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Python for Bioinformatics - #27624
5 point course, fall 2013
DTU's Studies Handbook about #27624
Note: This is a pilot course still under development
The first course will be held from September 2013. The course will run every thursday for a 13 week period (5th of September - 5th of December, room 062 in building 208), finishing with project hand-in on the 20th of December (May be subject to change!).
The course consists of short lectures with exercises and project work in the final period. The first part of the course will be tought using IPython. All course material are available on github.
Instructions:
Getting Course Material
Installing Python and IPython
Time: Thursdays 9am-12pm, September 5th - December 5th, 2013
Location: Aud. 062, building 208
Organizers: Anders Gorm Pedersen, Christian Skjødt
Evaluation form: Evaluation of projects, pass/not pass
Credits: 5 ECTS
Tools: Please plan to bring a laptop (Mac OS X, Windows, or Linux are all OK). We will be using Python 2.7.5 and IPython 1.0 (will be installed on day 1)
Text books:
- [Optional] Python for Bioinformatics by S. Bassi (there is an online version at DTU Digital Library)
- [Optional] Bioinformatics Programming Using Python by M. Model
- [Optional] Head First Python by P. Barry (for people coming from other programming languages)
Signing up:
Learning Objectives:
A student who has met the objectives of the course will be able to:
- Read and understand the Python syntax.
- Be familiar with Python's fundamentals and develop simple applications.
- Apply the principles and techniques of object-oriented programming.
- Use sophisticated techniques and Python modules that are particularly useful for bioinformatics programming.
- Build new Python software tools for life science research.
- Summarize text patterns using regular expressions.
- Apply different strategies for error handling of applications.
- Write applications in one of the most simplistic languages available.
Program:
The course program below is tentative and may be subjected to change.
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Date |
Lesson |
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1 |
5. Sep |
Welcome, Introduction to Python |
| 2 |
12. Sep |
Basic Python 1: Organising Data |
| 3 |
19. Sep |
Basic Python 2: Decisions and Control |
| 4 |
26. Sep |
Basic Python 3: Dealing with Files |
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5 |
3. Oct |
Functions, Modulization and Scripts |
| 6 |
10. Oct |
Error Handling |
| 7 |
24. Oct |
Classes |
| 8 |
31. Oct |
Regular Expressions |
| 9 |
7. Nov |
Biopython |
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14. Nov |
Working on project |
| 21. Nov |
| 28. Nov |
| 5. Dec |
| 20. Dec |
Hand in project |
More info on the projects will follow later in the course.
For more information, please contact course organizer Christian Skjødt or click on the links above.
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