Revision as of 11:32, 15 May 2014

Wellcome to Xenopus Bioinformatics Workshop 2014!

This wiki is for Xenopus Bioinformatics Workshop 2014 at the Marine Biological Laboratory (MBL) (May 11-18, 2014), hosted by National Xenopus Resrouce (NXR)

Instructors

• Leonid Peshkin, Harvard University
• Taejoon Kwon, Univerity of Texas at Austin
• Virginia Savova, Harvard University
• Ian Quigley, Salk Institute
• Martin Wühr, Harvard University (guest instructor)

Meals

• Breakfast: 7am - 8:30am
• Lunch: 12pm - 1:30pm
• Dinner: 5pm - 7pm

Course

Mainly we will use in-house workstation for most of sessions. Just in case, when you need high-performance computing (e.g. your own sequencing data), you can use guest account of the Orchestra clusters at Harvard Medical School. Check LSF_HowTo to learn how to use it.

• Workshop Outline & Rationale
• Syllabus

• List_of_sessions
• List_of_participants_2014
• Dataset
• https://github.com/taejoon/XenBioinfo2014 (Our primary github repository. See Github_HowTo to learn how to use it.)

Resources

• List_of_programs - programs used during the workshop
• List_of_links
• Point_of_significance - Articles published in Nature Method.
• List_of_databases
• http://www.rain.org/~mkummel/unix.html (Unix Cheat Sheet)
• http://www.ee.surrey.ac.uk/Teaching/Unix/index.html (A truly excellent UNIX primer, we recommend going through it a few times.)
• http://software-carpentry.org/v5/book.html ('Software Carpentry' Book, edited by Greg Wilson. Don't worry, we will not cover all of them, although we are happy to discuss about it.)
• https://github.com/stephenturner/oneliners ('Useful bash one-liners for bioinformatics')
• https://github.com/marcottelab/HTseq-toolbox/
• https://github.com/marcottelab/MSblender/

Alumni

Instructors

• Bob Freeman, Harvard University
• Mike Gilchrist, NIMR, UK

Participants

• List_of_participants_2012
• List_of_participants_2013