Software Carpentry at Scripps - Nov 2012 - postmortem

I am just returning from a trip to Southern California that included, among other things, the teaching of a two day Software Carpentry workshop at The Scripps Research Institute. There were two instructors, myself and Tracy Teal, a research scientist at MSU; and two external TAs, Qingpeng Zhang (one of my graduate students) and Cait Pickens (an MSU grad student studying computational learning). Andrew Su, the hosting faculty member, helped out quite a bit.

Justin Kitzes, a postdoc from Berkeley, was supposed to come but fell ill at the last minute :(.

Note that Cait has posted two reports on it as well; I like how touchingly naive she is about my preparation, where she thinks that I was only preparing things at the last minute because Justin fell ill ;).


The venue was pretty good, although we crammed 40 people into a room that was a bit small, and the screen was too small to be clearly seen from some positions in the room. There was a kitchen next door where the Scripps folk kept coffee and pastries all day, as well as bagels for breakfast and sandwiches for lunch - win!

One thing we had that I would have liked at other venues was a plethora of nearby conference rooms. This let me go to another room when I was preparing or modifying tutorials. It was also a good place to meet with the TAs to plan things.

One minor obstacle was that the "guest" network (which was all that was available to us as visitors) didn't initially have ssh enabled! This blocked us from ready access to some of our materials and demos. Andrew quickly got that changed, which was fantastic (lightning fast sysadmin response!); but then, later on, it proved to be impossible for me to get to non-canonical Web sites, which blocked me from easily setting up a multi-user Amazon machine running multiple ipython notebooks.

Recommendation: In addition to a main room, ask to have a nearby conference or breakout room where instructors can meet with students and with each other.

Recommendation: Make sure that the local network is open to both ssh and http/s for visitors; non-canonical ports (8000+?) would be a bonus. Best of all would be to enable login accounts for the instructors on the same network that the students are using.

Social hacking

It's always difficult to manage workshops, both in terms of short-term pacing and long-term retention. Cait and Tracy tried some new approaches out for this workshop: research paragraphs, minute cards, pairing into groups, and a formal concept roundup at the end.

I think the biggest win for me was the minute card concept. At the end of every session (before each break) we asked everyone to take a minute to write down one thing they had learned, and one thing they were confused about. They then turned these in to us (anonymously). This ended up being an excellent barometer of the session, and both let us pace lessons better and identify & address general points of confusion. Highly recommended.

At the beginning, we also asked everyone to email us research paragraphs, identifying a specific problem that they wanted to solve using what they learned in the workshop (this came from the discovery that a 15-minute writing exercise did cool things). This was when we realized that virtually every biologist in the room was hoping we could help them out with sequence analysis :). The only negative was that for this (and other evaluation mechanisms) we forgot to ask for explicit permission to share their paragraphs with the local professor, and so will only be able to give summaries to Andrew.

We asked everyone to go through a formal concept roundup at the end. Cait wrote down a bunch of concepts that we'd taught, and asked people to build a map showing which concepts connected to each other. (I don't know how this turned out, as I was decompressing.)

On the second day, we also asked people to sit in pairs, next to people they knew or saw regularly. Greg Wilson (via Tracy) had said that research showed that concepts were retained better when they had a friendly person nearby to discuss stuff with, and to connect with after the workshop. I'm not sure how this went but I did see a lot more useful on-topic chatter the second day.

Recommendation: Use minute cards! Before every break, ask everyone to write down one thing they learned and one thing they were confused about, and hand them in.

Recommendation: Ask everyone for research paragraphs at the beginning of the workshop.

Recommendation: Identify what student information and documents you want to share with the workshop host before starting the workshop, and get explicit permission to do so from the students. (To share them without permission is unethical.)


We covered: the shell; automating tasks; basic Python, including graphing and parsing; basic Python data structures; installing and using some Python packages, including a BLAST parser and a sequence parser; some useful UNIX tools (grep and find); and, at the end, a whirlwind tour of testing, version control, and analysis pipelines.

The main problem we faced up front was that we were teaching biologists, who generally do not encounter computation anywhere in their coursework. That had at least two direct consequences: we had to start at a very basic level, and we had to motivate people to pay attention to us, which in turn required that we speak their language. Luckily (well, ok, partly by design ;) Tracy and I are both biologists, and Qingpeng is in my lab, so we were familiar with the lingo and domain-specific problems.

We knew, going in, that the level of the students was going to be a problem -- we'd done a pre-workshop survey. But we still went into the workshop with material that was systematically too high level for the students. So we had to adapt on the fly.

I think we really need three "levels" of Software Carpentry material: a beginner level, an intermediate level, and an advanced level. I think most of the current SWC stuff focuses on the intermediate level of stuff that physicists and engineers need to know but never really get taught -- testing, version control, and automation. The beginner level should focus on issues like correctness, beginning automation, pipelines, and introduce testing and version control as concepts. The advanced level can focus on optimization, C/C++ integration, detailed testing advice, etc. -- stuff that only people deep into Python really get into -- if indeed we want to offer it at all. (See my Intermediate and Advanced Software Carpentry material for an example.)

A number of people came up to us after the workshop and said that we'd provided a great intro to and overview of computational concepts, and they were much clearer on where UNIX and programming could fit into their science. I think that's about as much as we can realistically hope for from a beginner workshop -- but that's already way more than we do in most biology training, and I think it's really worth it.

Recommendation: Make sure workshops are taught by domain experts, and motivate students with close-to-real-world examples from their domain.

Recommendation: Develop "libraries" of beginner, intermediate, and advanced topics that we can reuse as we move forward with Software Carpentry.

Teaching testing

I used IPython Notebook to implement a simple set of unit tests and regression tests -- you can see the notebook here.

The unit tests I developed by writing a function that calculated G/C content for a DNA sequence, and then working through issues like Ns, lower case letters, and null strings. I think everyone got the point, which was neat.

For the regression tests, I tried to motivate this by talking about the software lifecycle, specifically in research, and discussed how nice it was to be able to keep software consistent in terms of results. I then implemented a simple regression test that compared a "saved" output for a script to the current output. I don't know how successful I was, but I gather the more advanced users in the audience appreciated seeing some testing in action.

Teaching version control

We ended up not having time to teach command line git, although we did use it to distribute data (which worked really well, BTW). In some cases where git wasn't installed properly, we had to use the download button on the github project to grab a zip file, but that worked fine once we figured it out.

For people that haven't seen (distributed) version control before, the github workflow (fork, edit, send pull request) seems to make sense. At least, I felt very comfortable teaching it, and everyone completed a full pull request set.

I'd love to see how this interfaces with a follow-on command line git tutorial; next time!

Recommendation: Use git and github to distribute data for workshops. You can use either the repository or the 'download zip' button.

Something to try next time: Teach the github workflow as an intro to distributed version control.

Software installs

Software installation was, as usual, horrible. We squared several things away fairly quickly by settling on Anaconda CE for Mac OS X and telling everyone else to just use VirtualBox to run a virtual machine, but this left behind a bunch of people with old Windows machines (Anaconda CE just didn't work on Windows, at least not for me; and VirtualBox is a bit of a resource hog). There was also a fair bit of confusion about how to use Anaconda properly, aided and abetted by the fact that none of the tutors had any experience with it either.

BTW, even if we could have gotten Anaconda CE working on Windows, none of our pipeline examples would have worked, because they included shell commands. Windows really is just different.

What's the solution here?

From my experience in running a number of workshops, I give you the following set of points to consider.

  1. Cloud computing always just works, 'cause it's their business model to make things "just work".
  2. Windows is horrible and strange for most of what we want to teach, which is standard computational science practice -- which in turn generally involves UNIX.
  3. Software installs on Windows machines are always kind of weird anyway.
  4. VirtualBox works pretty well in general, but seems to fail (due to compute resource requirements) on some small number of machines.
  5. The less computationally experienced a person is, the more likely they are to have a weird/non-standard or resource-limited system that makes it impossible to install something we need.

So the question is, what do we want to be teaching people? If we want to teach people how to use their own laptops to do stuff, we're basically doomed; every laptop is different and we spend all our time debugging environments.


If we want to give people in-depth exposure to ideas and good computational practice, I think we're basically ok: some people will be able to install all the stuff just fine, while others will have to use a VM, and an unlucky few will have to resort to a cloud machine. But everyone will be able to follow along. If students can follow along with the course materials and are properly motivated, they should be able to go to their local computer support later on and get the software installed -- i.e. after the workshop, when it's not a melee situation.

We can definitely help future workshop tutors by providing up-to-date installation instructions, annotated by instructors based on experience, and also providing up-to-date VirtualBox and Amazon images. This would let instructors get on with the business of teaching as quickly as possible. And, more generally, other (non-Software Carpentry) courses could make use of our images for their classes - a total win.

So here are my recommendations:

Recommendation: Rely on Anaconda (for Mac OS X), virtual machines (for Windows), and cloud machines (for situations where neither work).

Recommendation: Keep an up-to-date Virtual Machine ready for workshop attendees to download. (The one we used had an out-of-date IPython Notebook install, for example.)

Recommendation: Develop a multi-user Amazon image that lets people use the shell and run IPython Notebook. (This requires some scut work but nothing terribly difficult.) If we base this off of StarCluster then instructors can (optionally) do a StarCluster lesson, too.

Recommendation: Provide Anaconda, virtualenv, and virtual machine instructions for each software install.

Recommendation: Provide video tutorials of the Anaconda and VM install, so that people can tell if they've done it properly.

And now it's time for a rant. We all suck. The fact that we, as computer people, put up with all of this hard to install software is incredibly depressing. Even worse, it's not for a good reason -- it's because computer people are lazy when writing software and happy to spend the time on the back end to figure out its complexities. We should stop using packages that are hard to install, or yell more loudly at the people building such packages. It's incredibly frustrating and infuriating, and it's holding us up as a society, at this point.

Hosting and editing workshop materials

The Software Carpentry tutors list continues go have "robust" conversations on how best to host and edit workshop materials, especially in a collaborative setting.

This was the first workshop where we tried out github's online editing capability of the ReadTheDocs-hosted site. It went OK -- the online editing was less important for the teachers than was the automatic updating of the course Web site (see Tracy kept on wanting to use the github site, which natively rendered the reStructuredText documents, instead of the Sphinx-based ReadTheDocs site. I personally think the extra structured offered by Sphinx is nice but don't have any real evidence of that ;).

Our workflow for the online materials was to outline our proposed tutorial sections, adapting existing materials as possible or writing new ones as needed, and then post those to the site in preparation. I used IPython Notebooks a fair bit for introducing Python code and shell commands, and added those to the online materials after each tutorial section.

This all worked pretty well but required a significant effort on post-session Web site cleanup and editing.

My takeaway from this was that, like anything else worthwhile, there is still a significant barrier to entry in reStructuredText, and because of this (as well as the general time and attention required to maintain things) that you need to have someone pretty dedicated to the site.

I still like the online editing but it wasn't as useful as I'd hoped. This might be because we didn't introduce people to github until late in the second day, though. I still hold out hope!

Recommendation: have someone whose job it is to keep the Web site updated and sane.

Recommendation: have a static site that is auto-updated from github; ReadTheDocs can do this for Sphinx/reStructuredText sites. (Q: can gh pages do this for Jekyll sites?)

Recommendation: use reStructuredText and Sphinx, or Jekyll and Markdown, to build full sites. Don't use individual pages. Students like having a single Web site to go to, and github just confuses them.

Recommendation: provide a simple alias for the Web site. We used (a domain that I own). Make it easy to remember and type in, so that students can do it even if they don't have access to e-mail. Software Carpentry should buy a simple domain for this purpose. (I'm happy to donate the namespace...)

Something to try next time: introduce Web site editing earlier!

In-class interaction

One of the problems I've always had during my shorter workshops is getting significant feedback and interaction during the workshop. For longer workshops, students and TAs get to know each other quite well, but during the shorter ones the stranger-danger and intimidation factor seem to block many of the students from grabbing us and asking questions. This is important for a successful workshop: I like to adapt my materials and presentations to what the students actually need and are concerned with, and pacing presentations correctly is much easier with feedback. It's also nice to get feedback on the various pages, e.g. "I couldn't follow these instructions, but this tweak helped."

As part of the ReadTheDocs site, I'd provided disqus commenting; for our two-week summer next-gen sequence analysis course, this was successful in terms of garnering topic-specific feedback during and after the course. I'd hoped that the zero-entry disqus system would encourage people to do that during shorter course. That turned out not to work at all for this course, or at least it wasn't used at all :).

The surprise success was hipchat, a realtime online discussion forum. As you can see from the transcripts, we started to get increasingly many comments and questions this way as the course progressed, and it was nice to see. I also took to posting bits of code from the IPython Notebooks to hipchat so that people could monitor the forum to grab code instead of typing it in from the screen.

I've tried things like hipchat before (there was a Python-related one, convore, a few years back that I used) and never found them all that useful. What was different this time?

I think the success of hipchat rested on Andrew's initial enthusiasm for it, and Cait's continued use of it to answer questions and post links. You really need someone monitoring this kind of forum full time, and Cait used it effectively to debug people's problems and (failing remote intervention) to get them to raise their hand so she could go help them in person.

I would definitely use hipchat (or something similar) again.

Recommendation: Use an online realtime discussion forum, but expect to need to have someone really focused on answering questions on it.

Real world applications

I implemented a "real" end-to-end example of a pipeline combining shell and Python on the first day, and Tracy wrote a full Python data munging script for a student's problem on the second day. I think this helped motivate the students to realize that this was both very useful stuff, and that while "complexity" awaited in every direction, it was nonetheless manageable.

Recommendation: embrace some real world complexity, if only to show the students what it looks like.

Miscellaneous points and problems

Paths are always a big sticking point. People just don't get paths. Everyone is on a different computer, running software from a different install, and no one can ever figure out what directory they're in or where the software they need to run is. It's not clear if we need more instruction up front, or if this is something that just takes time.

Speaking of things that just take time: don't bother trying to teach people who don't have any programming experience to program in a workshop! It takes weeks or months to do that. If they know some Perl or Ruby or Matlab, then I bet that you can usefully throw some Python at them.

I got my first really strong recommendations for OpenCourseWare (the MIT lectures) and the Khan Academy from a student in the workshop who said he'd learned to program from them -- never heard that before. He wanted to know why we weren't recommending them, or at least providing the links. I asked some CS profs and got answers that, on reflection, seemed somewhat strange; something to expand on later. My current take is that I'll recommend them for people who want to learn more Python, but not over taking a class or finding a good book.


There were a few really useful outcomes, apart from the generally positive comments from students.

First, most of the students in the class laughed at the 'sudo make me a sandwich' comic. That's real progress, folks -- more people being inculcated into nerd culture++.

Second, I got the sense that people came out of the class with some very specific requests for TSRI's computing infrastructure (like: provide UNIX workstations, running IPython Notebook). This kind of thing is good to see, especially when the requests and comments are coming from the field that's the ignored step-child of scientific computing, biology.

Third, Andrew seemed to get a lot of out of hosting the workshop. Maybe he'll host more! This one filled up in about 4 hours, and the class plus wait list had over 90 people on it. This is clear evidence of demand! (Warning, Andrew -- our rates will triple for the next one! ;)

Fourth, someone from the Salk Institute sat in and will be pitching SWC to the Salk.

Fifth, Tracy and Qingpeng and Cait all got to see what running a workshop was like, and seem to have thoroughly enjoyed it. So now they can run workshops all on their own!

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