Bioinformatics

Proposed work

• Through this study we will gain a general understanding of how topics in bioinformatics work and what the discipline has to offer biological researchers. We will each explore one particular area in-depth as an independent project.
• Topics will include: Programming basics (PERL and R), DNA sequences and strings, simulation of DNA mutations and other molecular events, regular expressions and finding motifs in data, arrays and hashes, databases (GenBank, Protein Data Bank, BLAST), among others.

Complements academic program

• Erika and Damian have both found over two summers of research that a general understanding of bioinformatics will come in very handy down the road. Through biology courses at Earlham we have briefly skimmed certain aspects of bioinformatics but not at a level that can be attained through in-depth study as we propose to do with this course.
• Charlie is interested in learning more about bioinformatics generally and to see if a lab can be built out of more basic material for the introduction to modeling class.

Evaluation

• We will create a wiki page (wiki.cs.earlham.edu) and update it throughout the course with summaries of the material we have studied together as well as the independent directions we will pursue with each topic.
• We will each pursue an independent topic throughout our study which will culminate at the end of the semester with a paper and colloquium presentation to the department.

Text/ Resources

• Beginning Perl for Bioinformatics. O'Reilly. James D. Tisdall.
• Bioinformatics for Dummies. Jean-Michel Claverie and Cedric Notredame.
• Genetics for Dummies. Tara Rodden Robinson.
• Developing Bioinformatics Computer Skills. O'Reilly. Cynthia Gibas and Per Jambeck.

Additional articles from various scientific journals.

• An online Beginning Perl book: http://www.perl.org/books/beginning-perl/

Excerpts from other bioinformatic texts (will be determined).

Meeting Times

• Damian and Erika meet Mondays at 8 pm and Thursdays at 7pm.
• D & E meet with Charlie at 11 am on Tuesdays.

SYLLABUS

Aug 30-Sept 5: Chp. 1-3 Beginning Perl, Install Perl and work through Chp 4. BI for Dummies : Chp. 1.

Sept 6-12: Chp. 5 Beginning Perl, Chp. 2 BI for Dummies

Sept 13-19: Chp. 6 Beginning Perl, Chp. 3 BI for Dummies. Personal Projects should be underway.

Sept 20-26: Chp. 7 Beginning Perl, Chp. 4 BI for Dummies

Sept 27-Oct 3: Chp. 8 Beginning Perl, Chp. 5 BI for Dummies

Oct 4-10: Chp. 9 Beginning Perl, Chp. 6 BI for Dummies

Oct 11-17: Chp. 10 Beginning Perl, Chp. 7 BI for Dummies

Oct 18-24: Chp. 11 Beginning Perl, Chp. 8 BI for Dummies

Oct 25-31: Chp. 12 Beginning Perl, Chp. 9 BI for Dummies

Nov 1-7: Chp. 12 Beginning Perl, Chp. 9 BI for Dummies

Nov 8-14: Writing codes for personal project

Nov 15-21: Focus on personal project, using modules

Nov 29-Dec 5: Focus on personal project, using modules

Colloquium
We will present a Biology colloquium on February, 11, to introduce the general topic of bioinformatics, applications in "the real world", and propose a syllabus for a course at Earlham, or another small liberal arts undergraduate college.

Our outline may be viewed here.