This site contains the teaching material for the course Computational Biology taught in the 1st year of the Master Computational and Mathematical Biology at Aix-Marseille Université.
| Doc | URL |
|---|---|
| Web site (git pages) | https://jvanheld.github.io/cmb-comp-bio/ |
| Github repo | https://github.com/jvanheld/cmb-comp-bio/ |
| [19-20] Computational Biology on Ametice | https://ametice.univ-amu.fr/course/view.php?id=51934 |
- Laurent Pezard
- Michael Kopp
- Jacques van Helden
- This course is conceived to be followed by a mixed audience of students having a background in either biology or mathematics.
- Biological and mathematical concepts will thus be introduced progressively.
- For the practicals, students will be encouraged to form interdisciplinary teams (1 biologist + 1 mathematician) in order to combine their respective skills.
Note: The first course (sequence similarity search) partly overlaps with the introductory courses of bioinformatics taught in Life Science Bachelor programs. However, the practical will go a bit further than what has been taught in bachelor.
- The practical will rely on a command-line use of the BLAST algorithm, with options specifically tuned to collect a family of proteins from the full proteome of an organism of interest.
- The practical will also introduce the way to run the analyses on a computer cluster (IFB core cluster), by sending them to a job scheduler (slurm).
| Session | Date | Topics | Type | Teaching material |
|---|---|---|---|---|
| 1 | 2019-11-25 | ¨Using the IFB NNCR cluster infrastructure | ||
| Introduction | Course | Slides [html] [Rmd] | ||
| IFB high performance computing usage | Practical | Slides [html] | ||
| First steps with the IFB HPC cluster | Practical | - IFB cluster doc - Quick start - Slurm user guide |
||
| 2 | 2019-11-25 | Collecting sequence families by sequence alignement | ||
| Background concepts for sequence analysis | Course | [Slides] | ||
| Pairwise sequence alignments | Course | [Slides] | ||
| Sequence search by similarity | Course | [Slides] | ||
| Collecting sequence families with BLAST | Practical | [html][Rmd] | ||
| 3 | 2019-11-29 | Segmenting sequences with HMMs | ||
| Hidden Markov Models (HMMs) | Course | [Slides] [Recording] (requires AMU login) | ||
| Analysing CpG islands with Markov models | Practical | [html] [Rmd] | ||
| 4 | 2019-12-11 | Analysing CpG islands with Markov models | Solutions (beginning) | [html] [Rmd] |
| Home work: detecting CpG islands in genomic sequences | [html] [pdf] [Rmd] |
For the practicals, we will use the IFB core cluster, which currently contains 4300 cores adn 400TB storage.
Attention: all tasks must imperatively run via the slurm task scheduler (never run them on the login node).
| Resource | URL |
|---|---|
| IFB NNCR cluster: info + account request | https://www.france-bioinformatique.fr/en/cluster |
| Slides: using the IFB core cluster | https://ifb-elixirfr.gitlab.io/cluster/trainings/slurm/ebai2019.html#1 |
| IFB cluster doc | https://ifb-elixirfr.gitlab.io/cluster/doc/ - Quick start - Slurm user guide |
| Resource | Description | URL |
|---|---|---|
| Ensembl | Genome database | www.ensembl.org |
| UniprotKB | Knowledge base of protein sequence and functional information | www.uniprot.org |
| PFAM | Database of protein families | pfam.xfam.org |
Introductory course of bioinformatics, for Bachelor students in biology.
- Home page of the course
- Pairwise alignments: global (Needleman-Wunsch) and local (Smith-Waterman) algorithms using dynamical programming
- Sequence similarity searches with BLAST