Bioinformatics

From Earlham Cluster Department

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Proposed work
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<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.
* 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.
* 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.
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Complements academic program
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<b>Complements academic program</b>
* 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.  
* 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.
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Evaluation  
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<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 our study which will culminate at the end of the semester with a paper and colloquium presentation to the department.
* 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.
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Text/ Resources
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<b>Text/ Resources</b>
*Beginning Perl for Bioinformatics. O'Reilly. James D. Tisdall.  
*Beginning Perl for Bioinformatics. O'Reilly. James D. Tisdall.  
*Bioinformatics for Dummies.  Jean-Michel Claverie and Cedric Notredame.  
*Bioinformatics for Dummies.  Jean-Michel Claverie and Cedric Notredame.  
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Additional articles from various scientific journals.
Additional articles from various scientific journals.
Excerpts from other bioinformatic texts (will be determined).
Excerpts from other bioinformatic texts (will be determined).
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<b><u>SYLLABUS</u></b>
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<i>Week 1</i>: Chp. 1-3 Beginning Perl, Install Perl and work through Chp 4. BI for Dummies : Chp. 1
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<i>Week 2</i>:
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<i>Week 3</i>:
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<i>Week 4</i>:
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<i>Week 5</i>:
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<i>Week 6</i>:
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<i>Week 7</i>:
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<i>Week 8</i>:
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<i>Week 9</i>:
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<i>Week 10</i>:
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<i>Week 11</i>:
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<i>Week 12</i>:
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<i>Week 13</i>: Presenting Independent Projects as a colloquium to the department
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Damian and Erika meet Mondays at 8 pm and Thursdays at 7pm.
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D & E meet with Charlie at 11 am on Tuesdays.

Revision as of 00:01, 7 September 2009

Proposed work

Complements academic program

Evaluation

Text/ Resources

Additional articles from various scientific journals. Excerpts from other bioinformatic texts (will be determined).


SYLLABUS

Week 1: Chp. 1-3 Beginning Perl, Install Perl and work through Chp 4. BI for Dummies : Chp. 1 Week 2: Week 3: Week 4: Week 5: Week 6: Week 7: Week 8: Week 9: Week 10: Week 11: Week 12: Week 13: Presenting Independent Projects as a colloquium to the department


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

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