Difference between revisions of "Bioinformatics"
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| − | Proposed work | + | <b>Proposed work</b> |
| − | * | + | * 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, databases (GenBank, Protein Data Bank, BLAST), among others. | + | * 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. |
| − | + | <b>Complements academic program</b> | |
| − | * Erika | + | * 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. | * 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 | + | <b>Evaluation</b> |
* 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 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 | + | * 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. |
| + | |||
| + | <b>Text/ Resources</b> | ||
| + | *<i>Beginning Perl for Bioinformatics</i>. O'Reilly. James D. Tisdall. | ||
| + | *<i>Bioinformatics for Dummies</i>. Jean-Michel Claverie and Cedric Notredame. | ||
| + | *<i>Genetics for Dummies</i>. Tara Rodden Robinson. | ||
| + | *<i>Developing Bioinformatics Computer Skills</i>. 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). | ||
| + | |||
| + | |||
| + | <b>Meeting Times</b> | ||
| + | *Damian and Erika meet Mondays at 8 pm and Thursdays at 7pm. | ||
| + | *D & E meet with Charlie at 11 am on Tuesdays. | ||
| + | |||
| + | <b><u>SYLLABUS</u></b> | ||
| + | |||
| + | <i>[[Aug 30-Sept 5]]</i>: Chp. 1-3 Beginning Perl, Install Perl and work through Chp 4. BI for Dummies : Chp. 1. | ||
| + | |||
| + | <i>[[Sept 6-12]]</i>: Chp. 5 Beginning Perl, Chp. 2 BI for Dummies | ||
| + | |||
| + | <i>[[Sept 13-19]]</i>: Chp. 6 Beginning Perl, Chp. 3 BI for Dummies. [[Personal Projects]] should be underway. | ||
| + | |||
| + | <i>[[Sept 20-26]]</i>: Chp. 7 Beginning Perl, Chp. 4 BI for Dummies | ||
| + | |||
| + | <i>[[Sept 27-Oct 3]]</i>: Chp. 8 Beginning Perl, Chp. 5 BI for Dummies | ||
| + | |||
| + | <i>[[Oct 4-10]]</i>: Chp. 9 Beginning Perl, Chp. 6 BI for Dummies | ||
| + | |||
| + | <i>[[Oct 11-17]]</i>: Chp. 10 Beginning Perl, Chp. 7 BI for Dummies | ||
| + | |||
| + | <i>[[Oct 18-24]]</i>: Chp. 11 Beginning Perl, Chp. 8 BI for Dummies | ||
| + | |||
| + | <i>[[Oct 25-31]]</i>: Chp. 12 Beginning Perl, Chp. 9 BI for Dummies | ||
| + | |||
| + | <i>[[Nov 1-7]]</i>: Chp. 12 Beginning Perl, Chp. 9 BI for Dummies | ||
| + | |||
| + | <i>[[Nov 8-14]]</i>: Writing codes for personal project | ||
| + | |||
| + | <i>[[Nov 15-21]]</i>: Focus on personal project, using modules | ||
| + | |||
| + | <i>[[Nov 29-Dec 5]]</i>: Focus on personal project, using modules | ||
| + | |||
| + | '''Colloquium''' | ||
| + | <BR> | ||
| + | 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]]. | ||
Latest revision as of 20:11, 10 February 2010
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.
