CS 59000 003
Computing for Life Sciences I
Fall 2009
Purdue University

Exams 1 and 2 are given concurrently Wednesday, October 7 in class.
Exam 1 covers Assignment #1 plus questions similar to the review questions from Sections 1.1-2.5 of the class notes.
Exam 2 covers Assignment #2 plus questions similar to the review questions from Sections 3.1-3.6 and 7.1-7.3.1 of the class notes.
There is a heavy emphasis on material of the Assignments.
A revision of the class notes will be available Friday, October 2 plus another further announcements concerning the exams.

CS 59000 003 is the first 5 weeks of CS 501. Final exam is midweek Oct 5-9 during normal class time.

The compansion course CS59000 006, Computing for Life Sciences II is offered during weeks 6-16 except for midweek Oct 5-9.
Here is a flyer (PDF). It is completely separate from CS 501. In 2009, it can be taken independently of part I.

Instructor Robert Skeel

This together with part II is a core course in the CLS Program .

Purpose of course:
to expose students to computational concepts, tools, and skills useful for research in computational life sciences, beyond what is learned in an elementary computing course. A related aim is to prepare students for other courses in CLS core by teaching CS material mostly unavailable in existing graduate level courses. (It does not count toward a graduate degree in Computer Science.)

CS 59000 003 Prerequisites:
Math/CS/Stats required of undergraduates in biology at Purdue. Students lacking scripting/programming experience might consider first taking BIOL 59500 Practical Biocomputing.

Course topics:
There will be considerable computer use: ideally all of it on whatever computer the student intends to use for his+ research, but an ITaP processor will be made available. The student will be expected to install the necessary (free) software on his/her computer.

Theme I: scripting to get things done
* introduction to computational sciences
* Unix & Python scripting
"objects don't improve productivity in the dramatic way that scripting does"
* files and text processing in Python, including regular expressions
* numerical computing in Python, including plotting
Theme IV: numerical computing
* algorithms; error

Theme IV is to be covered concurrently with Theme I.

Text Book:
Fairly detailed class notes will be made available.

Python Documentation
Good books:

Another reference is Software Carpentry

  Last updated 2009-4-4