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Return to Bioinformatics

Colloquium Outline:

1) General overview of bioinformatics
2) Our specific interests
3) Explorations with Perl

   *Other languages that could be used, too
   *Chp. 9
   *Chp. 10 (genebank)

4) Idea for a course
5) Present Syllabus
6) Scaffolded assignments
7) Future directions

1) General overview of bioinformatics

The application of computational techniques to understand and organize biological data


Informatics includes databases, text string comparison, finding patterns, geometry, and simulation

2) Our specific interests

Contrasting our experience with bioinfo in EC classes and in the "real world" Damian will talk about his work at ORNL and Wash U Erika will talk about her work at NIH

  • use this to illustrate why we felt an independent study was beneficial (as an introduction for the course proposal later in the talk)
  • also gives real examples of bioinfo applications that should be relevant to other students

3) Explorations with Perl

Introduce the idea that many other scripting languages could be used. Then talk about the subject of our independent study.

  • Easy to program
 -Many built in functions for common bioinformatics tasks
  • Faster to program
  • Fewer lines of code
  • Commonly used
  • Numerous modules

4) Idea for a Course

Discuss the increasing importance of cross-disciplinary interaction, especially in biology. We work with biologists, chemists, physicians, entemologists, statiticians.... It will be good for both biology students and CS students to learn to work with one another at the undergraduate level to share knowledge of different backgrounds and become familiar with a skillset from outside their own discipline.

Core requirements for bioinfomaticians (from conversations with companies such as Celera Genomics and Eli Lilly)

  • Fairly deep background in some aspect of molecular biology
  • Absolutely understand Biology’s Central Dogma
  • Substantial experience with at least 1-2 major molecular biology software packages
  • Comfortable with command-line computing
  • Experience with C/C+ and scripting language