Genome Biology and Bioinformatics) and conducted post-doctoral studies at the University of Geneva (Depts. of Molecular Biology and Plant Biology). He is currently working in bioinformatics support and training as a member of the SIB - Swiss Institute of Bioinformatics stationed at sciCORE - the Center for Scientific Computing at the University of Basel. He is interested in all aspects of structural biology, genomics, and empowering research through education in computational biology.
Tara Furstenau is a computational biologist working as a postdoc at Northern Arizona University's Informatics and Computing Program. She develops methods for pathogen detection and transmission in wildlife reservoirs.
Francis Gacenga works as an eResearch Analyst for the Queensland Cyber Infrastructure Foundation, which provides research computing services and infrastructure to Queensland universities. He is based at the University of Southern Queensland in Toowoomba, Australia. He have worked internationally in information systems development, support, training and management and has a PhD in Information Systems, certifications in research commercialisation, IT service management and training and assessment.
Jessica Gallinger is a research data management librarian on contract at Simon Fraser University. She delivers workshops on data management and consults with users to implement project-specific strategies for long-term data curation. She completed her Master of Information at the University of Toronto.
Emilia Gan is a student in the Pathobiology PhD Program at the University of Washington. She is a graduate of MIT (BS - Materials Science and Engineering) and the University of Massachusetts Medical School. Before entering grad school, Emilia homeschooled her three children and taught part-time at Bellevue College while taking math and CS classes.
Javier Garcia-Algarra leads a group of Operations Analysis in Telefónica R&D (Madrid, Spain), where he has worked in different innovation areas for the telecom industry during the last two decades. He holds a degree in Electronic Engineering and M.Sc. in Physics, and with the left side of the brain a Ph.D. in Art History. He collaborates with the Complex Systems Group of UPM, working in theoretical models of population biology.
Leonor Garcia-Gutierrez is a PhD student in Interdisciplinary Mathematics at the University of Warwick (UK), where she is working on a code to simulate blood flow in microvessels. She is passionate about public speaking, teaching and learning how to write better software.
Julián García is a computational scientist. He is a Lecturer at the Faculty of Information Technology at Monash University, where he uses computers to understand evolution and teaches Computer Programming and Computational Science. Before moving to Australia he lived in Colombia, the Netherlands and Germany.
Paul Gardner is a bioinformatics lecturer at the University of Canterbury, New Zealand. He teaches courses in bioinformatics, genomics and statistics. His research touches on non-coding RNAs, gene expression and functional characterisation of genome variation and he is enthusiastic about software benchmarks, Wikipedia editing, open source software and open access publishing.
Aaron Garoutte is a graduate student at Michigan State University studying microbial ecology and plant microbe interactions in the soil. His interest in programming stems from using bioinformatics tools to analyze metagenomic data.
Chris Gates has worked in software engineering including work in startups, consultancies, and academia across a range of domains and technologies. Since 2007, his focus has been on bioinformatics, mostly analysis and application of high-throughput genomics data. He is currently the lead software engineer at University of Michigan's Bioinformatics Core where he designs, implements, and maintains operational data pipelines.
Laurent Gatto is a computational biologist at the University of Cambridge, UK, an associated member of the Bioconductor project and a fellow of the Software Sustainability Institute. He works mainly on data analysis and method development for quantitative proteomics data using R and regularly teaches R and scientific programming in Cambridge and abroad.
Ge Baolai is a high performance computing consultant with the supercomputing consortium SHARCNET in Canada. Formally trained in numerical analysis and scientific computing, he has a wide research background in applied mathematics, engineering and finance. Baolai has been teaching courses in numerical methods and HPC for years.
Stuart Geiger is a postdoctoral scholar and ethnographer at the UC-Berkeley Institute for Data Science. He studies the infrastructures and institutions that support the production of knowledge, focusing on topics such as collaboration, interdisciplinarity, community governance, newcomer socialization, and diversity and inclusion.
Andre Geldenhuis works as an eResearch Specialist for ITS at Victoria University of Wellington. He received a Masters in Physics at Canterbury University focusing on atmospheric waves above Antarctica. Working for a central service unit rather than a specific department gives Andre the flexibility to work with researchers from diverse fields, from the humanities to the sciences.
Noushin Ghaffari received her Ph.D. degree in Electrical and Computer Engineering from Texas A&M University, focusing on complexity reduction of gene regulatory networks. She is currently a Bioinformatics Scientist at AgriLife Genomics and Bioinformatics, where she investigates the development of new bioinformatics tools, analyzes data from Next Generation Sequencing (NGS) technologies, supervises graduate students, and provides statistical/bioinformatics trainings for faculty/students across TAMU.
Heather Gibling is a Bioinformatics Research Assistant at the University of Guelph interested in human health genomics. She holds a master's degree in bioinformatics and has a background in molecular biology. Having recently been introduced to programming herself, she is aware of how frustrating it can be when starting out and hopes to help make this easier for others.
Molly Gibson is a Ph.D. candidate in Computational & Systems Biology at Washington University in Saint Louis. Her research focuses on the ecological resistance and resiliency of microbial community structures and functions to perturbation by antibiotic treatment.
Goble is Professor of Computer Science in the
University of Manchester, and has spent the past twenty years
developing innovative computing approaches in knowledge
management, distributed computing and social computing to support
scientific researchers in a wide variety of areas, including
Taverna, BioCatalogue, myExperiment, and SEEK. She is a partner
in the UK's Software Sustainability Institute.
Antonia Gogoglou is a Phd student in Aristotle University of Thessaloniki, Greece focusing on Complex Networks and Data Mining applied in the field of Scientometrics. As an Electrical and Computer engineer she has discovered how coding can be deployed for a variety of problems in mathematics and physics as well as engineering overall, so she is really invested in communicating this knowledge to others.
Gerard Gorman is a computational physicist at Imperial College London. His research interests include parallel algorithms, irregular computation, high performance computing, multi-scale and multi-physics modelling and inversion problems.
Laura Graham has a PhD in Geography from the University of Nottingham. She is a spatial/computational ecologist interested in what impacts environmental changes have on species' distributions and how we can use this information in landscape and conservation planning to reduce detrimental effects. Having previously been a mathematician and database developer, she applies skills learned there to ecological questions.
Bruno Grande is a PhD student at Simon Fraser University, where he studies cancer genomics. After completing an undergraduate degree in biochemistry, Bruno made the jump to computational biology in the area of cancer research, analyzing large cancer genome datasets to infer new knowledge about the biological processes involved in tumour initiation and progression. In doing so, he also discovered a passion for teaching digital literacy skills such as programming and version control and promoting open science/data/access.
Jeremy Gray is an evolutionary biologist based in Toronto. His research interests range through models of speciation, experimental evolution and bioinformatics. He received his PhD from the University of Auckland.
Jonathan Gross is a Ph.D. candidate in quantum information theory at the University of New Mexico where he works on quantum control and quantum measurement theory. Jonathan also has an undergraduate degree in computer engineering from the University of Arizona, where he learned the importance of good software engineering practices.
Thomas Guignard is a librarian and consultant based in Toronto, Ontario. He holds a PhD in Acoustics from the École Polytechnique Fédérale de Lausanne (EPFL) and has been working in academic libraries since 2006. He's also a maker and hobby programmer, and strongly believes in empowering kids and adults through a better understanding of technology.
Julia Gustavsen is a PhD student at the University of British Columbia in Biological Oceanography. Her thesis work focuses on the changes in marine viral communities over time and space. She received her BA and BSc from the University of New Brunswick.
Jonathan Guyer is leader of the Mechanical Performance Group at the National Institute of Standards and Technology. He is co-developer of the FiPy partial differential equation solver framework, which he uses for modeling phase transformations in materials. Jon received his PhD in Materials Science and Engineering from Northwestern University in 1997. Before that, he was a submarine officer.
Melissa Guzman is a PhD candidate in Ecology at the University of British Columbia. Her research focuses on understanding dispersal and species interactions using NGS.
Steven Haddock is a Research Scientist at the Monterey Bay Aquarium Research Institute and adjunct Associate Professor at U.C. Santa Cruz, studying bioluminescence and biodiversity of marine zooplankton. He co-authored Practical Computing for Biologists with Casey Dunn.
Denis Haine is a veterinarian and PhD candidate in veterinary epidemiology at the Université de Montréal, QC. For the last 10 years he has held several positions, as epidemiology and biostats consultant, director of biostatistics in a CRO and scientific assistant in a NSERC research centre.
Sam Hames is a PhD student at the University of Queensland. Coming from an engineering background, he is working on applying biomedical image analysis to understanding human skin. He is particularly interested in how software can be used to improve clinical understanding of imagery.
Christopher Hamm is a postdoc in the Department of Ecology and Evolutionary Biology at the University of Kansas. His research focuses on the evolution and ecology of insects (mostly butterflies). Chris earned his his PhD from Michigan State Universty in 2012 and his dog's name is Larry.
Jessica Hamrick is a graduate student in computational cognitive science at the University of California, Berkeley. Her research involves building formal mathematical models of human behavior using tools from psychology, statistics, and machine learning. In her spare time, Jessica enjoys contributing to open source projects and teaching others about tools like Python and Git.
Eilis Hannon has a background in mathematics and currently works as a Bioinformatician in the Complex Disease Epigenetics Group at the Univeristy of Exeter. Her research involvings integrating differnet 'omics data to understand the molecular causes of psychiatric disorders.
Mike Hansen is a PhD student in Computer Science and Cognitive Science at Indiana University. His research interests include quantifying the complexity of software using cognitive models of programmers. He has designed and developed software professionally for almost ten years, and enjoys teaching others the skill and art of programming.
Sumana Harihareswara a Python programmer, technical writer, and community manager living in New York City, is the founder of Changeset Consulting, which provides short-term project management and maintenance services to open source software projects. She holds an MS in Technology Management from Columbia University and and a BA in political science from UC Berkeley, and participated in the Recurse Center in 2013 and 2014. Her past and present open source communities include GNOME, MediaWiki, GNU Mailman, and Zulip.
Harris is a graduate student at the University of Texas in
Austin. She studies the neuromolecular basis of social behavior
and is involved in several initiatives to enhance training in the
Steering Committee (2016 Member)
Emelie Harstad received a PhD in Physics from the University of Oregon in 2013, and currently works as an Applications Specialist at the UNL Holland Computing Center, where she helps campus researchers use the local supercomputing resources. She also works part-time as User Support for the Open Science Grid.
Edmund (Ted) Hart is a senior data scientist in Silicon Valley and adjunct faculty in the biology department at the University of Vermont. He received his PhD in ecology from the University of Vermont, and did his post-doc at the University of British Columbia. In his spare time he develops open source software for ecology.
Wolfgang Hayek is a scientific programmer for the New Zealand eScience Infrastructure (NeSI) and for the National Institute of Water and Atmospheric research (NIWA) in Wellington, New Zealand. He has a PhD in astrophysics and supports scientists in using high-performance computers, helps them improve their scientific computing skills, and develops and looks after simulation codes with a focus on HPC.
Fabian Held is a postdoc at the University of Sydney's Charles Perkins Centre. In this interdisciplinary center for research on chronic disease, he enjoys working with experts from many fields, and he contributes to statistical analyses, computational modelling of complex adaptive systems and the analysis of social networks. His own research interests are collaborative networks and the way we can support, sustain and manage (in) them.
Donna Henderson is a PhD student in genomic medicine and statistics at the University of Oxford. Her research focuses on modeling population histories and migration events using genomic data. She uses programming primarily to visualize data, write statistical simulation algorithms, and process large files.
Ian Henry obtained his undergraduate degree from the University of Edinburgh in Molecular Biology and his Ph.D from the University of Nottingham in Genetics/Bioinformatics. He current leads the Scientific Computing Facility at the Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG) in Dresden, Germany, which provides bioinformatics, scientific software development and bioimage informatics services to research groups at the MPI-CBG and across the Dresden campus.
Martin Héroux is a physiotherapist by training. He received his PhD from Queen's University and completed a three year post-doctoral fellowship at the University of British Columbia. Martin currently works at Neuroscience Research Australia in Sydney where his research focuses on human sensory and motor physiology in both health and disease. He is interested in teaching computational skills to biomedical and clinical scientists to improve research transparency and reproducibility. Martin also co-authors Scientifically Sound, a blog on reproducible research in the digital age.
Josh Herr is an Assistant Professor at the University of Nebraska in the Center for Plant Science Innovation and the Plant Pathology Department. His research interests introduced him to phylogenetics at the command line and he has transitioned from the lab bench (almost entirely) to the computational analysis of microbial genomes and metagenomes. Josh blogs about his research interests at Cyme & Cystidium, is a moderator at the bioinformatics help forum Biostar.
is an assistant professor in the Department of Biology at the
University of Texas at Tyler. Her general research interests
include evolutionary biology, phylogenetics, and comparative
genomics, although she is particularly fond of transposable
elements, plant systematics, and next-generation sequencing
analysis. She is an alumna of Western Kentucky University (B.S),
University of Missouri (Ph.D.), and NESCent/Duke University
Steering Committee (2016 Member)
James Hetherington leads the Research Software Development Team at University College London. The team collaborates with research groups to create readable, reliable and efficient scientific software. He has experience as a scientific programmer in academia and industry on physics, physiology and climate.
James Hiebert is computer scientist who has worked extensively in the earth and ocean sciences. After earning his Masters in Computer Science from the University of Oregon, he helped map the ocean floors with NOAA's Office of Coast Survey and since has been working to project the impacts of climate change on British Columbia and the Pacific Northwest with the Pacific Climate Impacts Consortium. The common theme of his career has been writing software to scalably analyze massive amounts of spatio-temporal earth and ocean data.
Cody Hinchliff is a computational evolutionary biologist with a background in web development. He works primarily with large genetic datasets to address questions related to the origins and maintenance of biodiversity in plants, and programs primarily in Python, Java, and R (among other things).
Konrad Hinsen is a theoretical physicist by training who currently works on protein structure and dynamics and scientific computing at the Centre de Biophysique Moléculaire in Orléans (France) and at the Synchrotron Soleil in Saint Aubin (France). He is also a department editor for Computing in Science and Engineering.
Johan Hjelm is a Senior Scientist at the Department of Energy Conversion and Storage at the Technical University of Denmark. His research interests include electrochemical science and technology, physical chemistry, and materials science. He is also interested in open and reproducible science, and likes Git, Unix shell, and Python in particular.
Xavier Ho is a curiosity-driven designer, researcher and software engineer. He currently works for CSIRO creating interactive data visualisations. Pursuing a PhD part-time at University of Sydney keeps him busy, and sometimes he wonders about machines and humans and that philosophical lot. Previously, Xavier worked in a Sydney startup doing computer vision work, freelanced as a videographer, and taught a handful of programming classes to university design students. His passion lies somewhere in the spectrum of chocolates, video games, and a better world.
Daniel Hocking is a postdoctoral researcher in the Department of Environmental Conservation at the UMass-Amherst. He studies the effects of land-use and climate change on animal populations. He is currently using Hierarchical Bayesian methods to forecast brook trout populations in response to climate change throughout their native range.
Since July 2012, Amy Hodge has served as the Science Data Librarian at Stanford University Libraries, where she helps Stanford researchers with all aspects of data management, including teaching best practices for data organization and analysis. Before joining the Libraries, she spent nearly ten years in the business world working on science databases and learning the beauty of SQL. Amy has a PhD in Molecular Biophysics and Biochemistry from Yale University, where she studied ubiquitin-mediated regulation of the Saccharomyces cerevisiae cell cycle.
Toby Hodges is a bioinformatician and community coordinator in the Zeller Team at EMBL Heidelberg. He provides training and consultancy to community members and develops resources and tools to support computational biology at EMBL and beyond. He is also involved in organising the Heidelberg Unseminars in Bioinformatics series.
Alireza Hojjati is a postdoctoral fellow in the department of Physics and Astronomy at the University of British Columbia. He studies the origin and evolution of dark and visible matter in the universe through cosmological observations. His research aims at utilizing the ongoing and next generation of cosmological surveys to investigate possible signatures of new physics.
Chris Holdgraf studies cognitive and computational neuroscience at UC Berkeley. He is interested in linking higher-level theories of the mind with information processing in the brain, currently exploring how we make sense of noisy or incomplete auditory information. He's also an editor and manager for The Berkeley Science Review and serves as an advisor to Beyond Academia.
Jeff Hollister is a research ecologist with expertise in landscape ecology, GIS, and water quality. He works for the USEPA at the Office of Research and Development's Atlantic Ecology Division in Narragansett, RI. A large part of Jeff's work focuses on encouraging both his EPA colleagues and the broader community to increase their use of open science, reproducible research, and R.
Peter R. Hoyt has a PhD in Human Genetics and Cell Biology from the University of Texas Medical Branch in Galveston, TX. He spent 15 years at the Oak Ridge National Laboratory in Oak Ridge, TN, re-inventing himself through mouse genomics, scanning microscopy, and bioinformatics. He is now Graduate Program Director for the Bioinformatics Certificate at Oklahoma State University where he has 11-years of workshop experience through the Bioinformatics Core Facility, and works closely with the HPCC.
is a software engineer turned plant phylogeneticist turned
software engineer. Currently she is both a postdoctoral researcher
at the University of British Columbia, working on phylogenomics in
the genus Populus, and a software developer for the
Dryad Digital Repository.
Maintainer: Version Control with Git
Katy Huff is a
Postdoctoral Scholar and BIDS Data Science Fellow in Nuclear Engineering at
the University of California – Berkeley. She recently authored "Effective Computation in Physics: Field
Guide to Research in Python." She received her Ph.D. from the
University of Wisconsin – Madison, where she helped found The Hacker Within.
Katy is a former Chair of the Software Carpentry Foundation's Steering Committee.
Maintainer: Testing and Continuous Integration with Python
Fatma Imamoglu is a postdoctoral researcher at the International Computer Science Institute, UC Berkeley's Helen Wills Neuroscience Institute and a data science fellow at the Berkeley Institute for Data Science. She is interested in how sensory information is encoded in the brain and uses machine learning approaches to fit computational models to brain data acquired by functional magnetic resonance imaging. Her current research is on the representation of language and music in the human brain.
Damien Irving is a PhD candidate in Meteorology at the University of Melbourne, where his research focuses on the climate of the high southern latitudes. He also writes a blog about research best practice in the weather/climate sciences, teaches software skills to researchers through an innovative new project called the Research Bazaar, and is the unofficial coordinator of Software Carpentry activities in Australia.
Yuandra Ismiraldi is a student in the Master of Development Studies program in the University of Melbourne. Previously, he worked as a data engineer and consultant in the international development sector. His research interest is on how big data can help create better public policy. He is part of the Research Bazaar program in the University of Melbourne and teaches data collection tools, OpenRefine, and NLTK.
Paul Ivanov is a graduate student in the Vision Science program at UC Berkeley. His interests include eye tracking, GPGPU programming, and natural image statistics.
Christian Jacobs is a postdoctoral researcher in the Faculty of Engineering and the Environment at the University of Southampton. His research is primarily in the field of computational fluid dynamics, and currently focusses on multiphase flow modelling and the automated solution of partial differential equations using code generation. In addition to research, he thoroughly enjoys teaching and open-source software development, particularly with Python.
After a spell upgrading and maintaining a metrology company's statistical process control package written in C++ for Windows, Nick James is now almost retired. His personal interest in computing is centred around domain-specific languages, the parsing thereof, and code generation.
Dorota Jarecka has a PhD in Physics from University of Warsaw (Poland). She is a postdoctoral fellow in the National Center for Atmospheric Research (NCAR; Boulder, CO). She works on atmospheric numerical models, and she is interested in the scientific computing with Python.
Zbigniew Jędrzejewski-Szmek works in a mixed experimental-computational neuroscience lab and writes stochastic simulators and programs for the analysis of experimental data. He is active in the Fedora Linux distribution where he works on the init system. He also helps organize the Advanced Scientific Programming in Python summer school series.
Bo Ji is a postdoc in computational biology and bioinformatics at the Jackson Laboratory. She conducts research focused on large-scale association of genomic and genetic data to understand the molecular mechanisms that regulate human diseases. She obtained a Ph.D. in Animal Science and an M.S. in Statistics (University of Tennessee, Knoxville).
Ben Johnson is a Ph.D. student at Michigan State University studying microbiology and molecular genetics, focusing on drug discovery and intracellular adaptation pathways as new targets to treat Mycobacterium tuberculosis. He want to make the computational tools used to analyze large sequencing data sets accessible, useable, open, and reproducible.
Luke Johnston is a PhD student at the Department of Nutritional Sciences in the University of Toronto. His research is in diabetes epidemiology where he uses data to try to understand how and why some individuals develop diabetes and others don't. Teaching proper coding skills and fostering reproducible research is something he is very interested in, given that much of science relies on the results from these codes and analyses.
Myfanwy Johnston is a PhD student at the University California at Davis, studying the migratory behavior of native fishes in novel ecosystems. She has a particular passion for programming in R, as well as for helping scientists improve the visuals they use to communicate their research.
David Jones as been a software engineer for 15 years. He has a Masters in Applied Mathematics from UMass Lowell, and his main interests include algorithms, programming languages, and software tools.
Martin Jones is a biologist by training who learned to write code during his PhD and started teaching others to do the same shortly after. He uses Python every day in my own research and regularly teaches programming courses to biologists and bioinformaticians. He's currently Lecturer in Bioinformatics at Edinburgh University.
Blake Joyce is a benchtop molecular biologist and field agricultural ecologist by training, but has collaborated with a broader range of science professionals including mechanical engineers, chemists, physical scientists, and college educators by choice. He got his start in bioinformatics when next-generation DNA/RNA sequencing technologies were developed and quickly became a mainstay of academic research. Currently, he is a postdoctoral researcher for the CoGe bioinformatics platform which is a federated website with the iPlant Collaborative.
Ivana Kajić is a PhD student in Computer Science at University of Waterloo and Plymouth University. She investigates biologically constrained algorithms of cognitive functions related to semantic memory and problem solving using spiking neural networks. Apart from programming computers and robots she also enjoys teaching programming.
Saira Kazmi is currently working as the Scientific Data Architect for the Research Information Technologies group at The Jackson Laboratory for Genomic Medicine in Farmington, Connecticut. She loves working with high dimensional data; and enjoys designing and implementing solutions for problems that are associated with generating, storing and analyzing large amounts of data. She received her Ph.D. in Computer Science with a focus in Bioinformatics from the University of Connecticut and her post doctoral training in Medical Informatics is from Yale University.
Jonathan Keane is a Data Scientist at Mattersight, where he develops software and predictive models to improve interactions at call centers. Previously, he got a PhD in Linguistics from the University of Chicago with a focus on the phonetics of signed languages and laboratory methods in linguistics. He has a passion for developing software to not only help get a job done, but to do it in a way that is reproducible, reliable, and easy to understand.
Tom Kelly is a computational geneticist with research experience in evolution, epigenetics, and cancer genetics. He is currently studying towards a PhD on genetic interactions in breast cancer at the University of Otago in New Zealand. With a background in Mathematics and Life Sciences, he uses both data analysis and modelling approaches to problems. Facing the challenges of modern interdisciplinary research, he has become involved in science communication, education, and collaboration initiatives.
Jessica Kerr has channeled an undergraduate physics degree into a programming career. She loves computer science, especially when it intersects with math and complexity theory. Her goals include acquiring new tastes, sharing enthusiasm, and keeping two crazy-happy children alive.
David Ketcheson is an Associate Professor of Applied Mathematics at King Abdullah University of Science and Technology in Saudi Arabia. He is an advocate for reproducible research, affordable and accessible scientific publishing, and recognizing the value of software in science. He studies numerical discretizations of differential equations.
Radhika Khetani manages the training program at the Harvard Chan Bioinformatics Core, with a focus on developing bioinformatics workshops and training modules of various lengths for the Harvard community. Her passion is to make genomics data and its analysis more accessible to biologists. She has spent the last several years training wet lab researchers to independently perform genomic analyses.
Kalin Kiesling is a PhD student at the University of Wisconsin-Madison pursuing a degree in nuclear engineering and engineering physics. She studies computational nuclear engineering which focuses on developing software for nuclear engineering applications, in particular radiation transport. Kalin is interested in helping other students learn about best practices for software development.
Jan T. Kim is head of bioinformatics at The Pirbright Institute. His scientific interests revolve around information in biological systems and have led him to acquire principled knowledge in the biosciences as well as in computer science and mathematical fields relevant to information theory. Jan also has several years of experience in programming, scientific computing and machine learning. He very much likes interdisciplinary work and enjoys learning and teaching, where his favourites include explaining computing to bioscientists and illuminating biology to computer scientists.
W. Trevor King is a freelance software developer who moonlights as an evangelist for open source software in general, and Git and Python in particular.
Athanassios Kintsakis is an Electrical and Computer Engineering graduate and currently a Ph.D. student at the Aristotle University of Thessaloniki on the field of optimizing workflow parallelization. He is currently employed as a software engineer and researcher and his scientific interests lie across high performance computing in a cloud environment, big data analytics, workflow optimization, machine learning applied in data mining and bioinformatics.
completed a Ph.D. at the University of Melbourne,
and now works in the computational science team at IBM Research Australia.
As part of Bionic Vision Australia,
she focuses in her research on how to best convey information visually to an implant recipient to help in daily tasks,
such as reading.
Her newest passion is online data vizualisation.
She started programming in Basic on an Atari 8000XL when she was six years old and enjoys learning new languages.
Maintainer: Programming with MATLAB
Justin Kitzes is a postdoc in the Energy and Resources Group and a Data Science Fellow at the Berkeley Institute for Data Science at the University of California, Berkeley. His research centers on the intersection of quantitative ecology and conservation biology, with a focus on developing general methods to predict patterns of biodiversity in human-altered landscapes.
Sigrid Klerke is a PhD student at University of Copenhagen. She has a background in reading research and now studies how eye tracking data can improve natural language processing tools. This allows her to run experiments on both humans and computers. Her computational work is powered by Python, Git and the Unix shell.
Shelley Knuth is the Assistant Director of Research Data and Training at the University of Colorado Boulder. She currently works on assisting researchers on campus with their data and training needs. Previously, she spent twelve years as a soft money scientist working on atmospheric science issues in the Antarctic.
is a mathematician who loves people, computers and
helping people use computers. She currently works
as a research computing facilitator at the University
of Wisconsin, Madison, where she serves as a liaison between
researchers and campus compute resources.
Alexander Koeppel is an Analyst in the Bioinformatics Core Facility at the University of Virginia School of Medicine. He routinely performs data analysis on genome-scale biological datasets. His background is in microbial ecology and evolution.
Alexander Konovalov is a Senior Research Fellow in the Centre for Interdisciplinary Research in Computational Algebra and one of the developers of the open-source mathematical software system called GAP. He is involved in multiple aspects of GAP development, technical support and user training, especially through his participation in the CoDiMa and OpenDreamKit projects. He is a Fellow of the Software Sustainability Institute and an editor of the Journal of Software for Algebra and Geometry and the Journal of Open Research Software.
Bernhard Konrad is a PhD student in Mathematical Biology at the University of British Columbia. He studies how HIV spreads within a single host or a city network. Bernhard loves to work on and talk about Data Science and Machine Learning, both of which he likes to apply to his open source and volunteer-run side project Math Education Resources.
Michael Koontz is a PhD student in ecology at the University of California, Davis. He studies how heterogeneous spatial patterns of vegetation affect forest resilience to wildfires and bark beetle outbreaks. He works in R and Google Earth Engine, and is really excited by the challenge of teaching programming to folks that don’t know where to begin.
Igor Kozlov is pursuing a PhD in Nuclear Physics Theory at McGill University. He studies the process of melting hadronic matter, which was typical right after the Big Bang, and thus is instrumental in understanding the formation of the Universe.
Avishek Kumar is a postdoctoral researcher at Arizona State University. He received his PhD from Arizona State University. His research interests include condensed-matter physics, biophysics, genomic and personalized medicine. He greatly enjoyed and benefited from Software Carpentry workshops as a student and is excited to pass along these skills to others.
Kwasi Kwakwa was born and raised in Ghana, but now lives in colder, darker London working as a postdoctoral researcher at Imperial College London. He works in biophotonics, which mainly translates to long hours in dark, windowless rooms shining lasers on cells and then using computers to analyze the large stacks of pictures that are produced.
Stephanie Labou is a staff research assistant and data manager at Washington State University. She is an ecologist by training (B.S. ecology, M.S. marine science and management) and is always excited to help other environmental researchers harness the power of R for reproducible research.
Olivier Lafleur is a teacher in Computer Science at Cégep de Lévis-Lauzon. He likes to see the spark in the eyes of learning students. He is passionnate about Open Source and Open Science, and really likes clean code and clean architecture.
Isabelle Laforest-Lapointe is a Ph.D. candidate in Biology at Université du Québec à Montréal, where she is studying the interactions between plants and microbes. Her project focuses on the phyllosphere microbiome of trees across natural and urban ecosystems. She holds two master degrees: ecology and statistics. She loves sharing knowledge and teaching, especially on the use of R and statistics.
Karin Lagesen has a PhD in
bioinformatics and has since focused on the processing of high
throughput sequencing data in various forms. With a background in
both computational science and molecular biology, she has taught
programming and computational analysis to both master and PhD
students and believes that this should be an integral part of any
Steering Committee (2016 Vice-Chair, 2015 Secretary)
Sherry Lake is a digital curation librarian at the University of Virginia Library where she has taught many courses on databases and best practices for data collection and management. Sherry has been working with and teaching about UNIX systems since the late 1980s. Sherry describes herself as being the bridge between technology and its users. She has a BS in Computer Science from the University of Virginia, and a MS in Information Sciences.
Benjamin Laken has a background in Physical Geography and climate change, and holds a PhD from Sussex University. He has been a postdoc researcher in Spain and Norway, and currently works as a Research Software Engineer at UCL, England.
Jeremiah Lant is a Hydrologist for the U.S. Geological Survey (USGS) at the Kentucky Water Science Center in Louisville, Kentucky. His work includes hydrodynamic and hydrologic modeling with an emphasis on flood-inundation modeling. He enjoys rock climbing, teaching, programming, and sharing a passion for open science and open software.
Chris Lasher works at the interfaces of molecular biology, computer science, and software development. In 2007, he lead a weekly Software Carpentry boot camp at Virginia Tech for postdocs and graduate students. To this day, Chris continues to improve his good programming habits and extol the virtues of Python, his most beloved programming language.
Latornell is a professional engineer with post-graduate degrees
in experimental and computational fluid mechanics and
modeling and control of robotic manipulators. He
works for Nordion in Vancouver, where he helps produce
medical isotopes by proton irradiation from cyclotrons.
Side projects include work on a coupled biology and physics model of deep estuaries
that, through the winter
months, calculates a daily prediction of the date of the first
spring phytoplankton bloom in the Strait of Georgia.
Maintainer: Version Control with Mercurial
Mark Laufersweiler (BS Physics, MS and PhD meteorology) is the Research Data Specialist for the University of Oklahoma (OU) Libraries, which is now a institutional member of the Software Carpentry Foundation. He assists faculty, students, and staff with data management, best practices, and is helping to implement a digital asset repository for the OU libraries and research community. Previously he was the IT specialist and adjunct faculty for the OU School of Meteorology where he taught IT and weather visualization skills.
David LeBauer is research scientist at the University of Illinois and a Fellow at the National Center for Supercomputing Applications. His research objective is to understand, predict, and manage ecosystem function. To support the computational and informatics demands of ecological prediction and inference, he leads development of the Predictive Ecosystem Analyzer, a system for model-data synthesis as well as its database backend, BETYdb. In addition, he contributes to the development and assessment of statistical and simulation models.
Kate Lee has a plant science background and more recently has moved into bioinformatics. She is currently a research assistant in the University of Leicester where she organises training in Next Generation Sequencing data analysis and provides bioinformatics support on projects from around the college including epigenetics, GWAS, transcriptomics, evolution and various bespoke scripting.
Victor (Kwangchun) Lee is the founder of XWMOOC, a digital contents startup for computational thinking and software engineering in Korea. He set up business and system architecture for Free Trade Agreement (FTA) and Origin Management at the Hyundai Motor Company, and led automotive semiconductor developement and purchasing at Hyundai Autron. Victor has master's degrees in software engineering and statistics, and contributed to the Korean translation of Software Carpentry.
Over the last 10 years, Luke Lee has written software for everything from Python desktop and web applications to embedded C drivers for solid state disks. He currently writes scientific Python applications for Blueback Reservoir in Houston, Texas, and is an active member of the Houston Django and Python user groups.
John Leeman is a geoscience researcher and scientific instrumentation consultant dealing with making difficult measurements in the earth science and helping scientists interpret them. He received a B.S. in meteorology and in geophysics from the University of Oklahoma and is a Ph.D. Candidate at The Pennsylvania State University in geoscience.
Joona Lehtömaki is a postdoctoral researcher at the University of Helsinki working on spatial conservation planning. Developing and applying software tools in supporting decision-making and in knowledge co-production are in the core of his work. He is also an active member of the open science working group of Open Knowledge Finland.
Joanna Leng has moved between working on high performance computing support and research projects for almost 20 years. She has a wide variety of experience in a number of disciplines and enjoys working in cross-disciplinary teams. She is an expert in visualization and is particularly good at working with 3D data and models; she has a strong interest in all areas of computational science.
Jacob Levernier is a PhD student in Psychology at the University of Oregon, studying moral development, research ethics with digital data, and applied statistics. Jacob works between the disciplines of Psychology, Philosophy, and Computer Science. His interest in scientific computing centers on data management and workflow automation, both in the social sciences and related disciplines, including library science.
Jean-Christophe Leyder is a Research Fellow at the European Space Agency (ESA) and works at the European Space Astronomy Centre (ESAC) in Spain, where he studies the physical properties of massive stars, most often using X-rays and gamma-rays.
Peter Li is a bioinformatician at BGI-Hong Kong. He provides bioinformatics support for GigaScience to help this open-access journal improve reproducibility of the research that it publishes from the life and biomedical sciences.
Denise Liberton holds a PhD in biological anthropology from Pennsylvania State University and is currently a postdoctoral fellow at the National Institutes of Health. Her research interests focus on the quantitative analysis of 3D images for studies of human variation and dysmorphology.
Matthew Lightman is a Data Scientist at American Express in New York City. He received his PhD in physics from Columbia University, where he worked on simulating particle interactions on large computer clusters. Matthew is passionate about education, and believes that beginning researchers can learn to use scripting and programming tools effectively so that they can get closer to the "80% of the work with 20% of the effort" ideal of the Pareto Principle.
Willem Ligtenberg is a biomedical engineer by training, now working as a data scientist at Dr. Reddy's in Leiden. Previously, he worked as a bioinformatics/biostatistics consultant and has gained a lot of experience analysing data from various sources. He specifically likes to think about how to increase the performance. He is the author of ROpenCL, Rango and the author/maintainer of the reactome.db bioconductor package.
Philip Lijnzaad is a bioinformatician based in Utrecht, Holland. His experience ranges from structural biology to next generation sequencing. He has a special fascination for the mathematical side of bioinformatics. His latest interest is in pediatric oncogenomics.
Johnny Lin trained as a climate dynamicist but now is a Senior Lecturer and Director of Undergraduate Computing Education in the Computing and Software Systems Division at the University of Washington Bothell and an Affiliate Professor of Physics and Engineering at North Park University in Chicago.
Gang Liu received BS, MS, and PhD degrees in theoretical physics from Jilin University, Changchun, China in 1983-95. He has been a Scientific Computing Specialist at HPCVL at Queen's University in Ontario since 2001. His work has included the double-layer master-slave model, the HPCVL working template, and the dynamical equation of the period vectors of a periodic system even under external stress.
Clara Llebot Lorente is the Data Management Specialist at Oregon State University Libraries and Press. She supports researchers with their data management needs, including consultations and instruction. She has a PhD in oceanography, and used to be a biogeochemical modeler.
Andrew Lonsdale is a PhD candidate using bioinformatics approaches to study plant cell walls, in the ARC Centre of Excellence in Plant Cell Walls. He studied software engineering and worked in industry before returning to study. He is also involved in community groups including COMBINE, a group for Australian students in bioinformatics and computational biology.
Kathleen Lotterhos is an evolutionary geneticist and molecular ecologist. A central goal in her research is to understand how populations will respond both ecologically and evolutionarily to environmental change. To address these pressing issues in biological science, she uses a combination of field surveys, experiments, mathematical modeling, genomics, and bioinformatics.
Rebecca Love transitioned from the wet lab to computational biology and bioinformatics to study the population genomics of malaria vectors. She also works on improving reference assemblies. She is currently a PhD candidate in the Biological Sciences department at the University of Notre Dame.
Elijah Lowe is a Ph.D. candidate in Computer Science and Quantitative Biology at Michigan State University. His research focus is on tail loss and development of invertebrate chordates using RNA-seq data. Originally from Atlanta, he received a B.S. in Computer Science from Morehouse College, and is currently in the New York City area.
Julia Lowndes is a marine scientist practicing and promoting open science. She earned her PhD at Stanford University studying the behavior of Humboldt squid, and is now at NCEAS and the University of California, Santa Barbara with the Ocean Health Index, which is applied marine science at the interface of innovative scientific methods, open science tools, and coastal management.
Yuxi Luo works at the Institute of Modern Physics, Chinese Academy of Sciences. He loves data science, especially applying knowledge to solve problems in diverse areas. He believes that he can learn more when teaching others.
Eric Ma is a PhD candidate in the Department of Biological Engineering at MIT. He is a self-taught Pythonista, and uses data science methods to solve infectious disease problems.
Cam Macdonell is a faculty instructor at in the Department of Computer Science Grant MacEwan University in Edmonton, Alberta. His teaching and research relate to operating systems, software engineering, cloud computing and virtualization.
Gary Macindoe obtained his PhD in Computational Statistics from UCL developing hybrid algorithms for linear algebra operations on multicore CPUs and GPUs. He currently works as a Research Software Developer for UCL working with researchers and collaborators to produce and maintain readable, efficient and reliable research software.
Dan MacLean is Head of Bioinformatics at The Sainsbury Laboratory. His group works on projects ranging from genomics through bioinformatics and citizen science to evolutionary modelling in the field of Plant-Microbe Interactions.
Joshua Madin is a quantitative ecologist at Macquarie University in Sydney, Australia. His research focuses on marine systems, especially coral reefs, where he uses biophysics, ecological theory and informatics to address questions at a range of ecological scales. For example, I explore questions spanning from the ecological consequences of tropical cyclones to the biogeographical role of functional traits. Joshua, his students and collaborators rely heavily on the tools taught by Software Carpentry to address such questions.
Cindee Madison is a backend Data Engineer in Berkeley, CA, and a board member of NumFOCUS. She has been working in Python and Data Science for 8+ years. Her interests range from visualization and image processing to graph theory and machine learning.
Tobin Magle is a scientist turned data management specialist at the Morgan Library at Colorado State University. She studied parasites like malaria and toxoplasma in her PhD and postdoctoral research, and now she helps other researchers find the data, information, and tools they need to streamline their research.
Alexandre Manhães Savio is a post-doctoral researcher doing software engineering and data analysis in the Nuclear Medicine Department of the Klinikum rechts der Isar of the Technische University München, where he develops tools for brain PET-MR image processing and diagnosis. He received his PhD in machine learning in the University of the Basque Country, Spain, and is a co-founder of ACPySS, a local Basque non-profit free software organization. He has been on the board of the EuroPython Society since 2015 and co-organized EuroPython 2015 and EuroPython 2016.
Tamer Mansour is a postdoc at UC Davis. He graduated in medicine and hold a Master's degree in clinical pathology and a PhD of genetics and bioinformatics. His work focuses on applications of NGS in genetic disease discovery.
Sergio Marconi is a Ph.D student in Interdisciplinary Ecology at University of Florida. He is studying how combination of plant functional traits may explain vegetation structure across scales, how to forecast their dynamics with global change, in order to predict ecosystems services and resource availability. To do so, he is interested in using NEON airborne data to develop a generalized hybrid hierarchical model.
Naudene Maree has been studying non-stop for 8 years in Zoology and Botany, which isn't including a one-year fling with education. She is fascinated by all things animal and found coding to be capable of becoming my second fascination.
Diana Marek holds a PhD in Bioinformatics and Biostatistics from the University of Lausanne. She was involved in Statistical Genomics research at the SIB Swiss Institute of Bioinformatics, and now works at SIB, where she is involved in scientific collaborations, teaching bioinformatics for postgraduates, as well as in coordinating training and outreach activities, such as scientific fairs, conferences, seminars and workshops for the layperson as well as for scientists.
Camille Marini is a research engineer at the Paris-Saclay Center for Data Science. She holds a PhD in physical oceanography and has skills in data analysis. She is currently developing a data science platform to foster collaborations on machine learning challenges.
Paula Martinez is a PhD candidate in Applied Bioinformatics at the University of Queensland. She has a background in Computer Science and an MSc in Bioinformatics. Her current research interests include evolutionary biology, comparative genomics, and analysis of large-scale datasets. She wants to be more involved in research communities to empower participative work.
Kunal Marwaha is an undergraduate student in physics and computer science at the University of California, Berkeley. He currently thinks about quantum control and nonlinear spectroscopy, and gets excited by new computational methods in science. Kunal loves to communicate, often via teaching, learning, and musical expression.
Ben Marwick is an archaeologist at the University of Washington. He works on questions of prehistoric human-environment interaction in mainland Southeast Asia, Australia, and elsewhere. He enjoys programming in R and is active in the Reproducible Research and Open Science Group at the UW eScience Institute.
Jordan Masakuna is a computer scientist and a current Ph.D student in Computer Science at Stellenbosch University (South Africa). He completed a Master's in Mathematical Sciences at Stellenbosch University, and undergraduate and postgraduate degrees in Computer Science from University of Kinshasa (D.R. Congo). I worked as a software developer and network administrator at Agence Congolaise des Grands Travaux (DR. Congo), and as a teaching assistant at University of Kinshasa for 3 years. His research areas are Machine Learning, Fusion Data Techniques, Big Data, Random Graphs, Modelling, Design Space, Programming and High Performance Computing.
Sergey Mashchenko is a high performance computing analyst in the supercomputing consortium SHARCNET (Ontario, Canada) with a research background in computational astrophysics and cosmology. He is a lead in SHARCNET's Training and Outreach team, and has been teaching graduate and HPC Summer School courses on CUDA, MPI, and OpenMP for a number of years.
Sina Masoud-Ansari works as a high performance computing and eResearch consultant as the University of Auckland. His interests are in parallel and GPU computing as well as machine learning. He works with a range of researchers from various domains and helps develop tools and workflows to enable research.
Ryan May is a software engineer at Unidata, part of the University Corporation for Atmospheric Research (UCAR), working on python software and training for the atmospheric science community. He is the core developer of the MetPy and Siphon Python packages, as well as a member of the development team for the matplotlib Python visualization library. He received his B.S., M.S., and Ph.D. in meteorology from the University of Oklahoma.
Fernando Mayer is an Associate Professor in the Statistics Department at the Federal University of Paraná, Brazil. Originally, he have a bachelor degree in Oceanography with a master’s degree in Ecology, and now he is a Ph.D. candidate in Statistics & Experimentation at São Paulo University. He is a member of the Geoinformation and Statistics Laboratory (LEG), where he deals with statistical spatial models applied to environmental and ecological problems, specially those dealing with marine fisheries resources.
Sue McClatchy is a bioinformatician and research program manager at the Jackson Laboratory. She provides research training at all academic levels from high school to faculty. She mentors students and develops training materials for analysis of quantitative and high-throughput data. Her expertise in curriculum design and instruction stems from an eight-year science teaching career in schools in the U.S. and Latin America.
Daniel McCloy is a postdoctoral researcher in the Institute for Learning and Brain Sciences at the University of Washington in Seattle. His research centers around human speech perception, especially the processing and categorization of individual speech sounds and syllables. He writes open-source software in python and R for (among other things) running auditory psychophysics experiments and visualizing vowel spaces.
Bill McClung is an emeritus professor of computer science at Nebraska Wesleyan University. Prior to NWU he taught both mathematics and computer science at California State University, San Bernardino and the University of San Francisco. In between academic gigs, he worked for Hewlett-Packard Labs as member of the technical staff.
Daniel McDonald is a PhD student in linguistics at the University of Melbourne. His research involves combining corpus and computational linguistic methods with systemic functional linguistics in order to investigate (very) large amounts of text.
Stephen McGough is a Lecturer in Computing Sciences at Durham University and a member of the Institute of Advanced Research Computing (iARC). His research interests lie in the areas of high performance and high throughput computing along with their implications for green computing.
Catherine McGoveran is the Government Information Librarian at the University of Ottawa and a volunteer with Open Data Ottawa. Her current interests are in data literacy, visualization, and open government.
is a computational biologist with a background and interests in genetics, phylogenetics and comparative genomics.
He has participated in a number of biological database projects, including WormBase,
Maintainer: Using Databases and SQL
Jessica McKellar is a kernel engineer living in Cambridge, MA. She is a Python Software Foundation board member and an organizer for the largest Python user group in the world. With that group she runs the Boston Python Workshops for women and their friends—an introductory programming pipeline that has brought hundreds of women into the local Python community and is being replicated in cities across the US.
Maria McKinley is a software developer in a neuroscience lab at the University of Washington. She creates video games used to learn more about how our memory works, using Python and the 3D game engine, Panda3d. She is passionate about the craft of coding, and loves sharing what she has learned.
Cameron McLean is a PhD candidate in Computer Science at the University of Auckland. Hailing from the biological sciences originally, and a keen open science advocate, his current research is exploring the use of design patterns as a novel knowledge representation framework on the Semantic Web. He wants to make it easier to capture and share aspects of laboratory practice, and to help researchers find, understand, and reuse/reproduce appropriate laboratory methods.
Emily Jane McTavish is a Humboldt Research Fellow working on phylogenetics at the Heidelberg Institute for Theoretical Studies, in Germany. She is also a part-time postdoc at University of Kansas developing tools for updating and revising the tree of life, as part of the Open Tree project.
Chris Mędrela is a student of Automatics Control and Robotics at University of Science and Technology in Kraków, Poland. While being passionate about Python and open source movement, he's interested in teaching programming. He plays violin and loves every kind of music.
Prateek Mehta is a PhD student in Chemical Engineering at the University of Notre Dame. His research is powered by python, git, unix, and emacs, and is focused on designing new materials for energy conversion and storage.
Sarah Meister is a graduate student in the Biochemistry department at the Univeristy of Toronto. Currently she researches mRNA regulation during DNA replication stress. Her love for language started with French and German and then moved to R and Python.
Stefano Menegon is a geospatial information scientist and a geographical web developer, specialized in collaborative geospatial web applications, spatial data infrastructures, OGC standards, data sharing strategies, GIS analysis, geostatistics, geodatabase and complex data integration. He is an Environmental Engineer, holds a Ph.D. in New Technologies for the Environment, co-founder of MPA Solutions (an FBK spin-off) and Research Fellow by the Institute of Marine Science of the National Research Council of Italy.
Jeremy Metz is an Experimental Officer for Image Processing in the Biosciences at the University of Exeter. He develops tools to address a range of scientifically interesting questions using mainly Python, Matlab, and ImageJ macros and plugins. Being a physicist by training, Jeremy is interested in using quantitative techniques to help generate simulations of Biophysical systems.
Lauren Michael is a Research Computing Facilitator at the University of Wisconsin - Madison, where she helps researchers navigate the world of large-scale computing resources and related training opportunities. Lauren's own previous research examined the formation of RNA motifs and RNA-protein interactions using compute-intensive methods. She also has interests and experience in science communication, and serves as a member of the NSF-funded ACI-REF program.
Simon Michnowicz works at Monash Universtiy's e-Research group, where he helps researchers use High Performance Computing facilities to advance their work. He has a background in Computational Proteomics, and has a keen interest in educating users to find new ways to solve old problems.
François Michonneau is an evolutionary biologist interested in the origins of biodiversity, especially among marine invertebrates. He believes that the computing skills taught during Software Carpentry workshops are critical for a broad adoption of reproducible science, a topic he is passionate about.
James Mickley is a botanist and currently a PhD candidate at the University of Connecticut. He is captivated by why so many plants have five-petaled flowers and is interested in what has driven petal number evolution. He has long enjoyed coding and also loves logging plant observations on iNaturalist while sampling the edible ones.
Ryan Middleton is a computer science instructor at Northern Arizona University and a software engineer. In addition to teaching computer science and developing software, he also assists scientists and researchers in utilizing cloud computing and software engineering principles so as to improve efficiency and maximize reproducibility for their own work.
Brian Miles is a research scientist at the Institute for the Environment at the University of North Carolina at Chapel Hill. His research is focused on stormwater pollution in urbanized ecosystems, environmental modeling, and hydroinformatics. Brian was originally trained as a software developer, and current develops ecohydrology modeling tools to improve scientific reproducibility and researcher productivity.
Jackie Milhans currently manages the support services team for Research Computing, including computing, data storage, and visualization at Northwestern University. Her background is in computational materials science, including homogenization, molecular dynamics, and multi-scale modeling. She is passionate about adventure travel, especially backpacking, hiking, scuba, and enjoying new cuisines.
Bill Mills is a freelance scientific
software developer and open science advocate, currently at TRIUMF,
Canada's national lab for nuclear and particle physics. Bill sits
on the 2016 Software Carpentry Steering Committee, and has been
teaching for SWC since early 2014. He divides his time between
Vancouver and New York City.
Steering Committee (Treasurer)
Amanda Miotto is an eResearch Support Specialist in Griffith University's eResearch Services group. She graduated with a Bachelor of Science majoring in Bioinformatics before gaining hands-on experience developing software systems in support of a range of projects in genomics, systems biology and adult stem cell research. She writes in php, python and spends a lot of time in Bash.
Meeta Mistry is a member of the Bionformatics Core at the Harvard School of Public Health. Her training began in Biochemistry, however postgraduate interests in computational approaches fostered the transition to Bioinformatics. Her expertise includes complex statistical analysis of large-scale datasets, specifically those pertaining to next-generation sequencing data. She also has a passion for teaching bioinformatics with experience at the high school, graduate and postgraduate level. Meeta has a PhD in Bioinformatics from the University of British Columbia.
Ian M. Mitchell is an associate professor in the Department of Computer Science at the University of British Columbia. His research interests include scientific computing, cyber-physical systems, formal verification, and reproducible research.
Nora Mitchell is a PhD student at the University of Connecticut. Her research focuses on the ecology and evolution of plants in South Africa, particularly on the potential drivers of diversification at different taxonomic and spatial scales. She is interested in using (and teaching) the quantitative programming skills to connect naturalist intuition with statistical rigor.
Christian Mohr is a Ph.D. candidate in environmental and analytical chemistry at the University of Oslo. His main research is focused on improving our understanding of biogeochemical and photochemical processes governing the mobilization and degradation of phosphorus compounds and natural organic matter in the environment. A large part of his work involves utilising R for data processing and statistical analysis.
Hamid Mokhtarzadeh holds a PhD from the University of Minnesota for his research on estimators and sensor fusion systems for cooperative navigation applications. He is also interested in teaching and software tools for engineering analysis and design. During his graduate school Hamid designed and taught a 14-week course on Python for scientific and engineering applications to aerospace engineering undergraduate students.
Jason Moore is a postdoctoral researcher in biomechanical engineering and an advocate for open science and computational reproducibility.
Nathan Moore teaches physics on Minnesota's south-east coat, at Winona State University. His PhD work involved computational models of knotted loops of DNA, and in teaching undergraduates, his interests have expanded to include electronics, Arduino interfacing, and teaching elementary school teachers how to solder. With his children, he keeps honeybees and chickens.
Timothy Moore is an ecologist and evolutionary biologist currently working on his PhD at the University of Connecticut. His research interests include functional ecology, biogeography, and quantitative ecology. He is currently working on understanding species range limits in South African plants.
Thomas Morrell is a research data specialist at the Caltech Library. He manages the Caltech research data repository and works with researchers to preserve and share their results. He has a background in computational chemistry and has experience developing scientific software in Python and managing high performance computing systems.
Ben Morris is a backend engineer in Silicon Valley interested in distributed systems and analytics. He received his B.S. in Computational Biology from Utah State University, where he worked with Ethan White developing open source software to make scientific data more accessible.
Brook T. Moyers studies evolutionary ecology and genetics of plants, especially crops and their wild relatives. She received her PhD in "Botany" from the University of British Columbia in Vancouver, BC, although a lot of of her work involved large files of genomic sequence data rather than the plants themselves. She's currently a NSF National Plant Genome Initiative postdoctoral fellow based at Colorado State University, where she continues to enjoy spending a lot of time outdoors.
Erika Mudrak is on the staff at the Cornell Statistical Consulting Unit, where she consults with researchers across campus on a wide range of analytical research. She has a PhD in Ecology (Botany Dept) and an MS in Biometry (Statistics Dept) from the University of Wisconsin - Madison. Her research interests include multivariate and spatial analysis, data visualization, data management and reproducible research. She co-hosts a the blog accidental aRt with fellow SWC instructor Kara Woo, where they curate examples of data visualizations gone beautifully wrong.
Andreas Mueller is a research engineer at the NYU Center for Data Science. He works on the scikit-learn machine learning library and other python tools for machine learning and data science.
Markus Müller likes to call himself a computational geographer and is interested in remote sensing, high performance computing and data science. He is currently working as geospatial engineer for planet.
Madicken Munk is a PhD student in Nuclear Engineering at the University of California -- Berkeley. Her current research focuses on developing computational methods for analyzing nuclear systems, specifically for highly anisotropic, heavily shielded problems. She is interested in creating approachable and sustainable software tools for nuclear engineers.
Ian Muñoz is a scientific programmer at SESYNC, where he spends most of his time in R and Postgresql. Ian hails from Colorado State University, and has a Bachelors in Economics. He enjoys learning how different tools excel at different tasks and has a passion for open source.
Ghulam Murtaza received his PhD from University of New South Wales in Computer Science. His areas of research are Sensor Networks, Location based Social Networks and Overlay Networks. He is currently working with Intersect as an eResearch Analyst.
VP Nagraj is a Research Data Analyst at the University of Virginia. He programs, teaches and writes about data analysis, data visualization and web development.
Josh Nahum is a scientist interested in the intersection of evolutionary biology and computer science. During my doctorate, he investigated the nature of mutation and adaptive landscapes in microbes. After receiving his PhD from the University of Washington, he has been teaching and working with the evolution of digital organisms.
Hani Nakhoul is an MD/PhD student at Tulane University in New Orleans. In his research, he uses high-throughput sequencing and computational methods to study the role of viruses in cancer.
Sandeep Namburi is a Systems Analyst at The Jackson Laboratory. He is presently working at the nexus of bioinformatics and cloud computing to enable the bioinformatics big data analysis.
Jose Nandez did his PhD in Computational Astrophysics at the University of Alberta, Canada. He did his undergrad in Applied Math and Computer Sciences. His passion for computer coding, physics and mathematics led him to follows a data science path. He currently works as a data scientist for SHARCNET (Shared Hierarchical Academic Research Computing NETwork) part of Compute Canada, and he is based at the University of Western Ontario.
Nederbragt is a self-taught bioinformatician working
with high-throughput DNA sequencing data at Oslo University,
Norway. His speciality is the assembly of genomes from short
pieces of sequence information.
Moritz Neeb is studying computer science in a Master Programme at TU Berlin, where his interest is mainly in Machine Learning and it's applications to Biology and Medicine. He is applying this knowledge by hacking mainly Python at idalab, a data analysis agency. In his freetime he likes to enjoy Berlins cultural life, for example through swing dancing or theater visits.
Aleksandra Nenadic is ELIXIR-UK's Training Coordinator for ICT and Software, based at the School of Computer Science, University of Manchester, where she also completed a PhD in Internet security. She currently also oversees BioCatalogue, is involved with the Software Sustainability Institute, and when she has time still programs in Java and Ruby on Rails.
Ryan Neufeld is a graduate student at the University of Waterloo. His research goal is to develop a switchable adhesive device, using liquid crystalline elastomers as the main material. He is also interested in using simulations as teaching tools in science and mathematics.
Linh B. Ngo is the Director of Data Science division, Clemson University's Cyberinfrastructure and Technology Integration group. He holds a Ph.D. in Computer Science and is interested in all computational and data-enabled research. Linh is currently taking courses in Learning Sciences to better understand how computing skills, including system and programming, can be integrated into undergraduate curriculums across all disciplines.
Daiva Nielsen is a postdoc at Harvard Medical School and Brigham and Women's Hospital. Her research is in translational genomics, which aims to develop processes for integrating clinically relevant genomic information into medical practice to improve health outcomes. She is keen to continue to develop her data skills and promote reproducible research in science.
Jens Nielsen holds a PhD in experimental physics from Aarhus University, Denmark. He is now working as a Research Software Developer at UCL collaborating with researchers to write and maintain readable and reliable software for their research projects. He has been using git and programming in python for a number of years and is semi-regular contributor to Matplotlib.
Matthias Nilsson is a research software engineer at Chalmers University of Technology, writing user-friendly tools for analysis of RNA sequencing data and promoting best practices for software development. Before coming to academia, he worked as a developer in the finance industry.
Timothy Norris is a Council of Library and Information Resources Fellow in Data Curation at the University of Miami Libraries where he works on technical and human aspects of problems in research data management. He holds a PhD in Environmental Studies (a.k.a. Geography) from the University of California Santa Cruz (UCSC). In a prior life he started and maintained a small development NGO based on social justice and conservation in the Andes of Peru.
Juan Nunez-Iglesias is a bioinformatics researcher with special interests in neuroscience, image analysis, and computer vision. His undergraduate training was in genetics and biochemistry, but he gradually became more computationally-focused, and now he's a core developer for scikit-image, a major open-source library.
Alan O'Cais is a theoretical physicist by trade (PhD from Trinity College Dublin in 2006) who has spent the last number of years working within application and user support among some of worlds largest supercomputing centers. He is currently helping to develop virtual research communities (including remote support and training infrastructures) for computational researchers in the Eastern Mediterranean.
Allison Jai O'Dell is the Metadata Librarian for the University of Florida, George A. Smathers Libraries, where she focuses on data modeling, wrangling, and hygiene. Her side projects and publications target thesaurus and ontology design, front-end development for libraries and archives, and Linked Data education.
Tina O'Grady Tina O'Grady is a postdoc at the Université de Liège in Belgium. She uses high-throughput sequencing to study cell communication, RNA processing, viral transcriptomes and anything else she can think of. A former librarian, she loves to work with both data and the people who use data.
Aaron O'Leary is a PhD student at the University of Leeds, performing lab and field work looking at the dynamics of storms and doing lots of time series analysis. Aaron loves Git and Python and is currently working part-time as a software developer and cycle courier.
Jeffrey Oliver is the Bioinformationist at the University of Arizona Health Sciences Library. His domain knowledge is in phyloinformatics and population genetics, his skills include programming in R and python, and he thinks he understands git after using it for four years. He is currently working to make computational literacy ubiquitous in the life sciences and sometimes cannot believe his good fortune to be living in Tucson.
Randy Olson is a Computer Science graduate research assistant at Michigan State University in Dr. Chris Adami's lab specializing in artificial intelligence, artificial life, and evolutionary computation. He runs a research blog where he writes about scientific computing, data visualization, evolution, and AI. Randy is an ardent advocate of open science and regularly travels the U.S. to teach researchers scientific computing skills at Software Carpentry workshops.
Catherine Olsson is a scientist and programmer, with a background in computer science from MIT, and human neuroscience from NYU. Her research focuses on computational models of human vision with fMRI. She gets excited about teaching, tutoring, code, math, the mind, and the brain.
Shawn O'Neil s a Bioinformatics Trainer and Manager of the Advanced Cyberinfrastructure Teaching Facility at the Center for Genome Research and Biocomputing at Oregon State University. With a background in computer science, his research focuses on bioinformatics, including ecological informatics, transcriptomics, algorithms, and software development. He’s developed and taught several courses in computational biology and programming, and is the author of A Primer for Computational Biology (in press with OSU Press).
Anita Orendt is an Assistant Director at the Center for High Performance Computing, University of Utah, focusing on Faculty engagement and research consulting. In this position she oversees the faculty collaboration efforts of CHPC staff members and acts as the point person for communication with the CHPC user community. In addition she provides general user support and training. Anita has a PhD in Physical Chemistry, and consults with users of the computational chemistry software at the Center. She is an XSEDE Campus Champion for the University of Utah, part of the NSF funded ACIREF Program and an adjunct associate professor in the Department of Chemistry.
Adam Orr is a graduate student at Arizona State University. His research focuses on the mechanisms of mutation and the development of tools to analyze large genomic datasets.
Jeramia Ory is an Associate Professor of Biochemistry at the St. Louis College of Pharmacy in St. Louis, MO. A self-described "data junkie," he uses many of the tools Software Carpentry teaches to analyze genomic data sets when he is not teaching Biochemistry to pharmacy students. His educational interests include the use of metacognition to enable student learning, nontraditional lecture models, and the role of technology in science education.
Natalia Osiecka is a scientist at Institute of Nuclear Physics in Cracow Poland. Her research focuses on vitrification and phase transition, and she enjoys using Python in her work.
Reid Otsuji is the Data Curation Specialist and faculty liaison Librarian for the UC San Diego Library Research Data Curation Program, providing research data management plan support and data related training for campus researchers.
Kirill Palamartchouk is a Researcher in satellite geodesy at Newcastle University, UK. His science involves elements of geophysics and radioelectronics, meteorology and celestial mechanics, and, of course, computing. Kirill believes that following good computing practices is very important, and likes to help fellow researchers do things reliably and efficiently. He can teach in English, Russian, and Greek.
Francisco Palm is a Systems Engineer with Master in Applied Mathematics to Engineering and Diploma of Advanced Studies in Cartography, GIS and Remote Sensing. Professor at the University of Los Andes (Mérida, Venezuela) in Operations Research and activist of open technologies and open knowledge in various collectives. Researcher in Management Science and Geospatial Analysis applied to Grassroots Organizing.
Martin Paulo is a software developer who has had a long and varied career: he started out writing assembler for embedded systems. From there, via grid programming, he made the move to more conventional development, as a team lead in the in the financial services arena. For the last few years he has been active as a developer helping to support the research community. Martin has a particular interest in the human side of software development and cloud computing.
works for the Software Sustainability Institute at the University of Manchester.
She coordinates the Institute's training activities, including Software Carpentry workshops and
the Institute's collaboration with the Centers for Doctoral Training in the UK.
Aleksandra holds a PhD in Computing from the Open University and her PhD
research focused on documentation in scientific software. Aleksandra is a former member of the Steering Committee.
John Pearson was trained as a physicist but now works as a computational neuroscientist at the Duke Institute for Brain Sciences. His research focuses on applying machine learning to brain data, with particular interest in the cognitive processes underlying decision making. He is passionate about equipping undergraduate and graduate students with the computational tools needed to make the most of their data.
Ryan Peek works as an aquatic ecologist at the Center for Watershed Sciences at UC Davis. He is currently a PhD candidate in Ecology/Genetics, studying amphibians and spatial and temporal effects of anthropogenic and environmental change on river ecosystems. He is part of the Davis R Users Group, dad of two awesome kids, whitewater rafting guide, avid soccer player, and professional beard wearer.
Jason Pell is a Ph.D. student in Computer Science and Quantitative Biology at Michigan State University who is primarily interested in tackling large next-generation DNA sequencing datasets. He holds a B.A. in Computer Science from Grand Valley State University.
David Pérez-Suárez is a post-doc at the Mullard Space Science Laboratory (University College London), as a member of the Solar Physics group. He mainly works doing image processing and time-series analisys of solar data, but he is also active in a couple of projects involving webservices, workflows and grid computing. David is one of the developers of a Python library for solar physicists and one of the scientists behind a citizen science project to classify sunspots.
Fernando Perez is a research scientist at the Helen Wills Neuroscience Institute at U.C. Berkeley. His work involves the development and implementation of new algorithms and tools for neuroimaging, with a special interest in functional MRI. He is also actively involved with the development of new tools for high-level scientific computing, mostly using the Python language.
Mariela Perignon is a fluvial geomorphologist doing a post-doc at the University of Colorado at Boulder. She is interested in the movement of sediment across river networks and the contribution of individual floods to the long-term evolution of landscapes.
Heidi Perrett works as a Senior Software Engineer for eResearch Support Services at Griffith University in Australia. With a background in Information Systems and Biological Science her work involves requirement elicitation, development, support and maintenance of Research applications within the University.
Adam Perry writes some code in addition to his other responsibilities as a member of staff at Northern Arizona University. He focuses primarily on mining and analysis in enterprise databases, but is spending lots of time these days on a variety of scientific computing projects.
Giacomo Peru is a project officer at the Software Sustainability Institute. He helps with administration and coordination of workshops in the UK. His background is in Classics (Università di Sassari) and in European Studies (Rome).
Matthew Peterson is a Faculty Research Assistant at the Oregon State University Center for Genome Research and Biocomputing. Matthew develops bioinformatics processing pipelines for the Center's Illumina, PacBio, and Genotyping by Sequencing services, as well as data management strategies. As a CGRB Bioinformatics Trainer, he helps researchers learn the bioinformatic basics through workshops, user groups, and one-on-one training.
is a Professor of Computing at the Open University. She holds a
Royal Society/Wolfson Research Merit Award in recognition of her
research on expertise in software design. With degrees in both
Psycholinguistics and Computer Science, Marian's research spans
empirical studies of software development, representation and
visualisation for software design, psychology of programming,
human-centred computing, and computer science education.
Stefan Pfenninger is a PhD student at Imperial College London. His research is focused on energy policy and energy systems modeling, but he is also interested in climate policy more generally, including resilience and strategies for adapting society and infrastructure to a changing climate. His background is in environmental science and policy.
Tessa Pierce is a PhD student at Scripps Institution of Oceanography (UCSD). Her work focuses on using high-throughput sequencing data to investigate the response of marine organisms to changes in environmental pH, oxygen and temperature. Tessa is enthusiastic about open science, outreach, teaching, and supporting diversity, equity, and inclusion in bioinformatics and marine science.
Adrianna Pińska is a developer of scientific software and a postgraduate student of computer science. Her favourite language is Python. She lives in Cape Town, South Africa.
Jon Pipitone is a Research Methods Specialist in the Translational Imaging-Genetics Research Lab at the Centre for Addiction and Mental Health, Toronto, Canada where he works on neuroimaging-based studies of mental illness.
Will Pitchers started life as a behavioural ecologist, worked in quantitative genetics and now finds himself in evolutionary genomics. He is currently a post-doctoral researcher in the electric fish lab at Michigan State University, focussing on the evolution of electrical communication in West-African elephantfishes.
Plumbley is Director of the Centre for Digital Music
(C4DM) at Queen Mary, University of London, and leads
project. His work in audio signal analysis includes beat tracking,
music transcription, source separation and object coding, using
techniques such as neural networks, independent component
analysis, sparse representations and Bayesian modeling.
Tom Pollard is a PhD student at University College London, looking at models of acute physiological health in critical care patients. He is a @SoftwareSaved Fellow, and he'd like academic research to be less competitive and more collaborative.
Pawel Pomorski works for SHARCNET at the University of Waterloo as a High Performance Computing Programming Analyst. His interests span many areas of high performance computing, including parallel programming in various languages, using CUDA, OpenMP and MPI. Pawel has a PhD in physics, and presently lives in Waterloo, Ontario.
Likit Preeyanon works at the Faculty of Medical Technology, Mahidol university, Thailand where he builds cyberinfrastructure for big medical data analysis and tackles biological problems utilizing data from high-throughput technologies.
Leighton Pritchard works at the James Hutton Institute in Dundee, Scotland. Originally a chemist, he's now a computational biologist, with interests in plant pathology, systems biology, and bacterial metabolism and regulation.
Giuseppe Profiti is a research fellow in bioinformatics at the University of Bologna. He works on protein function prediction using graph algorithms, while teaching Python programming to the students. He enjoys helping people being more effective in their jobs thanks to new computational skills.
Françoise Provencher is a data analyst at Shopify. She received her PhD in physics from Université de Montreal. She organises the Montreal PyLadies group.
Fotis Psomopoulos is an Academic Fellow at the Aristotle University of Thessaloniki. His research interests lie across bioinformatics and the evolutionary analysis of genomes based on their protein data, data mining methods and techniques in order to analyse the vast amount of data involved, and grid and cloud computing in order to ensure the necessary computational power and to optimize the developed methods for large-scale approaches.
Sean Pue a literary historian and digital humanist, is the author of I Too Have Some Dreams: N. M. Rashed and Modernism in Urdu Poetry. He is eternally grateful to Software Carpentry for teaching him tab completion. Sean is an associate professor at Michigan State University and blogs at http://seanpue.com.
Karthik Ram is a quantitative ecologist at UC Berkeley broadly interested in the structure and dynamics of food webs in terrestrial systems. He blogs at Inundata, and is also the co-founder of rOpenSci, a project which aims to foster reproducible research and data reuse through open source software tools.
R Saravanan is a professor in the Department of Atmospheric Sciences at Texas A&M University. His research involves the use of supercomputers for numerical modeling and data analysis to study past, present, and future climates. He also dabbles in open source and teaches courses in meteorology, climate, and introductory programming (using Python).
Karina Ramos-Musalem is a PhD student in Physical Oceanography at the University of British Coulumbia. Her research focuses on modelling, either numerically or physically, various aspects of the flow within and around coastal submarine canyons and their impact on the exchange of nutrients between the continental shelf and the open ocean.
Louis Ranjard is a computational biologist currently working at the Australian National University, Canberra. His research interests include the development of algorithms and statistical learning methods to tackle questions in evolutionary biology and bioinformatics. He maintains several software packages that implement Bayesian MCMC and machine learning methods for the analysis of large phylogeographic and bioacoustic datasets.
Rohit Rawat is a Ph.D. candidate in the Department of Electrical Engineering at the University of Texas at Arlington. He researches machine learning and computer vision techniques and likes programming in C++, MATLAB, and R. He enjoys teaching and facilitates at the Linux User Group at UTA.
Alex Razoumov earned his PhD in computational astrophysics from the University of British Columbia. He has worked on numerical models ranging from galaxy formation to core-collapse supernovae and stellar hydrodynamics, and has developed a number of computational fluid dynamics and radiative transfer codes and techniques. He spent five years as HPC Analyst in SHARCNET helping researchers use large clusters, and more recently joined WestGrid as visualization specialist. Alex lives in Vancouver, British Columbia.
Emily Kara Read is a scientist at the U.S. Geological Survey Office of Water Information in Madison, Wisconsin. Emily earned a Ph.D. in Environmental Engineering from the University of Wisconsin, Madison, an M.S. in Environmental Science from Indiana University, and a B.S. in Environmental Science from the University of Arizona. Emily is interested in national scale aquatic science; building scientists' capacity in reproducible and efficient workflows; interdisciplinary team science; and data visualization.
Tim Rice has an Honours degree in Maths & Stats from University of Melbourne, focused on probability and applied maths. He writes open source software and presents on computational topics at Melbourne Linux Users Group.
Adam Richie-Halford is a PhD student and Department of Energy Computational Science Graduate Fellow in the Physics Department at the University of Washington, where he studies the dynamics of superfluid vortices. Before Adam became a PhD student, he was a Peace Corps Volunteer in a small Berber village in Morocco. He enjoys teaching and learning new things and hanging out with his Boston Terrier named Mousse.
Kristina Riemer is a PhD student in the Wildlife, Ecology, and Conservation department at the University of Florida. She is a macroecologist with a focus on the responses of species traits to climate change. Because her work has benefited greatly from learning computational skills, she likes to pay it forward by introducing other scientists to these skills.
Janet Riley is a programmer at Cantina Consulting, where she writes web applications for a variety of clients and industries. Her MS in Computer Science from Boston University nicely complements her BA in Classical Studies from the University of Massachusetts Amherst.
David Rio is a Software Engineer from Barcelona, Catalonia, Spain. He holds a B.S in Computer Science and is currently working at the Human Genome Sequencing Center in Baylor College of Medicine as a lead software engineer. He is passionate about using technology to help scientists with their research, an active contributor to all types of open source projects, and believes in the importance of teaching programming to non-computational scientists.
Scott Ritchie is a Ph.D. Student in the Medical Systems Biology lab at the University of Melbourne, Australia. He has a background in Computer Science and Bioinformatics, and his day-to-day research primarily consists of methods development and data analysis using R. His research interests include gene coexpression networks, and data visualisation.
Leah Roberts is a PhD student at the University of Queensland, Brisbane, with a BSc(Hons) in Microbiology and a BA in Japanese. Her current research topic focuses on microbial genomics, with specialised interests in mobile genetic elements and epidemiology.
James Robinson is a PhD student in marine ecology at the University of Victoria, BC. He uses large datasets to explore human impacts on aquatic ecosystems, from coral reefs to freshwater lakes He teaches introductory R workshops to biologists, and is a strong supporter of open science.
Natalie Robinson earned her PhD at the University of Colorado, Boulder, studying the causes of species diversity patterns in urban, fragmented ecosystems around the globe. She is currently a quantitative ecologist and biostatistician at NEON, where she processes and analyzes continental-scale ecological and spatial data that will be used by scientists worldwide to better understand the responses of species and ecosystems to such disturbances as climate and land-use change.
Rosario Robinson is working toward a more inclusive tech community by introducing women and underrepresented minorities to open source. Rose works with Her Systers' Keeper, a virtual community of technical women with more than 5,000 members from over 54 countries, manages Systers' open source projects, and is Systers' Google Summer of Code Administrator. She has more than 20 years tech consulting experience in various industries including telecommunications, geospatial and infrastructure.
Andrew Rohl is a computational materials scientist at Curtin University in Western Australia. His research focuses on crystal growth using both ab initio and forcefield techniques. He has been the director of a supercomputing centre and currently is leading an institute focussed on computation across all fields of research.
is a Data Scientist at the University of Washington eScience Institute,
where he builds software tools to conduct reproducible scientific research
and collaborates with scientists in a variety of fields. He received his
PhD in Neuroscience at UC Berkeley at 2010, followed by a postdoctoral
fellowship in Psychology at Stanford University.
Phil Rosenfield is a NSF Astronomy and Astrophysics post-doctoral fellow at the Harvard-Smithsonian Center for Astrophysics. He uses the Hubble Space Telescope to observe stars in other galaxies in order to constrain stellar evolution models. Phil also creates and engages in programs that teach science while combating the exclusion of people based on race, economic status, and disability. While at the University of Washington he co-created a program to train PhD students to communicate their research to the public, and co-created a planetarium outreach program for Seattle Middle and High Schools. He now works with the WorldWide Telescope Ambassador program to create affordable digital planetariums in the Boston area.
Jamie Rosner is the Life Sciences Analyst for the Advanced Research Computing group at the University of British Columbia. He also serves as co-lead of the Compute Canada Bioinformatics National Team, and is a member of the Compute Canada National Software Carpentry Team. He holds bachelor degrees in Computer Science from the University of Waterloo and Sociology from the University of Manitoba. Jamie worked at the Vancouver Prostate Centre in the mid-2000's, and has been involved since 2008 in bioinformatics, data management, and software development for (NGS) data in HPC cluster environments. Most recently, he worked at the BC Cancer Research Centre developing NGS analysis pipelines, data management and visualization solutions.
Noam Ross is a disease ecologist at EcoHealth Alliance in New York City, where he studies the dynamics of wildlife and plant diseases and the process of inter-species disease spillover. He is also a founder of the Davis R Users' Group, and is on the rOpenSci review board. Noam received his Ph.D. from the University of California-Davis in 2015.
Billy Rowell is a Research Specialist at Howard Hughes Medical Institute Janelia Research Campus, where he designs, runs, and analyzes data from high-throughput behavioral assays, and helps others automate workflow and analysis. He has an MA in Molecular and Cell Biology from the University of California, where he studied fruit fly genetics and development.
John Rugis is a Computer Scientist working for the New Zealand eScience Infrastructure (NeSI) at the University of Auckland. His primary research interests are 3D visualisation of scientific data, software design for GPU's in cluster computing and the geometry of 3D discrete point sets. He also studies the morphology and propagation of New Zealand endemic ferns.
Dan Russo is a PhD student at Rutgers University studying Computational and Integrative Biology. His current research involves the application of Machine Learning and Data Mining in the fields of pharmacology and toxicology. He has a strong passion for reading and discussing science of all disciplines, scientific communication, running, and Philadelphia Phillies baseball.
Matthew Ruttley was born in the UK and has lived in Japan and the USA, working on a variety of things related to data science and natural language processing. He is currently Manager of Data Science at Mozilla in New York City, where he works on interest signals, reporting, and site similarity metrics.
Halfdan Rydbeck is a bioinformatician at the Norwegian Sequencing Centre, Oslo, Norway. He works with post sequencing processing and analysis of genomic data from organisms ranging from bacteria to vertebrates.
Mahdi Sadjadi is a Ph.D. student in physics at Arizona State University where he models glassy materials and studies their low-temperature properties. He is passionate about implementing the best practices in software development in scientific computing.
Ramesh Sampath is a software engineer at a startup and tries to make sense of data. He is proficient with Python data tools and enjoys helping others learn the tools and techniques required to solve computational problems.
Shane Sanders is an HPC Systems Analyst at The Jackson Laboratory. His research interests include algorithm scalability, machine learning, genomics, proteomics, and evolutionary biology. He obtained a PhD in Molecular Biology (Mississippi State University), a B.S. in Biochemistry, a B.S. in Computer Science (both from Mississippi State University), and is currently completing a PhD in Computer Science (Mississippi State University).
Maneesha Sane has a background in education and nonprofit management. She has taught and managed school- and community-based educational programs for all ages in domains including cultural studies, literacy, and art. Maneesha is a self-taught programmer, skilled in Python, SQL, and VBA, among other technologies. She is the organizer of the Philadelphia Python Users Group and has taught several Python boot camps in Philadelphia, and is the Program Coordinator for Software Carpentry and Data Carpentry.
Michael Sarahan earned a PhD in materials science from UC Davis by writing some very scary Python code. He now does his penance by helping other people write better code. As director of software development at Nion Co., he enjoys enabling better science with computers. He moonlights as a tutor, and hopes to support his family by teaching one day.
Martin Schilling is a PhD candidate in Biology at Utah State University. He is interested in bioinformatic and statistical methods for next-generation sequencing in population genetics and evolutionary biology. He is working on the evolution and ecology of plant reproductive systems in a genomic context.
Pat Schloss is an Associate Professor in the Department of Microbiology & Immunology at the University of Michigan where he uses bioinformatics to enable his research into the role of human microbiota in maintaining health. He also develops the mothur open source project, which enables others to answer their own microbial ecology questions using microbial sequence data.
Sebastian Schmeier is a research group leader and lecturer in bioinformatics/genomics at the Institute of Natural and Mathematical Sciences at Massey University Auckland and a bioinformatics advisor to New Zealand Genomics Ltd, a genomics service company. His group uses a combination of computational methods and biology to answer questions in the fields of genomics and transcriptomics, with a focus on gene regulation, non-coding RNAs, and data-driven biomedical applications. Besides research, Sebastian is also highly interested in the computational and bioinformatics up-skilling of students and scientists.
Marian Schmidt is a PhD candidate in the Department of Ecology and Evolutionary Biology at the University of Michigan. She uses genomics data to study the spatial and seasonal distributions and activities of bacteria in freshwater lakes. She loves analyzing and visualizing microbial ecology data in R and is a believer in code sharing and reproducible research.
Juliane Schneider has had a long, weird career in data and libraries, from working as an insurance librarian on Wall Street, to designing databases for EBSCO, to working with ontologies and taxonomies to develop various tools for data discovery at NYU Medical Center and Countway Library, Harvard Medical School. She is currently Metadata Specialist for the Research Data Curation Program at UC San Diego, working with researchers to describe and organize their data for sharing, discovery and re-use.
Andrew Schoenrock is a postdoctoral researcher and high performance computing consultant at Carleton University. His main research interests include high performance parallel algorithms, computation biology, bioinformatics, and big data. He received his PhD in Computer Science from Carleton University in 2016.
Jory Schossau is a Ph.D. student at Michigan State University studying evolution through simulation, complexity measurement, and game theory. He is also involved in various outreach and education projects from educational game design to classroom teaching.
Anita Schürch is a bioinformatician at the Department of Medical Microbiology, University Medical Center Utrecht, the Netherlands. Her main research interest is the characterization of etiological agents of infectious diseases with sequencing data.
Rachel Schwartz is a research scientist at Arizona State University with a background in ecology and evolutionary biology. She currently develops methods for phylogenomics, including the software SISRS, which extracts phylogenetically useful data from raw next-generation sequencing reads.
Anthony Scopatz has a PhD in Mechanical and Nuclear Engineering from the University of Texas at Austin, and is now an assistant scientist in the Engineering Physics Department at the University of Wisconsin-Madison.
Michael Selik is a data scientist at Infochimps. Over his career, he has worked for major enterprises and venture-backed startups delivering sophisticated analysis and technology project management services from hyperlocal demographics inference to market share forecasting. He received a MS Economics, a BS Computer Science, and a BS International Affairs from the Georgia Institute of Technology.
Henry Senyondo is a data scientist and software developer for the Weecology lab at Univeristy of Florida. He is extremely passionate about open source technologies, and is a maintainer of the Data Retriever. He works on enhancing and supporting data-driven scientific discoveries in science. He is interested in machine learning, data analytics, knowledge representation, and statistics.
Neem Serra is an iOS developer in the St. Louis area with a background in genomics and evolutionary biology. Her interests include reading fantasy/scifi novels, playing board games, and eating cupcakes.
Afrah Shafquat is a Computational Biology PhD candidate at Cornell University. She is interested in the development of computational and statistical tools for biomarker discovery for her graduate research work. Before coming to Cornell, she received an S.B. in Biological Engineering from MIT (Class of 2012).
Brent Shambaugh has a Masters in Chemical Engineering and has taught undergraduate chemistry as a adjunct professor. Today he spends most of his time developing a concept for virtual organizations for peer production with linked data and semantic web technologies. He also started Code Norman.
Clara Shaw is a PhD student at the University of Michigan studying the ecology and evolution of Daphnia-parasite interactions. She is particularly interested in how abiotic factors may alter these interactions. Clara got involved with Software and Data Carpentry two years ago by participating in a workshop for women in science at the University of Michigan.
Jeff Shelton studies control aspects of human motion. Having spent more than two decades in industry before returning to Purdue University for his PhD in Mechanical Engineering, he is interested in aligning educational methods with the evolving societal roles performed by engineers.
Jennifer M Shelton is a Bioinformatics Analyst at the New York Genome Center. She finds the field rich with opportunities, and sees the "open science" model as a logical extension of the scientific method because it is a way to reduce redundancy and increase reproducibility.
Leigh Sheneman is a computer science Ph.D. student at Michigan State University, where she uses digital evolution to study epistasis between body and brain.She has spent many years helping non-profit organizations develop interactive applications that focus on efficiency. She holds degrees from Texas A&M University and the University of Texas at Tyler.
Jason Sherman is an Oklahoma native, a student of the liberal arts, and an IT Analyst at the University of Oklahoma Libraries. He spends much of his time building infrastructure for developers, but also pitches in by writing the occasional integration module or migration script.
Yu-Ching Shih is a computational scientist and engineer. He received his Ph.D in Applied Mechanics from National Taiwan University in 2013. He is now interested in applying his analytical and computational knowledge to the problems in machine learning and data science.
Alexey Shiklomanov is a Ph.D. Geography student at the Boston University Department of Earth and Environment advised by Michael Dietze. His research focuses on using airborne and satellite imagery to study forest composition, structure, and function. He is also a developer for the Predictive Ecosystem Analyzer (PEcAn) project aimed at facilitating model-data synthesis for ecological forecasting.
Ardita Shkurti is a Research Fellow at the School of Pharmacy of the University of Nottingham, funded by a joint EPRSC/NSF grant. She has a core expertise concerning Computer Science Engineering (BSc and MSc in Computer Science Engineering at respectively Università degli Studi di Modena e Reggio Emilia and Politecnico di Torino, and PhD in Information and Systems Engineering at Politecnico di Torino). In particular, Ardita's research focuses on software and hardware optimization of algorithms applied to molecular dynamics simulation and molecular simulation data analysis.
Patrick Shriwise works at the University of Wisconsin - Madison as a graduate student in the Engineering Physics department. He is currently doing research in improved methods for particle tracking in radiation transport simulations. His other computational interests include data visualization, mobile UI development, and discussing general software engineering topics.
has a BSc (Applied Mathematics) from the University of Campinas.
He works for the Software Sustainable Institute and the University of
Manchester trying to create a community around
"Better Software, Better Research".
Steering Committee (2016 Secretary, 2015 Member)
Sarah Simpkin is a GIS and geography librarian at the University of Ottawa. She is interested in digital curation, metadata, and historical GIS applications, and is also a volunteer with Open Data Ottawa.
Jack Simpson is a PhD student at the Australian National University researching honeybee behaviour. He spends most of his time filming bees and then writing software to track their movements.
John Simpson is currently the Digital Humanities Specialist for Compute Canada and is leading development of a national strategy to bring Arts-based research with HPC. He holds a PhD in philosophy based on research into rational behaviour using agent-based simulations that he wrote himself. Outside of academia a manipulator of strings on screens, in hands, and on ukulele and banjo fret boards.
Rachel Slaybaugh is an Assistant Professor of Nuclear Engineering at the University of California Berkeley where she develops radiation transport methods for application to reactors, shielding, and nuclear security applications. Rachel writes in C++, Python, and Fortran, and has research experience with massively parallel code systems.
Clare Sloggett is a research fellow and bioinformatician at the Victorian Life Sciences Computation Initiative. She works in genomics on a variety of projects, principally in cancer genomics, and is interested in the application of statistical and machine learning methods to bioinformatics. She also teaches a Masters-level subject in genomics algorithms at the University of Melbourne.
Luc Small works for Intersect Australia, a not-for-profit organisation helping researchers within New South Wales and Australian Capital Territory universities to achieve research impact through technology. Luc's hobbies include electronics, Arduino, single board computers and cycling. He holds a PhD in Philosophy.
Allison Smith is a postdoctoral fellow in the eScience Institute and the School of Oceanography at the University of Washington. Her research focuses on understanding and predicting the distribution of species in coastal and open ocean ecosystems. She has additional interests in reproducibility and data visualization.
Byron Smith Byron Smith is a PhD candidate in Ecology and Evolutionary Biology at the University of Michigan, where he studies evolutionary processes in microbial communities using a combination of culture-based physiology experiments and (meta)genomic sequence analysis. Previously he received a B.S. in biology from The College of William & Mary in Virginia and spent several years as a graduate student at Michigan State University. Byron is interested in sharing tools and best practices for scientific software with his colleagues to facilitate effective collaboration.
Daniel Smith is a Ph.D. candidate in Chemistry at Auburn University. His research focuses on elucidating the interactions between molecules and works on open source quantum chemistry software packages in his free time.
Joshua Ryan Smith specializes in electronic devices based on wide-bandgap semiconductor materials and in the past has done work in surface science and nanofabrication. Joshua is a native of North Carolina and received his Ph.D. in physics from North Carolina State University; he learned Python programming in graduate school and has an interest in understanding the design of experiments in terms of the practices of software development.
Brendan Smithyman is a geophysicist and software developer, currently working at 3point Science as Lead Backend Developer. Brendan continues to be involved in research at the University of Western Ontario, where he authored Zephyr (an open source seismic inversion package) during his second postdoctoral fellowship. He lives in Ontario, Canada with his wife and son.
Mike Smorul is the Associate Director for Cyberinfrastructure at SESYNC where he oversees development SESYNC's research computing infrastructure. He has a background in professional software development, system/network administration, high performance computing and digital archiving.
Abel Siqueira is a Professor in the Mathematics Department at Federal University of Paraná, Brazil. He's an applied mathematician working with nonlinear optimization, with interest on open source software and reproducible science. He works with Bash, Python, C/C++, Julia and Git.
Courtney Soderberg is the Statistical and Methodological Consultant at the Center for Open Science, a non-profit start-up in Charlottesville Virginia dedicated to increasing the openness, transparency, and reproducibility of scientific research. At the COS she creates training materials and works with researchers to enable them to use best statistical and methodological practice for reproducible research. She obtained a Ph.D. is Social Psychology with a minor in Quantitative Psychology at UC Davis, where she focused on attitude change and social cognitive processing.
Nancy Soontiens is a postdoctoral researcher at the University of British Columbia where she works on regional ocean modelling. She received her PhD in Applied Mathematics at the University of Waterloo.
Don Speer supports researchers in science and engineering at the three state universities in Arizona on a routine and daily basis. As a sysadmin he works to expand the infrastructure for informatics and computing in AZ through various projects like Arizona Environmental Grid Infrastructure Services. He volunteers his time in groups such as Software-Carpentry and hacker meetup groups to develop new software and startup ideas.
is a research associate at Clemson University's
Cyberinfrastructure Technology Integration (CITI) group
as well as a Ph.D. candidate in Mechanical Engineering
at Clemson University,
His research areas include computational fluid dynamics,
and high-performance computing.
He spends most days programming and making mistakes,
and some days teaching others how not to make them.
Maintainer: Programming with MATLAB, The Unix Shell Maintainer: The Unix Shell
Karthik Srinivasan is a PhD student at the MIS department in University of Arizona, where he applies statistical and machine learning approaches to research projects in environment and healthcare area. Previously, he was part of the data analytics team in the automobile firm Robert Bosch for a year after completing his masters from Indian Institute of Science.
Pier-Luc St-Onge earned a B.Eng degree in software engineering in 2006 and a M.A.Sc. degree in image processing in 2008 at École Polytechnique de Montréal. Since 2013, he has been working as a high performance computing specialist for Calcul Québec at McGill University. In fact, working for research groups in academic institutions has been the definition of his career so far.
Joseph Stachelek is an ecologist and research programmer at the South Florida Water Management District, USA. He develops software tools for interacting with large-scale coastal marine datasets. He started scientific programming in 2009 after completing Dave Roberts' R Labs for Community Ecologists tutorial.
Mark Stacy is a Senior Analyst in the Informatics group at the University of Oklahoma. In his career, Mark has worked within the federal government, healthcare, and higher education arenas. His expertise in the data lifecycle and information management system has empowered scientist, researchers, and management personnel with the ability to access pertinent information and drive data decision support capabilities. He has a MS in Computer Science from Oklahoma City University and a BS in Physical Therapy from the University of Oklahoma.
Jeff Stafford is a bioinformatician and system administrator with the Centre for Advanced Computing. Much of his current work revolves around managing HPC infrastructure, performing analyses, providing research support, and teaching computing to scientists throughout Ontario.
Daniel Standage is a Ph.D. candidate in the Computational Genome Science Lab at Indiana University. His general research interests are in genome biology and genome informatics, with a particular focus on genome annotation and analysis of high-throughput sequence data. When he's not writing research software or cleaning up data, he enjoys hiking/camping with his family and cooking breakfast.
Valentina Staneva is a data scientist
at the eScience Institute at University of Washington. Her
background is in applied mathematics and statistics and she enjoys
extracting information from heterogeneous data sets and teaching
others the skills and tools needed to perform data-intensive
Maintainer: Programming with Python
Mitchell Stanton-Cook is a Software Engineer and Systems Administrator in the Beatson Microbial Genomics Group at the University of Queensland, Australia. He manages nearing 1000 Next-Generation Sequencing data sets. His work involves developing solutions for the efficient storage, processing and analysis of ngs data sets.
Jim Stapleton is a research assistant professor at the University of Oregon. He develops new technologies that use high-throughput DNA sequencing to quickly evolve improved proteins.
Meg Staton is an assistant professor at the University of Tennessee Institute of Agriculture in the department of Entomology and Plant Pathology. Her research interests span bioinformatics, genomics and web development with a focus on hardwood trees. She maintains the hardwood genomics website and a lab website.
Peter Steinbach is a high-performance computing developer at the Max Planck Institute of Molecular Cell Biology and Genetics in Dresden (Germany). He has a PhD in Particle Physics and is now responsible of accelerating scientific applications in a myriad of languages as well as on a zoology of hardware platforms.
Sarah Stevens is a Ph.D candidate in Microbiology at the University of Wisconsin - Madison. She works in the McMahon Lab, studying how the whole genomes of freshwater bacterial populations change through time. She also organizes a Molecular Microbial Ecology and Evolution (MoMiEE) focus group, bringing together scientists at UW-Madison to learn computational/bioinformatics methods.
Mark Stillwell is a Researcher at Imperial College London in the United Kingdom. The main subjects of his research are scheduling algorithms for distributed systems and simulation of distributed computing platforms.
Marcel Stimberg is a postdoctoral researcher in the Computational Neuroscience of Sensory Systems group at the Institut de la Vision in Paris, working on software tools for neural simulations and on neural models of sensory systems and plasticity. He believes in quite a few principles based on the word "Open".
Dena Strong is an information design specialist at the University of Illinois. She has a MLIS in information science, with particular interests in user-centered design, data curation, and representing and organizing digital information. She loves to work at the intersections: connecting people with the information they need, connecting art and humanities with digital preservation and access, and connecting design to implementation to production.
Jonathan Strootman is a full-time software engineer on the iPlant Collaborative Core Software team. His experience with the command line began while playing Gorillas on MS-DOS 5.
Daniel Stubbs works as a high-performance computing analyst for Calcul Québec at the Université de Montréal, using his background in applied mathematics to help researchers use these resources as efficiently as possible. This includes training and outreach as well as creating documentation, in both French and English.
Oliver Stueker has a Ph.D. in computational chemistry, and in his time in academia working with biomolecular simulation, chem- and bioinformatics, he has picked up on several scripting and programming languages and version control tools. Now he helps profs, post-docs, and students in Atlantic Canada solve research problems involving high-performance computers.
Mike Sumner is a data munger at the Australian Antarctic Division, working in partnership with the Antarctic Climate and Ecosystems CRC and the Institute of Marine and Antarctic Studies at the University of Tasmania in Hobart. He develops and maintains tools to couple ecosystem models with remote sensing data and oceanographic model output, sailing the dire straits between scientific model data formats and geographic information systems. He loves teaching programming skills to new users, especially when map projections are involved and is excited by new web technologies to bring interactive exploratory data analysis out in the open.
Arvind Sundaram is a bioinformatician at the Norwegian Sequencing Centre, Oslo, Norway. He analyses high throughput sequence data from human, fish, plants and microbes and likes to provide a helping hand to biologists to learn computing. His background is in immunology and comparative genomics.
Sarah Supp is a postdoctoral associate at Stony Brook University where she studies the impacts of climate change on hummingbirds throughout the western hemisphere. She received her Ph.D. in Ecology from Utah State University, where she first learned about Software Carpentry.
Svaksha is a software developer and an active FOSS contributor with interests in open data, computational science, bioinformatics and open access.
Gayathri Swaminathan is a Linux Senior Systems Engineer and open source community advocate at Rackspace. Her team supports Enterprise infrastructure for Rackspace customers. She holds a Masters in Computer Science from the University of Oklahoma and several professional certifications. As an avid enthusiast of Opensource communities, Gayathri serves as volunteer for LinuxChix and Fedora Documentation project. She is passionate about science, data, reverse engineering and involving girls to new coding exercises and projects.
Brad Taber-Thomas is a cognitive neuroscientist studying the brain systems involved in social-emotional development. He works as a Postdoc at Penn State University, obtained his PhD in Neuroscience from the University of Iowa, and is a native of Western New York.
Yuka Takemon is a research assistant at The Jackson Laboratory working both as a wet lab biologist and a bioinformatic analysis for the Korstanje Lab. Her work mainly focuses on identifying causal and modifier genes for human age-related kidney disease such as Alport Syndrome, using bioinformatic tools to for QTL analysis, GWA studies, and RNA-seq analysis. If not in the lab, she can be found hiking around Acadia National Park, which she considers to be her backyard.
Leszek Tarkowski runs a small company czterybity.pl (Polish for "four bits") focused on teaching C, C++ and Python. He has a PhD in materials science, preceded by MSc in physics but after quite long time as scientist in IMIM he has left academia. My experience as a programmer is based of my needs for data processing and visualization. Leszek lives in Kraków, Poland.
Becca Tarvin is a PhD student at the University of Texas at Austin working to understand the evolution of aposematism and resistance to auto-intoxication in poison frogs. She uses Python, Bash, and R to deal with large genomic and ecological datasets.
Rachael Tatman is a PhD student in linguistics at the University of Washington. Her specializations include phonetics, phonology and sign linguistics and she's interested in how humans perceived and produce sub-lexical linguistics units. She is especially excited by computational methods for behavioural science.
Hugo Tavares is a post-doc at the University of Cambridge, with experience in evolutionary genetics and quantitative genetics, using whole-genome data. One of the most enjoyable parts of his work is to interact with colleagues to both learn and teach computational skills for data analysis.
Cody Taylor develops Open Educational Resources (OER) for the University of Oklahoma Libraries and also promotes the use of OER and Open Access publishing. He studied electrical engineering and is interested in embedded system design and implementation. His other interests include all things shared, especially open hardware designs, and open source software.
Brian Teague is a research scientist at the Massachusetts Institute of Technology Synthetic Biology Center. He studies how cells work together to form systems that are greater than the sum of their parts. Each summer, he advises the MIT International Genetically Engineered Machines (iGEM) team, a group of 12 undergraduates that design and execute an original research project in synthetic biology.
is a bioinformatics specialist at Michigan State University,
having completed an NSF Postdoctoral Fellowship in Biological
Informatics. She has developed open-source tools for metagenomics
analysis and, as a member of the Great Lakes Bioenergy Research
Center, studied the effects of land use change on microbial
communities and greenhouse gas flux.
Bartosz Teleńczuk is a computational neuroscientists and committed Pythonista. He has been advocating and teaching Free/Open Source Software in academia and non-profit organisations for 15+ years. He holds a PhD in theoretical biophysics from Humboldt University of Berlin.
Maria Teleńczuk is a computer scientist who strayed into the path of computational neuroscience. Currently she spends most of her day modelling neural activity.
Rochelle Terman is a Ph.D. candidate in Political Science at the University of California, Berkeley. In October 2016, she will join the Center for International Security and Cooperation at Stanford University as a post-doctoral fellow. She enjoys teaching a range of tech-y topics for people of all backgrounds, including WordPress, Drupal, git, R, python, computational text analysis and webscraping. In Fall 2015, she designed and taught a new graduate course in computational social science at UC Berkeley.
Andrew Teucher holds an MSc in terrestrial ecology, and currently works on analysis and public reporting of environmental status and trend indicators for the British Columbia government. He works with his colleagues to promote good data management and programming practices, and teaches introductory R courses to other government scientists.
Simon Thelwall is an epidemiologist working for Public Health England, where he uses R to analyse data from the surveillance of healthcare associated infections.
Florian Thöle is a PhD student in Materials Science at ETH Zurich, focussing on simulating magnetoelectric materials. In his work, he uses Python and the Unix shell to automate and streamline his high performance computing workflows.
Adam Thomas is a researcher in the Section on Functional Imaging Methods at the National Institute of Mental Health in Bethesda, Maryland and an honorary research fellow in the Nuffield Department of Clinical Neurosciences at the University of Oxford where he received his D.Phil in 2014. Adam uses neuroimaging techniques to study the mechanisms of brain plasticity associated with learning, experience, and physical exercise.
Samuel Thomson is a PhD student in Computational Astrophysics at the University of Edinburgh. He develops software for large-scale simulations of the universe's early history, with a focus on the period following the birth of the first stars. After attending a Software Carpentry course in 2012, Sam now enjoys teaching others about Python and Git.
Amali Thrimawithana is a Bioinformatician at the New Zealand Institute for Plant and Food Research Limited. She has been involved in research projects focusing on fungal pathogens, insect pests and plants where she has undertaken bioinformatics analysis including de novo assembly and annotation of genomes and transcriptomes, differential expression as well as comparative genomics. Her current major areas of interest focus on understanding insect pests of important horticultural crops as well as genome exploration of native New Zealand plant species. She also has a keen interest in upskilling people in bioinformatics/computation space and reproducible research.
Robert Till is an Associate Professor of Fire Science at John Jay College of Criminal Justice, City University of New York. He regularly teaches courses in Fire Risk Analysis, Fire Dynamics and Special Suppression Systems. His main area of research is simulating fire and disasters in urban infrastructure.
Tiffany Timbers obtained her Ph.D. in Neuroscience from the University of British Columbia in Vancouver, and is currently a Postdoctoral Fellow at Simon Fraser University. Her research uses uses genomics in combination with high-throughput automated phenotyping to uncover how nervous systems enable animals to sense and respond appropriately to the external environment.
Katherine Todd-Brown is a computational biogeochemist at the Pacific Northwest National Lab in Richland, WA where she makes computer models of how soil breathes. She is passionate about reproducible open science, data provenance, and bringing computational tools to scientists of all types.
Christopher Tomlinson provides data management and software support for high throughput biological experiments performed within Imperial College London, and teaches software development skills to MSc Bioinformatics students. He has been involved in providing software and hardware support for science for over 20 years, during which time he has worked with psychologists, economists, physicists, health care professionals, computer scientists and biologists.
Richard Tomsett did his PhD research in theoretical neuroscience at Newcastle University, modelling electrode measurements of brain activity. After a year's postdoctoral research at the Okinawa Institute of Science and Technology in Japan, he returned to the UK to seek his fortune outside of academia.
Lina Tran is a neuroscience graduate student at the University of Toronto studying learning and memory. her research involves using graph theory to perform network analysis on the rodent brain during fear learning. She is also particularly interested in machine learning in biological contexts.
Will Trimble is a postdoc in the metagenomic annotation group at Argonne National Laboratory led by Folker Meyer, the group which provides and maintains MG-RAST. He was trained in experimental physics and has moved into computational biology, using computers and math to analyze bulky high-throughput sequence data. He switched fields out of a desire to participate in inderdisciplinary research and teaches Software Carpentry because he regrets using computers so much for years without learning the tricks.
Tim Tröndle is a system scientist working in the energy sector with a strong focus on collaboration. He is constantly trying to make his work more traceable and reproducible and to convince others to do the same.
Daniel Turek is a postdoc in the Department of Statistics at the University of California, Berkeley, and also a Fellow with the Berkeley Institute for Data Science. Daniel completed his PhD at the University of Otago located in Dunedin, New Zealand, where he studied multi-model inference and model averaging. His current research interests include computational statistics, efficient MCMC algorithms, and the evolving field of data science.
Stephen Turner is an assistant professor in public health sciences at the University of Virginia, and director of UVA's bioinformatics core. He works closely with other life scientists at UVA and abroad in the study design and data analysis of experiments involving large, genome-scale biological data.
holds a PhD in Ancient History from the University of Sydney. She
now leads a program at the University of Melbourne training
researchers in digital research tools and methods, with a focus on
capacity-building in the Digital Humanities. She volunteers with
Open Knowledge Australia and is an unrepentant fabulist.
Juan Ugalde is a research professor and bioinformatics core leader at the School of Medicine, Universidad del Desarrollo. His research focuses in genomics approaches to study microbial diversity, from extreme environments to pathogens. He tries to promote (hopefully with some success), the learning of basic programming and data analysis skills in colleagues and students (at all levels), as well as reproducible analysis and open data.
Daniela Ushizima is the head deputy of the Data Analytics and Visualization group and a staff scientist at the Lawrence Berkeley National Lab. She is also a data scientist fellow with the Berkeley Institute for Data Sciences, UC Berkeley. Her interests include pattern recognition, computer vision, machine learning, signal processing, quantitative microscopy, and high-performance computing.
Olav Vahtras is a professor of theoretical chemistry at the KTH Royal Institute of Technology, Stockholm. His research involves development of quantum chemical methods for prediction of molecular properties and he teaches Python in a national program for computational sciences.
Ramnath Vaidyanathan is an Assistant Professor of Operations Management at McGill University. He holds a PhD in Operations Management from the Wharton School, and has worked at McKinsey and Company. He is addicted to R and has developed two R packages, Slidify and rCharts, both aimed at simplifying the creation and sharing of interactive web-based content with R.
Roman Valls Guimerà completed his MSc in Computational Biology in KTH, Sweden. He has been working on high throughput bioinformatics pipelines and distributed computing environments at Science for Life Laboratory in Stockholm and taught courses on software engineering best practices to scientists, primarily in Python.
Edwin van der Helm is working on a PhD in computational astrophysics at Leiden Observatory in the Netherlands. His research is about hydrodynamics in young star clusters and near masssive black holes. He also works as a software developer for minds.ai, a company specialized in training deep neural networks.
Anelda van der Walt
obtained a MSc in Bioinformatics from the South African National
Bioinformatics Institute and have worked as bioinformatics analyst
at national genomics and next generation sequencing platforms.
She enjoys working with software developers as well as applied
researchers and have a passion for training post graduate
Peter van Heusden is a software developer and bioinformaticist working at the South African National Bioinformatics Institute (SANBI) in Cape Town, South Africa. He enjoys trying to build better workflows for genomic research, teaching Python programming and advocating for research and teaching with a positive social and ecological impact.
Thea Van Rossum is a PhD student in bioinformatics at Simon Fraser University in Vancouver. She's using metagenomics to investigate how microbial communities change in response to contamination, and whether these changes can be used to monitor for environmental contamination.
Jay van Schyndel worked as a software developer on commercial insurance systems coding in COBOL and Java. While at JCU his programming experience has been widened to include Python, Git and Bash. He is currently the Research Data Services Manager in the eResearch Centre at James Cook University, Townsville, Australia.
Steve Van Tuyl is the Digital Repository Librarian at Oregon State University Libraries & Press, working in the areas of digital repositories, research data management services, and open research. He goes on and on about these things and more on twitter @badgerbouse. In a former life, Steve studied disturbance impacts on carbon cycling in the forests of Oregon and New Jersey.
Steven van Der Valk is a Data Scientist at Fino Consulting in NYC, where he applies statistical and machine learning approaches to projects in the education and energy sectors. Previously, he was a postdoc at Tufts University where he performed neuroscience research aimed at better understanding learning and memory using high throughput RNA sequencing. As someone who had to slowly gain programming skills to understand the large biological data sets generated by his research, he is excited to make the process a bit easier for others.
Darya Vanichkina is a bioinformatics PhD student at the University of Queensland. She is passionate about understanding how the genome works to underpin the complexity of the mammalian nervous system, and what goes wrong at the molecular level in human neurological disease. Combining her PhD-derived bioinformatics knowledge with that obtained via a Specialist Degree in Molecular Biology & Biochemistry from Lomonosov Moscow State University, she enjoys initiating her (often unsuspecting) students to the magic of data analysis using R, python, awk and bash.
Horacio Vargas Guzmán is a postdoctoral researcher at the Max Planck Institute of Polymer Research in Mainz. He works on the theoretical development and implementation of analytical and computational methods for modeling materials properties, with special interest on physical phenomena of soft matter systems. He is also developing new algorithms for high performance computing environments, and actively contributing to scientific computing tools, using Fortran, C/C++ and Python.
After working as a Python software engineer, Nelle Varoquaux returned to university in 2011 to pursue an applied mathematics degree, specializing in machine learning. She is now using her skills to solve biological problems, such as reconstructing the 3D architecture of the genome.
Bogdan Vera is a PhD student in the Centre for Digital Music, at Queen Mary University of London, and previously studied at the University of York and Bournemouth University. His research is about distributed music technologies that can enable musicians to more effectively perform and compose music over great distances using the internet.
Allegra Via is a physicist and a scientific researcher at the National Research Council (CNR) and Sapienza University of Rome (IT). Her main research interests include protein structural bioinformatics, protein function prediction and analysis, and protein interactions. She has a long track record of training and academic teaching (Python programming, Bioinformatics, Biochemistry) and, since 2015, she is the ELIXIR Italy Training Coordinator. As such, she is involved in the design, organisation and delivery of bioinformatics training courses, Train-The-Trainer activities, and collaborations on many training-related initiatives with other ELIXIR's nodes.
Alex Viana is a Software Engineer at Terbium Labs, an Information Security startup based in Baltimore, MD, USA. Previously, he was a Research and Instrument Analyst at the Space Telescope Science Institute where he supported the operations of the Hubble Space Telescope. Alex works primarily in Python and has taught workshops in the US and Brazil in both English and Portuguese.
Kevin Vilbig is a polyglot programmer with a B.Sc. in Social Science via the Portland State University Honors College. He is currently a first year Master's in Social Work student at the University of Texas at Arlington, but understands more than enough mathematics to get into trouble. You can find him in the deep end or riding a bicycle in traffic, both figuratively and literally. He is planning to write a Master's thesis in the area of structural equation modeling in R.
Philipp von Bieberstein is an undergraduate student at the University of Arizona studying Plant Science, Chemistry and Informatics. His main goal is to use and develop computational methods to better understand biology.
Jens von der Linden is a PhD student in plasma physics at the University of Washington. He is designing and building an experiment to simulate astrophysical jets in the lab. His focus is the interaction between twisted magnetic fields and twisted flows in the jets and their stabilizing effects. He uses Python for data analysis, and has also worked on plasma fluid simulations in Fortran and Python.
Leanne Wake is an early career researcher based in Newcastle, UK specialising in modelling the solid Earth and geoid response to the evolution of ice sheets, specifically Greenland. She became involved with Software Carpentry via the Software Sustainability Institute because she believes everyone should have the opportunity to learn to code.
Andrew Walker is an Associate Professor in computational geophysics at the University of Leeds. After a degree in geology, a PhD in mineral physics, and ten years of postdoctoral research, he now holds a personal fellowship from the Natural Environment Research Council in the Institute of Geophysics and Tectonics. Andrew's research focuses on modelling the way that the Earth's interior deforms from the atomic to the planetary scale.
Dawn Walker is a information studies graduate student at the University of Toronto. Her research interests include design practises for civic engagement as well as community-led data collection for urban food security and environmental monitoring. An avid gardener, Dawn has volunteered in community gardens and urban agriculture projects across Canada.
Mike Wallis is a sysadmin at the University of Leeds with 16 years of experience in the HPC field, with many years of working in biosciences alongside that. He is one of a small team who keep the tier 2 N8 HPC facilities running, alongside several t3 machines used for advanced research computing in multiple academic disciplines. He has far too many different hobbies.
is about to be a PhD candidate at the University of Melbourne in
Australia. He holds an Honours Degree in Cognitive Neuroscience
and a BSc in Psychology/Psychophysiology, and has worked at the
Defence Science Technology Organisation in Adelaide and led a
research agreement between Swinburne University and the Land
Operations Division of the DSTO into the use of open source
biological sensors in human factors research. Alistair is the
co-ordinator of NeuralCode at Swinburne University, Hawthorn,
which is a resource for brain scientists to learn coding.
Dan Warren is an evolutionary ecologist with a strong focus on developing new analytical methods. He is currently working as a DECRA postdoctoral fellow at Macquarie University in Sydney, Australia. In his spare time he makes music, and lately has been doing a lot of soundtracks for nature documentaries.
Leah Wasser works as a remote sensing data scientist/senior science educator at the National Ecological Observatory Network (NEON). She received her PhD in ecology at Penn State, and has a passion for ecology, remote sensing, and GIS.
Josh Waterfall is a senior research fellow at the National Cancer Institute in Bethesda, MD. He works at the interface of computational methods, chromatin biology, and clinical oncology, revealing fundamental biology and translational opportunities from deep characterization of striking clinical cancer phenotypes.
works for the Queensland Cyber Infrastructure Foundation,
which provides eResearch infrastructure, including cloud resources, to Queensland universities.
Based at The University of Queensland in Brisbane, Australia,
she leads a team of nine eResearch Analysts statewide.
Belinda tweets as @cloudaus.
Steering Committee (2016 Member)
Lukas Weber is a PhD student in biostatistics at the University of Zurich in Switzerland. His research work is on the development of statistical and computational methods for analyzing bioinformatics data, and he uses R for most of his programming. He grew up in Perth, Australia, and previously worked for the Australian government on climate policy and the national greenhouse gas inventory.
Ben Weinstein is a PhD student at Stony Brook University studying tropical ecology. His research interests include automated monitoring for biodiversity, network analysis and community ecology of plants and pollinators. When not working in Ecuador, Ben enjoys climbing and birding with his wife and dog.
Mark Wheelhouse is a Teaching Fellow in the Department of Computing at Imperial College London. He is the coordinator for the second year of their Undergraduate Computer Science degree primarily supporting labs on compilers and operating systems. He is a big science-fiction and fantasy fan, eagerly devouring everything he can read/watch/play.
Melissa Whitaker is a post-doctoral researcher at Harvard University studying diet and ant-association among lycaenid butterflies. She enjoys Unix, Straus vanilla softserve, and digging up ant nests.
is an Associate Professor in the Department of Biology and the
Ecology Center at Utah State University. He is
Investigator in Data-Driven Discovery and a recipient of the
National Science Foundation CAREER "Young Investigators" Award. He
is a proponent of open and reproducible science and serves on
the Data Carpentry
the Impactstory board of
directors, and the editorial boards
of PLOS ONE
Easton White is a PhD student in Population Biology at the University of California, Davis. His research uses mathematical and statistical tools to answer questions related to population dynamics, evolution of life history traits, and eco-evolutionary dynamics.
Shawn Whitefield is a PhD student in Microbiology & Immunology at the University of Michigan Medical School. She received her MPH in hospital and molecular epidemiology from the University of Michigan School of Public Health in 2014. Her work focuses on integrating epidemiology and genomics to study pathogen evolution and transmission of hospital acquired infections.
Tyson Whitehead works at SHARCNET (a supercomputing facility in Canada) as a high performance computing (HPC) programming specialist. His official training is in Computer Engineering and Applied Mathematics, although he is interested in a wide variety of topics including pretty much anything computer, science, or math related. His latest hobby is soaring, and his near term ambitions include making it through the Feynman Lectures and becoming involved in the maker scene.
Alexander Whitlock is a PhD student at the University of North Carolina at Chapel Hill. In his research, he uses a computational model of an evolving artificial gene network to study the origin and maintenance of sexual reproduction.
Asela Wijeratne works as a Research Scientist at the Molecular and Cellular Imaging Center at the Ohio Agriculture Research and Development Center at Ohio State University. His research interest is in high-throughput genomics and has keen interest in sharing knowledge and expertise to help others. He received his PhD from Penn State in 2007.
Mark Wilber is a PhD student at University of California, Santa Barbara. His research interests include understanding how disease and disturbance can affect the structure of ecological communities.
Chandler Wilkerson has supported Linux and Unix systems for academic users since 2001. Since 2007, he has specialized in high-performance computing in support of researchers at Rice University. Chandler is also a husband, father, juggler, and disc golfer in his spare time. He sometimes blogs at http://chwilk.blogs.rice.edu/ and helps maintain his group's website at http://www.rcsg.rice.edu/.
Jason is Assistant Director, External Collaborations at Cold Spring Harbor Laboratory’s DNA Learning Center (www.dnalc.org)
and is the Education, Outreach, and Training lead for CyVerse. Jason organizes, instructs, and speaks at more than dozen
bioinformatics workshops annually. In addition to Cold Spring Harbor, Jason is faculty at Yeshiva University in New York,
where he created and instructs a research program for their Girl's High School. Jason also serves on committees and boards
for several projects that advance science and science.
Steering Committee (2016 Chair, 2015 Member)
Lynne Williams works at the Rotman-Baycrest Research Institute, where she studies the cognitive neuroscience of language development over the lifespan and develops statistical techniques to analyze large multivariate data sets. Her most recent work is concerned with pattern classifiers in brain imaging and age-associated patterns of variability in brain activation.
Ryan Williams is a postdoctoral researcher at Iowa State University in Agricultural and Biosystems Engineering. He uses ecological theory to understand complex patterns within microbial communities and metagenomic data that relate to changes in the environment. Away from the computer, Ryan applies his research findings to educate local farmers about microbial ecology and agricultural sustainability.
Evan Williamson is the Digital Infrastructure Librarian at University of Idaho. Despite a background in Art History, Anthropology, and Philosophy, he always manages to get involved in all things digital. At the library he works with Data & Digital Services to bring cool projects, enlightening workshops, and innovative services to life.
Anna Williford is a research scientist at the University of Texas at Arlington with a PhD from the University of Iowa in evolutionary biology. Her research relies heavily on the analysis of next generation sequence data in hope of identifying genetic changes that contribute to functional divergence within and between species. It seems like whenever she is not doing NGS analysis, she is preparing for some sort of Software Carpentry activity (and loving it!)
Frank Willmore received his PhD in chemical engineering from the University of Texas after a career in software engineering. He served as a research associate at the Texas Advanced Computing Center before leaving to pursue consulting interests. He currently lives in Taipei where he is lead editor on a book on scientific and technical computing, to be available from CRC/Taylor and Francis.
Aidan Wilson is an eResearch Analyst at Intersect Australia, a not-for-profit organisation that helps researchers at Australian universities achieve research impact through technology. Before that, Aidan was a linguist and spent his postgraduate years researching Aboriginal Australian languages. He also worked as an archivist and data manager at PARADISEC, an archive for digital material relating to endangered cultures in the Australia-Pacific region, a role in which he taught himself basic coding and unix competency so as to work more efficiently.
co-founded the Software Carpentry project in 1998. He has been a
professional software developer, an author, and a university
professor. Greg received his PhD in Computer Science from the
University of Edinburgh in 1993.
Director of Instructor Training
Maintainer: Instructor Training
Paul Wilson is a Professor at the U. Wisconsin-Madison where he teaches nuclear engineering. His research group, CNERG, delivers new capability for the simulation of complex nuclear systems. The Hacker Within was born from his research group as he tried to impart Software Carpentry skills upon his graduate students.
Donny Winston studied scanning-charged-particle-beam lithography before shifting professional focus to software-as-a-service. He maintains and develops open, web-based tools for data-driven discovery of advanced materials (see materialsproject.org) at the Lawrence Berkeley National Laboratory. He uses hyphens extensively.
Jared Winton is the Application Services Manager at V3 Alliance and part of the V3 Alliance leadership team. He has had extensive practical experience in management and oversight of projects for a wide range of research disciplines and organizations. Jared worked at the Victorian eResearch Strategic Initiative (VeRSI) for six years in roles from software engineer to program manager, and prior to that was a research fellow for the Experimental Particle Physics group at the University of Melbourne.
Christopher Woods is a researcher at the University of Bristol, where he develops software for modelling medicinal drugs and proteins. He obtained his PhD in physical chemistry at the University of Southampton, where four years hacking through established academic codes gave him a keen appreciation of the importance of clean design, good documentation, testing and version control.
is researching the effect of disease on the human eye. He creates
tools to analyse high resolution imaging and electro-physiological
signals and integrate the results with demographic and phenotypic
information scrapped from a variety of sources. His love of the
command line started with
10 PRINT "hello" GOTO 10.
Maintainer: R for Reproducible Scientific Analysis
Steven Wu is a computational biologist and currently he is a postdoctoral researcher at Arizona State University. He focus on developing novel statistical methods to address evolutionary questions.
Stefan Wyder is a postdoctoral bioinformatician working at the University of Zurich in Switzerland. He is currently working in bioinformatics support and training mainly dealing with high-throughput sequencing data.
Xiao Xiao is a postdoc at the University of Maine. Her research area is macroecology, which identifies ecological patterns and processes at broad spatial and/or temporal scales using large amount of data. She finds programming to be an essential part of her research, and looks forward to sharing the skills she has learned at workshops with others.
Fan Yang is currently a postdoctoral research scientist at Iowa State University. Her research interest is studying microbial communities and extrapolating their functions and impacts from integrated datasets, such as sequence data and biogeochemistry data. She was greatly benefited by attending a Software Carpentry course when she was in graduate school and would like to pass on the great experience and learn more through teaching.
Hsi-Kai Yang was a software engineer at Microsoft and Sony Electronics, and is currently is working on data science projects. He wrote his master's thesis on specification languages and did post-graduate research on mathematical modeling of network switches. He is enthusiastic about teaching better software practices and paradigms.
Isaac Ye works for Compute-Canada/SHARCNET at York University in Toronto, Ontario as a High Performance Computing Programming Specialist with a research specialty in the Computational Fluid Dynamics. He has been involved in various research field such as the Meteorology, Bioinformatics, Crystal modelling and mainly turbulent combustion which requires massive computation.
Lynn Young is a bioinformaticist specializing in the analysis of high-throughput data. She is with the National Institutes of Health Library Bioinformatics Support Program which provides services for data analysis, consulting, training, and computer programming. She studied the vibrational modes of DNA for her thesis in solid state physics.
Constantine Zakkaroff is a Post-doctoral Research Fellow at the BlueFern Supercomputing Centre, University of Canterbury, New Zealand. Constantine has a BSc and MSc in Computer Science and Software Engineering from the University of Canterbury, New Zealand. Constantine's PhD in medical image analysis is from the University of Leeds, UK. Constantine's current research is focused on large-scale physiological simulation and parallel computing. His expertise covers object-oriented software design, scientific visualization and supercomputing.
Jingchao Zhang received his PhD in Mechanical Engineering from Iowa State University in 2013. He currently works as an HPC applications specialist at University of Nebraska-Lincoln Holland Computing Center, where he works to promote the use of high performance cyberinfrastructure and a wide variety of research projects requiring high performance and/or high throughput computing, storage, and other cyberinfrastructure.
Qingpeng Zhang is a Ph.D. candidate in Computer Science and Quantitative Biology at Michigan State University. Broadly his research interest is developing novel computational method to make sense of the big data generated in biological research, especially large metagenomic data. He obtained a bachelor degree in Physics from Nanjing University in China.
a postdoctoral fellow in the University of Arizona School of Plant
Sciences studying the microbial ecology of plants and their
associated fungi. He has a PhD from Stanford in Ecology and
Evolutionary Biology. His love of the command line started way
back with the Commodore 64 and
Maintainer: R for Reproducible Scientific Analysis
Tiziano Zito moved from theoretical physics through neuroscience to finally become a full-time system administrator. He is now working as a Scientific Computing Coordinator at the Jülich Forschungszentrum in Germany. He is the main organizer of the Advanced Scientific Programming in Python summer school series.
Andrea Zonca has a background in astrophysics and now works helping other scientists deploy their data analysis software on supercomputers as staff at the San Diego Supercomputing Center.
Juan Carlos Zuniga is a research software engineer. He has a PhD in systems theory and is specialized in the development of fast algorithms for matrix and polynomial matrix computations. He worked as an assistant professor and later as a computational science consultant and technical software developer for the industry and different private research companies. He has years of experience developing technical software to solve complex problems in different areas of science and engineering. Juan Carlos currently works as an advanced computing research analyst and HPC specialist at the University of Saskatchewan, and for Westgrid/Compute Canada.
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