COMS W1005.002 Course Homepage

Introduction to Computer Science and Programming in MATLAB

Life Sciences Section

Syllabus

Topics are listed according to the computer-science curriculum, with tentative examples covered in brackets.

  1. Introduction: Administration; Why computer science and programming?
  2. Calculating with MATLAB (the MATLAB environment, built-in numeric functions and operators, command history) [BMI calculator]
  3. Using variables (motivation, practice, conventions, several MATLAB commands, saving workspace) [BMI calculator, genetic risk]
  4. Writing programs (motivation, practice, editing, saving, conventions, printing, debugging ) [BMI calculator, genetic risk]
  5. Writing your own functions (motivation, practice, conventions, namespace) [BMI calculator, genetic risk]
  6. Vectors with data (motivation, access and assignment, properties, visualization, operators, builtin functions, strings) [genome statistics, GC content]
  7. Matrices with data (motivation, access and assignment, properties, visualization, operators, builtin functions, vectors of strings) [translation, translation, gene expression]
  8. Files (motivation, saving and loading tabular data) [gene expression]
  9. GUI [evolution]
  10. Flow control (motivation, conditionals, loops, algorithms)[evolution, ungapped sequence comparison, biochemical reaction simulation]
  11. Matlab solvers (MATLAB modules, [reaction kinetics]
  12. Recursion [evolution]
  13. Structures [Gene annotation]
  14. Cell arrays [Gene and exon annotation]
  15. Writing larger projects[High throughput sequencing]

Pre-requisites

None. The course is aimed at non-Computer-Science students, seeking to acquire computing skills to support biomedically-oriented careers. No previous knowledge is assumed, in neither computer science nor biology.

Mode of Instruction

Course intended for very interactive work in a PC-per-student setting, taking advantage of the CLIC lab. Classes will include both lecture-type frontal teaching, as well as practical exercises.

Grading

Problem sets 40% [Submitted through courseworks]
Midterm        25%
Final             35%

Administration

  • Teacher: Itsik Pe'er
  • Time: TuTh 1:10p - 2:25p
  • Regular place: 486 Computer Science Bldg (CLIC computer lab)
  • First lecture, Sep 2nd: 717 Hamilton Hall, joint between the two sections, 1005.001 and 1005.002, by Paul Blaer and Itsik Pe'er
  • Students can be registered to only one of the two sections, and can change their enrollment to the two classes until Sep 12th, per university policy.
  • Enrollment to 1005.002 is limited by computers in the CLIC lab, on a first-come-first-serve basis.
  • Students in 1005.002 are required to open a Computer Science account or purchase a MATLAB license (details in the first lecture) during the first week of classes.
  • All course material is being accumulated on CourseWorks , so please see there for the most up-to-date content.

 

 

FAQ
  1. Q: What are the office hours?
    A: See my contacts.
  2. Q: Is there a book with the course material?
    A: Sorry, but no. The course is given in this form for the first time, We will be using the MATLAB Documentation. A lot of the material is available in i Mastering MATLAB 7 by Duane C. Hanselman, Bruce L. Littlefield, Prentice Hall, ISBN 0-13-143018-1