Michigan State University on The Carpentries

Feedback from Michigan State

Sat, 12 May 2012 00:00:00 +0000

This post originally appeared on the Software Carpentry website.

Our workshop at Michigan State University this week was three days long instead of two, and included two topics (Git and the IPython notebook) that we haven't tried before. Feedback was generally positive, but we've got lots to work on for next time as well.

Good

Bad

Using history
Ending with general theory
Pen and paper database design
Version control was useful
Good practice in software
Concise and module programming in Python
Console segment
Smooth flow between Bash and Python
Challenging and flowed nicely
Futher reading material
Desktop setup
Instructor teaching style
Permission to spend less time coding
iPython notebook looks great
Paired programming model
Git script (tutorials used were available)
Legal issues (opensource)
Good for beginners
Free course (and food!)
Variety
Practical (reality-based)
Overview of DB options
Testing
Better ways to do things
Somewhat static seating created helpful partners

Typing speed is too fast
Class time chunks too long
Why iPython
Need more 'why'
Curriculum
Advanced Git bounced
Too much switching screens
Some things failed
Beverages included only caffeine
Need snacks at breaks
Lacked connection between course material and applicability
Tuesday way too long
Wanted a cheat sheet
Not enough exercises
How to create DB
Anti-Windows bigotry
Next day install at end of day
Some concepts skipped
Don't know where to start (registrationg etc.)
Inappropriate room size
Breadth
PPT for CS

The Hacker Within at MSU in June

Tue, 03 May 2011 00:00:00 +0000

This post originally appeared on the Software Carpentry website.

The University of Wisconsin's Hacker Within team are running a bootcamp at Michigan State University June 4-5 2011—see the announcement for details. Space is limited, so sign up now!

Next-Generation Sequencing Course at MSU

Wed, 16 Mar 2011 00:00:00 +0000

This post originally appeared on the Software Carpentry website.

Analyzing Next-Generation Sequencing Data

June 6th — June 17th, 2011

Kellogg Biological Station, Michigan State University

Instructors: Dr. C. Titus Brown, Dr. Ian Dworkin, and Dr. Istvan Albert.

Applications must be received by March 25th for full consideration. See the full announcement at http://bioinformatics.msu.edu/ngs-summer-course-2011 for more information.

Course Description:

This intensive two week summer course will introduce students with a strong biology background to the practice of analyzing short-read sequencing data from Roche 454, Illumina GA2, ABI SOLiD, Pacific Biosciences, 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.

Interview with Michigan State's Titus Brown

Sun, 11 Jul 2010 00:00:00 +0000

This post originally appeared on the Software Carpentry website.

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.

Next-Gen Sequencing Course at MSU: It Went Well

Tue, 15 Jun 2010 00:00:00 +0000

This post originally appeared on the Software Carpentry website.

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.

Summer Course: Analyzing Next-Generation Sequencing Data

Thu, 25 Mar 2010 00:00:00 +0000

This post originally appeared on the Software Carpentry website.

Analyzing Next-Generation Sequencing Data

May 31 — June 11th, 2010
Kellogg Biological Station, Michigan State University
CSE 891 s431 / MMG 890 s433, 2 cr

http://bioinformatics.msu.edu/ngs-summer-course-2010

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.

BEACON Funded!

Mon, 22 Feb 2010 00:00:00 +0000

This post originally appeared on the Software Carpentry website.

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."