We're running another hackathon!

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We ran a successful pilot hackathon, and we will run a second one soon!

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It takes constant work to make a welcoming teaching/learning environment!

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We just finished teaching a second version of our two-day shotgun metagenome analysis workshop, this time at UC Santa Cruz (the first one was in October 2016, at Scripps Institute of Oceanography). Harriet Alexander led the workshop and Phillip Brooks and I co-taught; Luiz Irber, Shannon Joslin, and Taylor Reiter …

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We just finished teaching a two day workshop at the Scripps Institute of Oceanography down at UC San Diego. Dr. Harriet Alexander, a postdoc in my lab, and I spent two days going through cloud computing, short read quality and k-mer trimming, metagenome assembly, quantification of gene abundance, mapping of …

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This March, Andreas Hejnol invited me to give a talk in Bergen, Norway, and as part of the trip I arranged to also give a trial workshop on "computational reproducibility" at the University in Oslo, where my friend & colleague Lex Nederbragt works.

(The workshop materials are here, under CC0.)

The …

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A few days, I gave an invited lecture on code review here at UC Davis. The class was the ECS capstone class, consisting of about 100 CS majors who were all working on some form of group project - all but a few were doing something with programming. I was told …

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We're running three half-day workshops for your remote viewing pleasure! All three will be live-streamed via YouTube (well, Hangouts on Air).

Today 2/17, at 9:15am PT, Tiffany Timbers (Simon Fraser U.) is going to be going through regular expressions in Python - see the workshop description.

On Friday, 2 …

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Today at 9:15am PT, Raniere Silva will be giving a lesson on advanced git usage, including bisect, branches, pull requests, and rebasing.

This lesson will be broadcast via YouTube as a Hangout on Air - if you're interested in watching it, we will post the link on the workshop page …

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We just finished the second day of a workshop on Docker at the Berkeley Institute for Data Science. I was invited to organize the workshop after some Berkeley folk couldn't make our Davis workshop in November, and so I trundled on down for two days to give it a try …

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When I decided to move to UC Davis, I was also seizing the opportunity to dramatically expand my training efforts. At Davis, it was made clear to me that I could substitute skills training -- in whatever guise I chose -- for my for-credit teaching; in consequence, I'd asked for money for …

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On Friday, Emily Dolson, a doctoral student at Michigan State University in Charles Ofria's lab, walked a bunch of us through d3.js for data visualization. Crucially, she did this from Michigan, and in addition to a local classroom, taught three other classrooms -- one in Florida, one in Virginia, and …

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Every year since 2010, I've been the primary organizer for a summer workshop on Analyzing Next Generation Sequencing Data. In 2010 and 2011, I was funded internally by the Gene Expression in Disease and Development group at MSU; since 2012, I've had a $50,000/yr grant from the NIH …

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What are the most concretely useful, interesting, awesome or neat things about Project Jupyter?

Over here at the Lab for Data Intensive Biology, we're putting on a workshop on Project Jupyter notebooks (the notebook system formerly known as IPython Notebook). This will be a two-day hands-on workshop, Carpentry-style, with the …

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I've often wanted to mark up arbitrary Web sites with annotations and reminders, and it's always been puzzling to me that this is missing from the Web. In recent years, I've heard more and more about a small non-profit called Hypothesis, which provides this general functionality via both a Chrome …

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On June 11th, 2010, I remember dropping the last workshop attendee off at the Kalamazoo train station, turning the car towards home, and nearly sobbing in relief that workshop was over and done and I could finally get some sleep now. That workshop was the first of a series of …

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Yesterday morning, we announced a Software Carpentry workshop here at UC Davis, running July 6-7 -- see the Web site for more information. I'm organizing, and Easton White and Noam Ross are co-lead instructors. (This is the first workshop I'm running since we became an affiliate!)

I'd love it if you …

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We just finished teaching the second of my RNAseq workshops at UC Davis -- the fifth workshop I've hosted since I took a faculty position here in VetMed. In order, we've done a Train the Trainers, a Data Carpentry, a reference-guided RNAseq assembly workshop, a mothur (microbial ecology) workshop, and a …

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Here are some statistics from this year's applications to the NGS course. Briefly, this is a two-week workshop on sequence analysis at the command line and in the cloud.

The short version is that demand remains high; note that we admit only 24 applicants, so generally < 20%...

Year	Number of …

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Here at the Lab for Data-Intensive Biology (TM) we are constantly trying to explore new ideas for advancing the practice of biological data sciences. Below are some ideas that originated with or were sharpened by conversations with Greg Wilson (Executive Director, Software Carpentry) and Tracy Teal (Project Lead, Data Carpentry …

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I've just opened applications for the 2015 summer course on Analyzing Next Generation Sequencing Data. The course will run from August 10th through August 21st; for details, see the course information page.

This year there will also be a third week of the course that is invitation-only. This third week …

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Note: this hackathon report was written by ArisKnight Winfree.

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This past weekend was the University of Michigan’s hackathon, MHacks IV. Over 1100 students from universities and high schools across the United States took over Ann Arbor from September 5th through September 7th to participate in one of the most …

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At the NIH ADDS meeting, we had several breakout sessions. Michelle Dunn and I led the training session. For this breakout, we had the following agenda:

First, build "sticky-note clouds", with one sticky-note cloud with notes for each of the following topics:

1. Desired outcomes of biomedical data science training;
2. Other …

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I am pleased to announce that Dr. Greg Wilson will be giving a two-day Software Carpentry Instructor Training workshop at UC Davis, January 6-7, 2015. This will be an in-person version of the instructor training that Greg runs every quarter; see my blog post about the first such instructor training …

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As I mentioned, I am hoping to significantly scale up my training efforts at UC Davis; it's one of the reasons they hired me, it's a big need in biology, and I'm enthusiastic about the whole thing! A key point is that, at least at the beginning, it may replace …

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tl;dr? The Software Carpentry train-the-trainers workshop in Toronto this past M-W was just fantastic. I can't recommend it enough.

A bit of background: Software Carpentry is a project to teach scientists to use computing more effectively. Started by Greg Wilson about 16 years ago, the project has progressed through …

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This term, I'm once again teaching my upper-division CSE undergrad course in Web Dev here at MSU. For the second time, I'm requiring students to use github for their homework; unlike last year, I now understand pull requests and have integrated them into the process.

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I've started to think more broadly about bioinformatics training, and after some conversations with Vicky Schneider at TGAC, Terri Atwood at GOBLET, and others, I thought I'd write down some thoughts on bioinformatics classrooms. In particular, what kind of compute infrastructure is needed?

Before I get started, my assumptions and …

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Julia Gustavsen and I just finished teaching one room of a 3-room Software Carpentry boot camp at University of Washington, Seattle.

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Randy Olson, who is watching amusedly from the side lines as I struggle once again to teach programming to graduate students in biology, asked a really good question (it's rare, yes, but it should be acknowledged for encouragement) --

Had a student from your class ask me today if it's typical …

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One of the most important jobs a professor has is to pay it forward: that is, to teach, train, mentor, support, and open up opportunities for their students and postdocs. It's a job that is undervalued by those who focus on the short term -- the administrators and review committees that …

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The second iteration of our bioinformatics summer course, Analyzing Next-Generation Sequencing Data, just finished. It was a great success, at least judging from the comments that people made to us personally; the evaluations aren't yet complete.

The what: a two week course on analyzing next-gen sequencing data, using the Amazon …

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I'm just finishing up my Computational Science for Evolutionary Biologists course, and I'm finding it tricky to come up with a good high-level summary of what I would like them to take away. As you can see from the class notes they've done some reasonably neat stuff with Digital Life …

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PLoS Biology published an article entitled Open Education, Open Minds, in which they solicited ideas for contributions to a series on life sciences education:

Contributions to the Education Series are encouraged; ideas should be sent to plosbiology@plos.org.

So I sent in an e-mail and got back

> This message …

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On the heels of my aggressive competence post, about (among other things) my failure to outline my expectations for students, I've started putting together a page to help manage student expectations for the pony-build project, which is participating in the Undergraduate Capstone Open-Source Projects (UCOSP) course this term.

(Please comment …

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This last term I facilitated the participation of five MSU students in the Undergraduate Capstone Open Source Projects (UCOSP) program, in which students do distributed open source software development and receive home institution credit. UCOSP was managed out of U Toronto by Greg Wilson, and I was (and am) enthusiastic …

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I'm looking for examples of frustratingly simple-yet-wrong Python code, suitable for an undergrad class to debug. I'd prefer things that don't rely on tricky features of Python (like shared list references), but rather code where subtly bad logic or program flow leads to bad behavior.

Comment below, or e-mail me …

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After being on the new Python diversity mailing list for a bit, I've just unsubscribed. While there was an unpleasant personal incident that catalyzed my decision, I also don't think I'm a good fit for the style of discussion taking place. (YMMV ;)

That having been said, I want to give …

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Just a short note with characteristic inhumility (ahumility? abhumility?) -- for my Concepts in Database-Backed Web Programming course, I received the Withrow Award for Teaching Excellence from the students.

This means a lot to me, because I spent a huge amount of time on that course (and will have to do …

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(This blog post is a long, rambling retrospective on my recent undergrad comp-sci course at Michigan State U., newly renamed to "Concepts in Database-backed Web Programming".)

I set out this term to teach a CS class in the way I would have wanted it taught when I was an undergrad …

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On Tuesday (June 12), Wednesday, and Thursday I taught the course "Intermediate and Advanced Software Carpentry in Python" at Lawrence Livermore National Labs. This was intended to be an extension of some of the ideas from the Software Carpentry course.

The pre-course course advert, the handouts distributed at the course …

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