Workshop overview
The Computational Metagenomics Workshop at the University of Mauritius will provide a week-long series of training seminars, practical demonstrations, hands-on tutorials and research talks on the use of software tools to analyze and interpret metagenomics data. The scope is quite broad and offers an overview of cutting-edge fundamental theory and practical applications of metagenomics.

This workshop is aimed primarily at biologists but also at computational scientists who intend to use public metagenomics data in their research or start new projects in the field of metagenomics.

Keywords: Genetics, Genomics, Nucleic acids analysis, Phylogenetics

Skill level of training: beginner

Language: English

Credential awarded: no credential awarded

Type of training: face-to-face / in person

Any pre-requisites / requirements for attending the workshop
Practical workshop sessions assume a basic usage of Unix/Linux command line. Familiarity with other software tools would be an advantage.

Organisers and  presenters
The Computational Metagenomics Workshop is supported by the University of Mauritius and H3ABioNet, as well as the instructors of: University of Cape Town (SA), Linnaeus University (Sweden), CERTH (Thessalonica, Greece) and the University of Cyprus. The instructors are:
Shakuntala Baichoo | University of Mauritius, Mauritius
Gerrit Botha | University of Cape Town, South Africa
Daniel Lundin | Linnaeus University, Sweden
Christos Ouzounis | CERTH Thessalonica, Greece
Vasilis Promponas | University of Cyprus Nicosia, Cyprus

Topics that will be covered during the workshop

Day 1
Fundamentals of Biology: genes, genomes, habitats | Ouzounis
Fundamentals of Computing: data, databases, algorithms | Baichoo
Fundamentals of Bioinformatics: computation, biology, computational biology | Promponas
Practical: Introduction to Linux | Baichoo, Botha

Day 2
Principles of molecular structure, DNA/RNA/proteins, -omics | Promponas
Principles of sequence alignment: sequence comparison, database searches | Ouzounis
Principles of multiple sequence alignment: phylogenetics, phylogenomics | Promponas
Practical: Sequence comparison, tricks of the trade | Ouzounis, Promponas

Day 3
Metagenomics: genomes, pangenomes, paleogenomes | Lundin, Ouzounis
Metagenomics: New sequencing technologies, assembly, pathway inference | Lundin
Metagenomics: Genomic/Functional Encyclopedia of Bacteria & Archaea | TBA
Practical: LAST, MEGAN & Web resources for Metagenomics | Lundin, Ouzounis

Day 4
Metagenomics Platforms I: EBI's metagenomics portal, data standards | TBA
Metagenomics Platforms II: JGI's IMG/M, Microbial Earth Project (MEP) | TBA
Practical: Data analysis of 16S rRNA amplicons with QIIME, uparse & phyloseq | Botha
Practical: Environmental genomics, metagenomics, metatranscriptomics | Lundin

Day 5
Thematic Areas: microbial ecology, bioprospecting, 16S rRNA, metaomics | Lundin
Thematic Areas: human microbiome, biosecurity, highlights/milestones | TBA
Thematic Areas: extreme environments, exobiology | TBA
Practical: Analysis of reduced or simulated datasets, student challenges | Ouzounis, Lundin, Promponas, Botha

The application form for the Computational Metagenomics Workshop can be accessed here.

Application deadline date
The deadline for applications for the Computational Metagenomics workshop is the 20th October 2014

Application restrictions
Please note due to the recent Ebola outbreak there are travel restrictions to Mauritius imposed on nationals from Guinea, Liberia, Sierra Leone, Nigeria, Senegal and the Democratic Republic of Congo by the Government of Mauritius.

Applicant notification deadline
Successful candidates will be notified of their acceptance to the Computational Metagenomics Workshop by the 31st October 2014

Contact Person: Dr. Shakuntala Baichoo

Training Materials Availability:

Training materials for this course are available as a single downloadable archive here: Should you re-use any of these materials, please ensure that both the author/s of the material AND H3ABioNet are clearly credited.