Archive for the ‘Venues’ Category
Hans-Martin von Gaudecker is planning to teach a Software Carpentry-style course for economists at Universität Mannheim this autumn — as his announcement says, “I think it is amazing that a profession obsessed with efficiency affords a very obvious inefficiency: Most researchers nowadays spend a fair share of their time programming, but hardly anyone has been taught to do that well.” I’ll post updates here as he sends them.
Thanks to the initiative of Dominique Vuvan (who took Software Carpentry last summer), we ran a semi-formal version of the course from last November through to this past week for grad students in Psychology, Linguistics, and a few other disciplines at the University of Toronto. Weekly tutorials were offered in both Python and MATLAB by graduate teaching assistants from Computer Science, covering roughly half of the existing material.
Analyzing Next-Generation Sequencing Data
May 31 – June 11th, 2010
Kellogg Biological Station, Michigan State University
CSE 891 s431 / MMG 890 s433, 2 cr
Applications are due by midnight EST, April 9th, 2010.
Course sponsor: Gene Expression in Disease and Development Focus Group at Michigan State University.
Instructors: Dr. C. Titus Brown and Dr. Gregory V. Wilson
This intensive two week summer course will introduce students with a strong biology background to the practice of analyzing short-read sequencing data from the Illumina GA2 and other next-gen platforms. The first week will introduce students to computational thinking and large-scale data analysis on UNIX platforms. The second week will focus on mapping, assembly, and analysis of short-read data for resequencing, ChIP-seq, and RNAseq.
No prior programming experience is required, although familiarity with some programming concepts is suggested, and bravery in the face of the unknown is necessary. 2 years or more of graduate school in a biological science is strongly suggested.
Congratulations to Titus Brown and others on the NSF’s announcement that it will fund the BEACON (Bio/computational Evolution in Action Consortium) Science and Technology Center. BEACON “…BEACON is focused on studying the evolution of organization across multiple scales—from genomic and cellular, to multicellular, to inter-multicellular (a.k.a. social)—using techniques from experimental evolution, modeling, and digital life systems.” Long story short, this means that Michigan State University and its partner institutions “…has money explicitly for supporting students doing really sexy interdisciplinary work combining computation and biology.”
The warmup tutorials for our grassroots Software Carpentry course started this week, and we’d like to send a “thank you” to Jamie Winter at The MathWorks, who has provided students with temporary licenses for MATLAB. It’s all been very last minute, and we’re grateful to Jamie for pulling this off on such short notice.
After a lot of hard work from Dominique and Jon, we’re kicking off warmup tutorials for Software Carpentry this week. 65 students from Psychology, Linguistics, Chemical Engineering, and a couple of other departments will get three weeks of review on basic programming, then start the regular material in January. Our thanks to MITACS, the MathWorks, SciNet, and DCS for their support.
Some graduate students at the University of Toronto have asked us to run the course for them later this fall or during the winter. There’s an obvious selection bias (if they were expert programmers, they wouldn’t need this course), but I think they’re pretty representative of scientists at their level:
|03.||Level of study|
|04.||Primary programming language|
|05.||Knowledge of primary language|
|Don’t know how to use it||28/39||72%|
|Understand basic commands||10/39||26%|
|Can program competently||1/39||2%|
|06.||What other languages do you know?|
|Other (VB, Java, Perl, etc.)||10/27||37%|
|07.||Would you like pre-class tutorial on
|programming basics (loops, files, if/else)?|
|08.||Do you have a laptop?|
|Mac OS X||7/39||18%|
|10.||Do you have a MATLAB license?|
|11.||Which topics are you interested in?|
|Functions and Modules||14/39||41%|
|Web Application Programming||9/39||26%|
|Web Client Programming||7/39||21%|
|How Web Servers Work||6/39||18%|
|Sets and Dictionaries||5/39||15%|
|Unix Shell Scripting||5/39||15%|
|Empirical Software Engineering||3/39||9%|
|Software Development Lifecycles||1/39||3%|
|Other (please specify)||10/39||30%|