Center for Infectious Disease and Vector Research

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Bioinformatics Workshop: Linux Part I: Linux Essentials

Chris Webber, Grant Brady & Thomas Girke

Friday, December 7, 2012
14 p.m.


Genomics Building , Genomics Auditorium, RM 1102A
Parking Information


Description: The majority of bioinformatics software, especially in the next generation sequence analysis field, is only available for Unix/Linux-based operating systems. Basic knowledge about its usage provides free access to the most powerful and up-to-date applications for high-throughput data analysis. The workshop will teach beginners the basic command-line syntax for running applications on large data sets on LINUX systems. During the workshop users will work on IIGB's Linux cluster by logging in remotely from their laptops. The following topics will be covered: (1) overview of the Linux operating system, (2) file system organization, (3) getting around, (4) basic Shell commands and scripts, (5) available software, (6) running software like Bowtie, BWA, BLAST, HMMER, PHYLIP, EMBOSS, etc.
Manual for this workshop
Maximum number of participants: 40

How to sign up: send chosen workshop date, your name, email address, title of your position, lab affiliation (PI) and department information to thomas.girke@ucr.edu.

Registration fee*: no charge for participants from registered labs, $23 for UCR members, $75 for participants from external academic institutions, and $102 for participants from commercial institutions.

Laptop requirements: Participants will work during the course on a Linux cluster. Personal laptops are required to log remotely into the cluster. For this, all laptops need to have a functional wireless connection. In addition, they will need a terminal application and a SCP software for file exchange. Windows users should install for this purpose PuTTY and WinSCP. On Mac OS X systems, one can use the native terminal application and Fugu for file exchange. Linux systems usually have similar applications pre-configured.

Additional Information:

Open to:

General Public



Institute for Integrative Genome Biology


Thomas Girke

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University of California, Riverside
900 University Ave.
Riverside, CA 92521
Tel: (951) 827-1012

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Institute of Integrative Genomics Biology
2150 Batchelor Hall

Tel: (951) 827-7177