We are pleased to announce that Enthought has generously given us a grant to support some of the travel costs associated with our boot camps. Along with hosting an earlier version of our material for several years and preparing a rock-solid Python distribution for scientific computing, this is one more good deed we’d like to thank them for.

Enthought, Inc is delighted to provide funding to Software Carpentry to support educating scientists in basic computing skills.  Enthought was founded with a mission to improve the way scientific computing is accomplished, which we do through our support of open source initiatives, applications we build for customers, and through a goal we share with Software Carpentry: teaching scientists computing skills that improve their productivity and advances their contributions to science.

One of the things we need to do in the next six months along with running boot camps and updating our online content is to create some sort of badging to recognize people’s skills and contributions. As we said in the proposal to the Sloan Foundation, “A badge program will provide near-term incentives for both learning and mentoring; a framework to support viral, peer-driven engagement with the program; and facilitate recognition by partner institutions and potential employers.”

Read more…

A couple of people have recently asked, “How do you go about asking for money?” Applying for grants from NSERC, the NSF, and other agencies is something they understand (though it never actually worked for me), but cold-calling people, or emailing them out of the blue, isn’t something most academics have ever done.

I’m now doing another round of this, and since this is supposed to be an open-everything project, I’ve posted the short pitch I use as a starting point when approaching someone new. I hope you find it useful, and of course, feedback is always welcome.

Today’s interview is with Indiana University’s Professor Andrew Lumsdaine.

Tell us a bit about your organization and its goals.

One of the reasons the School of Informatics and Computing exists is that computing of various kinds has become part of almost all academic disciplines. The school’s goal is to educate students in computer-related areas, as well as traditional computer science, and it’s important that the principles of software development be taught. The same holds for my research group, which works in HPC (where the ‘P’ means both “performance” and “productivity”). There’s a huge need for reproducibility in CS research, both for the sake of sound science and also so that people actually can build on each other’s work. In order for that to happen, we need some guarantees about quality and reusability, and improving basic skills is a necessary prerequisite.

Tell us a bit about the software your group uses.

The first group (students in the school) uses every kind of off-the-shelf application you can think of. It’s mostly closed source; they do relatively little development. My research group mostly build their own tools, and tend to be pretty zealous about open source.

Tell us a bit about what software your group develops.

We started by building a version of MPI, and are now part of the Open MPI collaboration. Working with dozens of collaborators around the world requires the same skill set as other open source projects: having a software repository, nightly build, regression tests, and proper licensing protocols is essential. We also contribute to the BOOST C++ library, in particular a parallel version of the BOOST graph library.

How do you hope the course will help them?

Bill Gropp once said, “Computers should be a labor saving device,” but it often doesn’t feel that way. We think that adopting basic development practices will allow people to do more and better science. We also think that organizing this material, instead of having grad students tutoring each other erratically, will give us a common base of knowledge that we can then rely on.

It’s important for us institutionally that the course is self-contained. Introducing a bit of computing here and there across the curriculum is an idea that comes up a lot in faculty meetings, but I don’t know of any successful across-the-curriculum efforts. Putting this training in one place is more efficient, and makes it someone’s job to ensure success.

How do you plan to evaluate the impact the course has had?

(laughs) That’s a forbidden question in Computer Science.

Today’s interview is with Professor Titus Brown, from Michigan State University.

Tell us a bit about your organization and its goals.

Michigan State is one of the Big Ten and hence a really big place. We do a lot of research, in particular, and a lot of that research is in biology. The Gene Expression in Disease and Development focus group is a collection of molecular biologists at MSU that are interested in gene expression and methods (experimental, genomic, and bioinformatic) for understanding it.

Tell us a bit about the software your group uses.

Most molecular biologists either use pre-packaged analysis tools, or nothing at all. Even the local bioinformaticians have generally not picked up on version control or anything more complex than Perl analysis scripts.

Tell us a bit about what software your group develops.

My lab develops software for our own research, as well as working on reusable libraries for others to use, and eventually we hope to build GUIs or Web applications for even more general use. We’re interested in soup-to-nuts—basic sequence analysis all the way through to database curation and genome-scale visualization.

Who are you hoping Software Carpentry will help?

Any biology graduate student that needs to do anything unoriginal, computationally speaking. Computational students should find it particularly useful: someone who has been through the normal CS curriculum, for example, but has never learned about SQL databases, version control, Web services, testing, etc. We get a pretty wide range of backgrounds in our interdisciplinary grad students, so it is impossible to identify a single training track that will serve even a majority. Hopefully the SWC material can backstop the material we are already developing on the subject of “being effective at computation.”

How do you hope the course will help them?

Like many other biology research institutions, we’re finding ourselves overwhelmed with genome-scale data; all the new sequencing platforms (along with tandem mass spec, and a host of other systems) deliver stunning amounts of data. We are not well prepared to deal with the data, and the old molecular biologist standby of loading everything into Excel doesn’t scale at all. So molecular biologists are starting to have to learn to program in order to do pretty much anything with this data. But while we at least have courses that teach people how to program, we have basically no computational science curriculum, and what we do have is targeted less at being effective than at being minimally capable in a given field.

I’m not a fan of big ideas. I would just like students to have the ability to improve their general scientific computation skills iteratively, without having to go through a class.

How will you tell what impact the course has had?

I will be happy the day one of my own students casually (and correctly) uses a technique that s/he could only have learned from the SWC material. I will be thrilled when somebody else’s computational student name-drops SWC as the source of a technique that sped up their research. And I will be ecstatic when a previously purely experimental students tells me how great SWC has been for helping them learn how to do computational science better.

We don’t have any systematic way of assessing the impact of the course, however.

Today’s interview is with Dr. Daniel Gruner of SciNet.

Tell us a bit about your organization and its goals.

SciNet is a High Performance Computing (HPC) consortium. We provide hardware and software platforms for researchers who require HPC in their work. We are also enabling this research, in ways that had not even been thought of before. The enabling is partly due to us having the largest systems in Canada, and partly by helping people port their codes to run on these very large systems.

Tell us a bit about the software your group uses.

We are not a research group, but rather we provide help to researchers. We have expert HPC developers and practitioners, who use the traditional tools of HPC, namely Message Passing (MPI) or shared memory (OpenMP) multithreading techniques to scale out scientific codes.

Tell us a bit about what software your group develops.

Our system administrators mostly develop tools for systems management. Our parallel programming analysts assist in porting users’ codes to the parallel HPC platforms, and being scientists themselves they write their own codes as well. The software developed here is mostly for scientific simulations and data analysis.

How do you hope the course will help them?

The course is not really geared to our group, but rather to scientists who are users of our systems. Some of our users are highly skilled software carpenters, but many of them are not. Some develop their own codes, while others use existing software for their simulations or data analysis. Those users who are not skilled carpenters should learn techniques from workflow planning to data management, software development tools to development lifecycle management, data analysis, documentation techniques to version management.

We have found that most students in science and engineering who need to use HPC in their work lack the basic education that your course provides. Not to speak of those disciplines where HPC has not been traditionally used…

How will you tell what impact the course has had?

Hopefully we’ll see it in better systems’ utilization, smarter approaches to problem solving because the tools will be available and known to the users. We should notice in the way users approach us for help in coding and in running their jobs, and we should be able to interact with users at a higher level of understanding. We should be able to see more and better parallelized codes, more efficient data management, better understanding of how HPC systems operate and how to optimize their utilization.

The Centre for Digital Music (C4DM) at Queen Mary, University of London, is seeking an experienced Software Developer with a background and knowledge in Audio and Digital Music, to work on a new EPSRC-funded project “Sustainable Software for Digital Music and Audio Research”. The aim of this project is to provide a Service to support the development and use of software, data and metadata to enable high quality research in the Audio and Digital Music research community. Please see the job posting for more information.

The latest in our series of interviews with Software Carpentry sponsors is with Microsoft’s David Rich.

Tell us a bit about your organization and its goals.

Microsoft has very recently expanded the group working on HPC (clusters and similar) to address a broader “technical computing” solution set. This includes areas such as parallel programming, and making it easier for scientists and engineers to apply computational power to their work.

Tell us a bit about the software your group uses.

As a software vendor, we are concerned with both our own products and the myriad of applications that form the full solution set for our customers.

Tell us a bit about what software your group develops.

We build tools for others, but also use them ourselves!

How are you hoping Software Carpentry will help?

Today, there are few disciplines (any?) where some form of computer based analysis or at least reporting is not an important part of success. Few individuals have the time to become expert in computer science as well as their primary field. A course participant might be a grad student looking at their first large dataset or an experienced scientist in industry who wishes to improve their efficiency.

How do you hope the course will help them?

Professional chefs keep their knives sharp. Musicians take care of their instruments. We hope that software carpentry students learn to think of their software and computing resources as a primary tool and develop the habit of thinking about how to use that tool more efficiently.

How will you tell what impact the course has had?

All world problems solved by a huge increase in productivity! Or if not that, students who report increased efficiency in their work.

Titus Brown has posted a summary of his course on next-generation sequencing data analysis for biologists with little or no previous training in computing. It went very well, and he’s already trying to figure out how to do it again next year. If you can help, please give him a shout!

Later: Titus and his students used Amazon’s web services in the course, which earned them a post on Amazon’s blog.

Today’s interview is with Prof. Mark Plumbley, of the Department of Electronic Engineering & Computer Science at Queen Mary University of London.

Tell us a bit about your organization and its goals.

We are a new project “Sustainable Software for Digital Music and Audio Research”, funded by the UK Engineering and Physical Sciences Research Council (EPSRC), and based at the Centre for Digital Music (C4DM) at Queen Mary University of London. The aim of the project is to provide a Service to support the development and use of software, data and metadata to enable high quality research in the Audio and Digital Music research community. It’s really about getting research results—including robust software to implement that research—out to the people who should be able to use them, and then keep it working.

Tell us a bit about the software your group uses.

We use some generic signal processing development tools like Matlab, as well as C/C++, Python, Prolog, etc. We also use some music-specific software, like Max/MSP, SuperCollider, and Ableton Live. Some people use Subversion for version control (even occasionally for writing joint research papers in LaTeX).

Tell us a bit about what software your group develops.

Some of the software we’ve already developed is for our own research, but we are increasinly making more and more available for others to use: see http://www.isophonics.net/ for a selection. Some of this includes:

• Sonic Visualiser: an application for viewing and analysing the contents of music audio files.
• SoundBite: an iTunes plugin to create great-sounding playlists.
• BeatFx: a suite of real-time musical audio effects which are automatically synchronized to the beat.

Who are you hoping Software Carpentry will help?

The new project includes software developers whose job it is to take flaky research software and turn it into robust software usable by other researchers. We hope that the Software Carpentry course will train up a next generation of PhD students and researchers that can create robust research software for themselves, so they don’t have to rely on some other developers to come along later and clear up the mess.

How do you hope the course will help them?

We hope that the course will help researchers to think about robust software development from the outset of their research, not as an afterthought. Therefore when the paper is published, or the thesis is finished, the software that implements that research will be available for others to use in a robust and sustainable form. This should also benefit the researcher themselves, since people using their software will cite their research papers when acknowledging their software.

How will you tell what impact the course has had?

We would like to follow up the students who attended the course, and see how well they are producing well-written and well-documented research code, in comparison to what they would have done without it. Some of the impact will be more nebulous, about changing attitudes to the role of software in research. But if we get this right we should be pushing at an open door. “Research Impact” is the name of the game at the moment, and what better way to help your audio research have impact than make software for it available in as sustainable software which is usable by the people who need to use it!