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Bioinformatic Assignments in Computer Science Courses
 
 
Authors          Audiences          Overview           Materials          Resources           Future Directions
 

 


Authors


Jim Mahoney
Marlboro College


Peter Wilkinson
McGill University


 
   
 


Possible Audiences:

Computer Science instructors for classes at various levels, or programming in biology classes  

 
 


Brief Overview

The two of us spent an hour on Saturday afternoon tossing around ideas on how to put bioinformatics material into computer science courses, particularly in open-ended exploratory projects. In this case the point is not primarily to help the students learn NCBI tools to study a biology question, but instead to use the biological problems as examples of the computer science issues behind these tools.  

 
   
 


Project Materials

Some examples of these kinds of problems include

  • information management issues
    • various types of datbases, file formats, API's
    • relational databases / SQL
    • XML
    • parsing text files (.fasta, ...)
  • genetic sequences as codes, including
    • parsing it (finding open reading frames, start,stop, ...)
    • differences between nucleic, mitochondrial, chloroplast
    • how to characterize it (codon frequency, Shannon's entropy, ...)
  • discrete mathematics of phylogenetic trees
    • calculating distances between given sequences
    • creating trees by hand, then with a program
  • scripting techniques and WWW agents
    • automating routine tasks like those seen this weekend
    • web scraping, parsing, ...
  • user interface issues
  • 3D graphics and data visualization techniques
 

 
 


Resources and References

http://bioquest.org/bedrock/sunnyvale_workshop/project3.htm
a similar effort at another BEDROCK workshop

http://www.bio.cam.ac.uk/seqlogo/
Sequence Logos - another way to graphically present bioinformatic data

http://cm.bell-labs.com/cm/ms/what/shannonday/paper.html
Claude Shannon's paper on information theory

http://www.maths.abdn.ac.uk/~igc/tch/mx4002/notes/node59.html
background on Huffman codes

http://aleph0.clarku.edu/~djoyce/java/Phyltree/cover.html
phylogenetic trees

http://bioweb.uwlax.edu/GenWeb/Molecular/Seq_Anal/Translation/translation.html
translation and open reading frames

http://www.bioperl.org
perl Bio module

http://www.biopython.org
python Bio module

http://www.biosql.org
Bio SQL project

http://www.mysql.org
mysql database

 

 
   
 


Future Directions

 

 
 


Attachments


- ESTproblem.doc