Bioinformatics: Computational Analysis for a Molecular Biologist
MCDB 6440 and 4110
Registration call number for MCDB 6440 ---> 24473
Registration call number for MCDB 4110 ---> 24472
MCDB 6440 and MCDB 4110 - Spring 2002
Instructors: Ravinder
Singh, and Scott Kelley
Time/Location/Credits: Friday;
2:30 PM - 4:10 PM; MCDB A2B07, 2 Cr. hr
Organizer: rsingh@colorado.edu
This course is designed for molecular biology students who wish to quickly develop skills
for mining available genomic databases and analyzing sequence information. This course will emphasize programming skills
as well as existing tools and resources relevant to studying molecular biology problems. Most importantly, it will focus on molecular
biology applications that are not addressed in standard programming classes. The major inspiration behind this course is that although
the majority of molecular biologists are adept at blasting sequences at the NCBI or other sites, only a few of us have the expertise for
further analysis of the output by more powerful computational means. The majority of the commercial software for molecular biology,
although user-friendly for some tasks, offers limited flexibity for specific scientific needs. Therefore, we will focus on the concept
of object-oriented programming (OOP) and how it can be applied towards obtaining relevant sequence information for addressing specific
biological problems. For programming, we will use Python, which is a simple, elegant, easy to learn and powerful programming language.
We will discuss Python syntax, including object types, data structures, conditional loops, modules and classes (encapsulation,
inheritance and polymorphism, which are the three pillars of OOP). We will use Python scripts for parsing GENBANK,
FASTA, PUBMED and BLAST records. The programming skills developed here should be directly applicable to other languages and provide a springboard
for those who wish to become serious bioinformaticians or computational biologists. Although prior programming knowledge is not required,
homework will be assigned to encourage students to practice and hone new programming skills.
Prereq. instructor's consent. Approved for arts and sciences core curriculum. Limited to no more than 15 students because of
the space limitation in our computer lab; MCDB graduate and undergraduate students will have priority.
Lecture Schedule
|
|
|
|
|
| January | 18 | Introduction and Grades: Getting Started - Types and Operators (RS) |
|
| 25 | Basic Statements (RS) |
|
|
| February | 1 | Functions (RS) |
|
| 8 | Modules and Built-in Tools (RS) |
|
|
| 15 | Built-in Tools and Exceptions (RS) |
| |
| 22 | Classes - Encapsulation (SK) |
Excercise 1 Due | |
| March | 1 | Classes - Inheritance (SK) |
|
| 8 | Classes - Polymorphism (SK) |
| |
| 15 | Biopython - Sequence objects (RS) |
| |
| 22 | Biopython - Parsing data files ; (RS) |
| |
| 29 | Spring Break |
| |
| April | 5 | Biopython - Parsing data files (RS) |
|
| 12 | Biopython - Advanced Sequence classes (SK) |
| |
| 19 | Let's face the issue of computational speed - python/C++- (Fernando Perez) |
| |
| 26 | Scott's final sage advice - (SK) and "Where to go from here" (Chuck Robertson) |
| |
| May | 3 | Review of the entire course, Exam and closing comments (RS) |
|
| 6 | Final Examination |
| |
Books and Readings
Online Tutorials
Optional Books for further reading:
Additional Useful Sites:
Questions about this information should be directed to Ravinder Singh.