Unix and Perl workshop using the Amazon cloud

Also available to undergraduates.

This course provides the basic platform onto which other genomic, transcriptomic and mass-spectrometry skills will build. It covers some of the simple but powerful skills all scientists should know in a world of increasingly complex analyses.

The target audience is anyone wanting further training in bioinformatics: PhD, post-docs, technicians, and faculty staff and undergraduates.

The course provides the basic computational and programming skills needed to perform analyses within the Linux environment. It is not a bioinformatics course, although the lessons are applicable to molecular data. The skills are applicable to any subdiscipline where gathering and analysing moderate to large data sets are involved.

Participants will be able to take the techniques and skills they learn back to their groups to continue making their own research easier and more effective.

All of the tools discussed are freely available.

Course content

• Setting up and accessing your own Linux virtual machine in the Amazon cloud computing environment.
• Accessing the virtual machine using the NX client.
• Using the Linux command line terminal.
• Basic Linux commands.
• Creating and editing files.
• Basic scripting using Bash.
• Advanced Linux topics.
• Searching files.
• An introduction to Perl.
• Variables, loops.
• Regular expressions.
• Subroutines and modules.
• How to transfer your data into the Amazon cloud and get your results out.

Course details