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ARANGS12
Automated and reproducible analysis of NGS dataCourse Timetable |
| PW12 | Automated and reproducible analysis of NGS data |
| Tue, Sep 11th |
Day #1
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| 09:30 - 10:30 |
Course methodology. Self-introductions. Automated and reproducible analysis of NGS data: Introductory lecture |
| 10:30 - 11:00 | Coffee Break |
| 11:00 - 12:30 |
NGS data, file formats, 'big data' (hands-on, looking at files) |
| 12:30 - 14:00 | Lunch Break |
| 14:00 - 16:00 | The UNIX command line |
| 16:00 - 16:30 | Tea Break |
| 16:30 - 18:00 | Running analysis steps on the command line |
| Wed, Sep 12th |
Day #2
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| 09:30 - 10:30 |
Wrap-up session about Day 1 Command line scripting (shell) |
| 10:30 - 11:00 | Coffee Break |
| 11:00 - 12:30 | Programming toolkits (i.e. scripting with objects) |
| 12:30 - 14:00 | Lunch Break |
| 14:00 - 16:00 | Organizing computational biology projects (i.e. data and scripts)
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| 16:00 - 16:30 | Tea Break |
| 16:30 - 18:00 | Tracking project versions using distributed version control systems |
| Thu, Sep 13th |
Day #3
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| 09:30 - 10:30 |
Wrap-up session about Day 2 Chaining things together on the command line (i.e. with shell/perl/make/unix pipes) |
| 10:30 - 11:00 | Coffee Break |
| 11:00 - 12:30 | Make (i.e. recipes, pattern rules) |
| 12:30 - 14:00 | Lunch Break |
| 14:00 - 16:00 |
Parallelization with make
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| 16:00 - 16:30 | Tea Break |
| 16:30 - 18:00 | Massive parallelization (e.g. MapReduce) |
| Fri, Sep 14th |
Day #4
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| 09:30 - 10:30 |
Wrap-up session about Day 3 Visual environments for workflows (galaxy) |
| 10:30 - 11:00 | Coffee Break |
| 11:00 - 12:30 | Data sharing, reproducibility, open data |
| 12:30 - 14:00 | Lunch Break |
| 14:00 - 16:00 | Running existing workflows in Galaxy |
| 16:00 - 16:30 | Tea Break |
| 16:30 - 18:00 | Final wrap-up session Development of a Galaxy tool. |
| Course Homepage |
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Instituto Gulbenkian de Ciência, Apartado 14, 2781-901 Oeiras, Portugal Last updated: July 30th 2012 |