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BPB11
Bioinformatics using Python for BiologistsDetailed description |
| Course Timetable (provisional) |
| BPB10 | Bioinformatics using Python for Biologists |
| Mon, May 2nd |
Day #1
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| 09:30 - 11:00 | Introduction to Linux commands |
| 11:00 - 11:30 | Coffee Break |
| 11:30 - 12:30 | Introduction to the Python Programming Language: Python interpreter, interactive mode, scripts, modules, variables, functions, built-ins, namespaces |
| 12:30 - 14:00 | Lunch Break |
| 14:00 - 16:00 | Practicals |
| 16:00 - 16:30 | Tea Break |
| 16:30 - 18:00 | Data structures: numbers, strings, lists, dictionaries , tuples, sets |
| Tue, May 3rd |
Day #2
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| 09:30 - 11:00 | More on data structures |
| 11:00 - 11:30 | Coffee Break |
| 11:30 - 12:30 | Control flow tools (if, for, while, break, continue, else, pass) |
| 12:30 - 14:00 | Lunch Break |
| 14:00 - 16:00 | Practicals |
| 16:00 - 16:30 | Tea Break |
| 16:30 - 18:00 | Input and Output |
| Wed, May 4tht |
Day #3
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| 09:30 - 11:00 | Classes and instances |
| 11:00 - 11:30 | Coffee Break |
| 11:30 - 12:30 | Error handling |
| 12:30 - 14:00 | Lunch Break |
| 14:00 - 16:00 | Practicals |
| 16:00 - 16:30 | Tea Break |
| 16:30 - 18:00 | Important modules: sys, os, os.path, re, cPickle, copy, math, numpy |
| Thu, May 5th |
Day #4
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| 09:30 - 11:00 | Introduction to Biopython (I) |
| 11:00 - 11:30 | Coffee Break |
| 11:30 - 12:30 | Introduction to Biopython (II) |
| 12:30 - 14:00 | Lunch Break |
| 14:00 - 16:00 | Practicals |
| 16:00 - 16:30 | Tea Break |
| 16:30 - 18:00 | Working with DNA and protein sequences |
| Fri, May 6th |
Day #5
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| 09:30 - 11:00 | Extracting information from biological resources: parsing Swiss-Prot files, PDB files, ENSEMBLE records, blast output files, etc. (I) |
| 11:00 - 11:30 | Coffee Break |
| 11:30 - 12:30 | Extracting information from biological resources: parsing Swiss-Prot files, PDB files, ENSEMBLE records, blast output files, etc. (II) |
| 12:30 - 14:00 | Lunch Break |
| 14:00 - 16:00 | Running external applications (e.g. BLAST) locally and from a script |
| 16:00 - 16:30 | Tea Break |
| 16:30 - 18:00 | Working with motifs. Final wrap-up session. |
| Course Homepage |
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Instituto Gulbenkian de Ciência, Apartado 14, 2781-901 Oeiras, Portugal Last updated: February 26th 2011 |