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| INFO0097-2 | Introduction to linux programming
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| Duration : | 40h Th, 60h Mon. WS |
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| Number of credits : |
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| Lecturer : | Denis Baurain |
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Language(s) of instruction :
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| French language |
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Organisation and examination :
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| All year long |
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Course contents :
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| 1. Linux
- UNIX environment (Bio-Linux)
- text files and file formats
- CLI features (jokers, variables, loops, history...)
- bash shell
2. Perl
- Perl basics and Modern Perl
- Perl Object-Oriented Programming using Moose
- Perl for Bioinformatics (Bioperl, Ensembl Perl API)
3. other Open Source technologies
- LaTeX (XeTeX) and co
- WWW programming (HTML/CSS and PHP)
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Learning outcomes of the course :
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| This course is the first of three courses -- "Introduction to linux programming" [INFO0097-2], "Introduction to databases for biology" [INFO0099-2], "Introduction to algorithms in bioinformatics" [INFO0094-3] -- taught by the same teacher in the context of the specialized approach in bioinformatics of M2-BBMC. The course "Introduction to biological data analysis" [INFO0115-2] by Prof. Patrick Meyer shares the same goals.
At the end of this series of courses, students will be able to use the computer as a scientific instrument. More specifically, they will have been trained towards the following objectives:
1. Experimental design
- how to choose appropriate controls
- how to think in a statistical framework
2. Conducting experiments
- how to run large series of analyzes
- how to harness the power of grid computing
3. Interpretation of results
- how to automate the analysis of output files
- how to generate informative but nice looking graphs
- how to draw statistically sound conclusions
4. Documentation and archiving
- how to document experimental protocols
- how to reorganize a series of past analyzes
- how to manage multiple versions of the data sets, of the required programs and of the generated results
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Prerequisites and co-requisites/ Recommended optional programme components :
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| This course is part of a specialized approach in bioinformatics. Even if it requires no special knowledge in computer science, it is nevertheless based on the Genomics [GENE0003-1] and Bioinformatics [BIOL0008-1] courses of the M1-BBMC. |
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Planned learning activities and teaching methods :
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- brief theoretical lectures
- challenges to solve
- computer practicals
- self-learning (textbooks and online tutorials)
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Mode of delivery (face-to-face ; distance-learning) :
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| This course is partly face-to-face but as a problem-oriented course, it will require that students work also outside of the classroom. |
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Recommended or required readings :
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Assessment methods and criteria :
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| Course assessment will be based on both the work carried out during the academic year and the development of a personal project, in principle distinct from the Master's thesis. |
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Work placement(s) :
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Organizational remarks :
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| Taking notes on a laptop or tablet is allowed. However, students are expected not to surf or chat in the classroom. |
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Contacts :
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| Prof. Denis Baurain
Institut de Botanique B22 (P70)
denis.baurain@ulg.ac.be
Assistant: Dr. Damien Sirjacobs
Institut de Botanique B22 (P70)
04/366.38.54
D.Sirjacobs@ulg.ac.be |
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