Essential Computing for Bioinformatics (Fall 2007)

This course provides a broad introductory discussion of essential computer science concepts that have wide applicability in the natural sciences. Particular emphasis will be placed on applications to Bioinformatics.  The concepts will be motivated by practical problems arising from the use of bioinformatics research tools such as genetic sequence databases. Concepts will be discussed in a weekly lecture and will be practiced via simple programming exercises using Python, an easy to learn and widely available scripting language.


General Information

- Course Information Sheet A.K.A. Prontuario (PDF)
- Course Outline  (PDF)

Lectures Tuesday & Thursday (4:10 – 5:25) @ Stefani 228

- Lecture   1 – First Steps in Computing (PDF)
- Lecture   2 – Using Biological Databases (PDF)
- Lecture   3 – The Nature of Computing (PDF)
- Lecture   4 – Conreolling the Flow of your Programs (PDF)
- Lecture  5 – Cotainer Data Structures (PDF)
- Lecture 6 – Files and Directories (PDF)
- Lecture 7 – Interfacing with Bioinformatics Data Sources (PDF)
- Lecture 8 – Exploiting Relational Databases (PDF)


- Exam 1:TBA (Topics, Practice, Solution, Stats)
- Exam 2: TBA (Topics, Practice, Solution, Stats)
- Exam 3: TBA (Topics, Practice, Solution, Stats)
- Final Exam: (Topics, Practice, Solution, Stats)

Problem Sets

- Problem Set 1. TBA (PDF, Solution)
- Problem Set 2. TBA (PDF, Solution)
- Problem Set 3. TBA (PDF, Solution)
- Problem Set 4. TBA (Doc, Solution)

Programming Assignments

- Programming Assignment 1. TBA  (Word, PDF, Solution)
- Programming Assignment 2. TBA (Word, PDF, Solution)
- Programming Assignment 3. TBA (RefCode, Doc, Solution)
- Programming Assignment 4. TBA (RefCode, Doc, Solution)

Email Lists

- icom4995-profs
- icom4995-students  (Subscribe) (Archives)
- icom4995-forum (staff & students)(Archives)

Software Tools

- Standard Python Software Downloads
- BioPython Download Page
- MySQL Downloads Page

Supplementary Readings

- Computability and Turing Machines
  1. CS 110 Notes University of Alberta
  2. Turing Machines in Stanford’s Encyclopedia of Philosophy

Language References and Documentation

- Python

  1. Python Tutorial
  2. Python Language Reference
  3. Python Documentation Index
  4. BioPython Tutorial and Cookbook

Other Reference Links

- Pasteur Institute Course in Bioinformatics
-   Pasteur Institute Introduction to Programming Using Python

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