Building Bioinformatics Applications: USC Software Carpentry Boot Camp

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Davidson Continuing Education Conference Center

3415 S Figueroa St

Los Angeles, CA 90007

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WORKSHOP AGENDA: http://arokem.github.io/2013-09-16-ISI/

This boot camp is an example-driven two-day workshop on basic computing skills needed for people that want to develop good software. Particular emphasis will be given to bioinformatics applications. Short tutorials alternate with hands-on practical exercises, and participants are encouraged both to help one another, and to try applying what they have learned to their own research problems during and between sessions. Participants should bring their own laptops to work on.

Prerequesites: basic knowledge of programming and data structures.

The boot camp will include modules on:

  • shell programming
  • using good software programming practices
Most of the material is taught in Python.

See http://software-carpentry.org/bootcamps/ for more info.

There will be also two custom modules:

  • workflow technologies for bioinformatics, particularly the Pegasus Workflow Management System, which is developed at the USC Information Sciences Institute
  • demonstration of the RNA-Seq pipeline that is built using Pegasus, this pipeline has been develped by Keck and USC Bioinformatics researchers.

Tentative agenda:

Day 1:
The UNIX Shell - shell basics, processes, job control, pipes, variables, scripts, advanced commands (find, grep, awk, sed, xargs), ssh
Version Control - intro, Git basics, branching, development workflows, GitHub
Testing - types of tests, unit testing, xUnit, test-driven development, testing in Python
Day 2:
Craftsmanship - documentation, best practices, programming tips and tricks, refactoring, debugging, reproducibility
USC HPCC - How to run your jobs on Campus HPCC resources: HPC clusters, allocations, PBS basics, job submission, job status
Workflows - intro to workflows, how to create and run workflows
Running RNA-Seq analysis as an example of a bioinformatics pipeline

Registration is limited to 40 participants on a first-come-first-served basis. The $50 registration fee covers two breakfasts, two lunches, and morning and afternoon breaks.

Registration closses September 9, 2013

For more information please email pegasus@isi.edu

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Location

Davidson Continuing Education Conference Center

3415 S Figueroa St

Los Angeles, CA 90007

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