Teaching  BioE131

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Biowiki . Teaching . BioE131

Biowiki . Teaching . BioE131

THIS PAGE IS OUTDATED - PLEASE GO TO BCOURSES FOR CURRENT INFO ON THIS CLASS: https://bcourses.berkeley.edu/courses/1377149/


Introduction to Computational Biology.

Course info

Calendar & announcements

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Lecture slides will be posted on the BioE131 lecture notes page after each group of lectures has concluded and corrections have been applied.

BioE131 weekly exercises

The following self-directed exercises may be used to assess knowledge of examinable material.

These exercises are not for credit, except where otherwise stated.

Except for sample examination questions, each of the following should take roughly 2 hours.

For midterms 1 & 2

For midterm 2 only

BioE131 policies

See also the BioE131 fact sheet.

Student wiki


Approximate sequence of lectures (see also BioE131 weekly schedule):

Lab practicals

  1. Unix
  2. UsingWiki
  3. Biological Databases
  4. PythonBasicsLab
  5. Python Lists & Dictionaries
  6. PythonPatternMatchingLab
  7. RNA folding
  8. Sequence Alignment
  9. InformationContentOfDNA
  10. BacterialGenePrediction
  11. PrimatePhylogeny
  12. PathwayMining
  13. Protein Visualization
  14. Catch-up lab; project work

Homework exercises

Homework exercises will be assigned in labs and posted on the individual lab pages. Programming assignments will be graded both for form (style) and function (correctness). Stylistic expectations will be outlined on the style guidelines page by the time the first assignment is given.


No textbook purchase is required to take the class.

References to the following textbook (which can be freely downloaded) appear occasionally as recommended reading:

The DurbinBook is also a very useful guide to probabilistic biological sequence analysis.

The following Python books may be a useful supplement to what's taught in class:

Other resources


Academic calendar




Final project

See FinalProject

----- Revision r510 - 2012-12-14 - 18:40:36 - IanHolmes
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