Computer Programming in Systems Biology and Bioinformatics
BSR6803.05 Pharmacology and Systems Biology of Disease and Therapeutics CMC(customized mini-course)
Course Director: Avi Ma'ayan PhD
E-mail: avi.maayan@mssm.edu
The course meets at 12-34 IMI from 4:00-5:30PM every Tuesday for 10 weeks
Course Description:
This mini course covers computer programming methodologies applied to processing data and analysis of data in the broad fields of Bioinformatics and Systems Biology. Topics covered would include an overview of data structures and algorithms, Python scripting for processing text files, computational platforms such as R and MATLAB as well as web technologies using JavaScript, HTML, XML, PHP, SQL, MySql, and CGI. Students will be required to complete small programming assignments throughout the course
Course Schedule Spring 2012
Date |
Topic |
Assignment |
| 2/21 | Mutual Information and Decision Trees | Decision Tree Classifier |
| 2/28 | MATLAB Programming | M-file assignment |
| 3/6 | Data Structures | Linked list program |
| 3/13 | Python Programming | Interactive web-page |
| 3/20 | Database Systems | Creating a database |
| 3/27 | Web Programming | Interactive web-page |
| 4/3 | GSEA | GSEA in R |
| 4/10 | PCA | PCA in R |
| 4/17 | PubMed E-utils, AERS, GeneRIF, OMIM | Final project |
| 4/24 | Final Project Q & A | |
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