Analyzing Next Generation Sequencing Data - 2012 Course

We held the 2012 workshop on Analyzing Next Generation Sequencing Data from June 4 to June 15, at the Kellogg Biological Station in western Michigan, about 30 minutes north of Kalamazoo.

(This is a long delayed blog post. :)

The goal of the workshop is to take biologists with little in the way of computational knowledge and bring them up to speed on doing bioinformatics data analysis of next-gen data. We don't want to turn them into practicing computer science researchers, but rather we want to get them to the point where they can run their own analyses using other tools and some small amount of scripting. It's a tricky thing to manage!

This year the course was sponsored by NIH (through an R25 grant), which let us expand our set of invited faculty. The faculty this year included Ian Dworkin from MSU, Istvan Albert from PSU, Corbin Jones from UNC, Erich Schwarz from Caltech & Cornell, and Julian Catchen from Oregon State.

We also had 4 TAs from my lab: Adina Howe, Qingpeng Zhang, Jaron Guo, and Likit Preeyanon. Many people came up to me and told me what a great job they'd done, which is always nice to hear; no heads need roll.

Applicants

We received a total of 168 applications from researchers. 110 researchers were from the US; 25% of US applicants come from Michigan, with the remaining 75% split across 35 other states, including 12 from California, 8 applicants from Arizona, 6 from Wisconsin and North Carolina, and 5 or fewer from each of the other 31 states. We also had over three dozen international applicants, including applicants from Germany, Norway, Brazil, Slovenia, Portugal, Spain, Australia, New Zealand, and France.

Most notably, we had over 22 tenure-line faculty apply to the workshop!

We used biological system of choice, data sets already available, bioinformatics approaches needed, and existing knowledge/background to choose a broad range of students that included vertebrate, invertebrate, microbial, and plant researchers.

We admitted 8 graduate students, 10 postdocs, 4 tenure-line faculty, and 3 industry or independent researchers. The workshop participants are spread across the US and the world, with 4 from Michigan, 2 from Pennsylvania, and participants from several other states including CA, OH, KA, NH, IL. International participants included people working in Mexico, Canada, France, Spain, and Switzerland.

Workshop

We spent between 6 and 10 hours each day on lectures, tutorials, and free working time. (We also included plenty of time for frisbee, volleyball, swimming, napping, and running -- think summer camp for scientists!) Several people told us that they really liked the balance of activities, which let them stay sharp and alert during the lessons without getting bored by too much instruction.

Course Materials

As always, the majority of the course materials are available online under a CC-BY-SA license. This year we put the disqus commenting system in place, which let students ask questions and provide feedback that was recorded. (Seemed to work well!)

One big shift this year was in using the ipython notebook. Some people found it distracting (it's one more thing to learn, on top of the shell and some minimal programming and a bunch of tools!) while others found it super-awesome; either way, we produced a bunch of notebooks that illustrate how to run BLASTs, use khmer and screed, etc. (You can see video introductions to the ipython notebook here, under my current fall course.)

Another big shift this year was that I had personal research content to introduce. While I didn't want to make the course all about our stuff, which is still in the process of being published, every third student had a problem that could be addressed with digital normalization. So, I introduced digital normalization early in the second week, and had the TAs talk about their research then as well. (It went better than expected.)

Critiques

Every year, at the end of the course we do a post-mortem, where people are supposed to say mostly negative things. As in previous years, most of the critiques were about how we handled basic UNIX and programming knowledge; we try to walk the line between motivating the UNIX shell, Python, etc., and actually teaching them about it. It's tough! But nothing terribly serious other than the usual "more stuff/ better taught"...

Evaluation

This is the first year where we had a formal external evaluation done for us. As I've mentioned before, I think assessment and evaluation are critical: they let us determine whether or not the students are learning what we want to teach them, and helps us target future efforts more precisely.

The evaluation results came in a week or two ago -- and, I quote:

A pre-workshop evaluation of the NGS Summer Workshop 2012 - Analyzing Next-Generation Sequencing Data was conducted on June 4, with a post-workshop evaluation occurring June 15, 2012. Observations were also conducted at the start, middle, and end of the workshop. In all, 25 participants completed the pre-survey and 23 completed both the pre- and post-surveys.

EXECUTIVE SUMMARY OF RESULTS

We summarize evaluation results below. [ ... ]

In summary, we found that:

  1. Scores on the Perception of Computational Ability scale were calculated for both the pre- and post-workshop surveys. Results from the Wilcoxon Signed Ranks Test indicate that pre- and post-workshop results are statistically different (Z = -4.116, p <= 0.001), with higher post-workshop scores. This indicates that participants perceived greater computational ability after engagement in the workshop.
  2. Scores on the Computational Understanding - Sequencing Data scale were calculated for both the pre- and post-workshop surveys. Results from the Wilcoxon Signed Ranks Test indicate that pre- and post-workshop results are statistically different (Z = -4.111, p <= 0.001), with higher post-workshop scores. This indicates that participants perceived greater understanding after engagement in the workshop.
  3. Scores on the Python Coding Ability scale were calculated for both the pre- and post- workshop surveys. Results from the Wilcoxon Signed Ranks Test indicate that pre- and post-workshop results are statistically different (Z = -4.374, p <= 0.001), with higher post- workshop scores. This indicates that participants perceived greater coding ability after engagement in the workshop.
  4. Participants were generally very satisfied with the workshop. On average, participants rated the workshop components as Good-Very Good.
  5. Participants generally felt the workshop met their needs and would overwhelmingly recommend it to others.
  6. Participants were generally positive about the workshop in their open-ended comments. Suggestions for improvement include: more time on RNA sequencing and differential expression/data, less focus on why tools are not good, more focus on basics of programming, scripts and/or UNIX early on, and more details about daily activities.

The informal summary by our evaluator was "you nailed it" - always nice to hear! The above results are slightly squishy because they are based on self-perception; we are hoping to get more objectively quantifiable results out of the free form essays. However, I think we can be reasonably certain that if the students hated the course, they would not be learning very much, so ... so far, so good.

We are currently working on coding the free-form essays in preparation for a publication on educating advanced biologists in computation; I'll post those results when I can.

2013 and Beyond

The course is funded for one more year, through 2013. I've done some hand-wringing about whether or not I should run the course in the future. There are lots of reasons not to run the course: it's not strongly valued by MSU, it doesn't bring in much money, it consumes a big chunk of my summer time, and frankly it's a lot of work! But... in many ways it's strongly affected my research program for the better. I understood de Bruijn graph assembly because I had to learn it to teach the 2010 course, for example; and now I'm publishing in the area, two years later. Each year I get a dose of opinion about what is holding people back, and this lets me target and refine my bioinformatics research. This year, I figured out how to apply digital normalization to 454 data (or, rather, how to evaluate it ON such data, which is more important); and I developed some potentially great ideas on how to do better mRNAseq quantitation. Teaching is good for research! (There's also evidence that graduate students' teaching improves their research, too.)

It also serves as a great networking tool, of course -- I've been invited to give 4 or 5 talks by previous students so far -- and this year we had some really excellent sequencing center folk who could give me the skinny on the various platforms, which was valuable. Admitting senior faculty has its pluses as well; one of the attending full professors offered to write me a tenure evaluation letter based on the high quality of the course (!).

So, largely because of these research impacts, I've decided to apply again to the NIH to run the course in the future, and I may also be trying to figure out a Research Coordination Network (NSF) of some kind to expand our efforts. I'm trying to figure out how to continue bringing in new ideas and tools to the course; one idea is run an additional "advanced tools" discussion breakout at something like Plant & Animal Genome, where we could get some candid opinions on tools and figure out what tools are good/better/best.

...suggestions welcome.

Anyhoo, the application is due next Tuesday. Wish me luck!

--titus

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