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Course 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.
Intended Audience
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
Venue of the course: University of Mauritius
Dates for the course: 1st Dec 2014 to 5th Dec 2014
Course organisers: 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
Participation: This workshop is available to biologists but also to computational scientists who intend to use public metagenomics data in their research or start new projects in the field of metagenomics.
Course Sponsors: University of Mauritius, H3ABioNet, University of Cape Town (SA), Linnaeus University (Sweden), CERTH (Thessalonica, Greece) and the University of Cyprus
Course objectives
 

Classroom applications

Registration for classrooms opens: Thu, 01/01/1970
Registration for classrooms closes: Thu, 01/01/1970
Link to classroom application form:
Notification date for successful classrooms: Thu, 01/01/1970
Maximum number of participants that may be accepted per classroom will be capped at

Participant applications

Registration for participants opens: Mon, 06/10/2014
Registration for participants closes: Mon, 20/10/2014
Participant registration link: https://docs.google.com/forms/d/1yJpTXDyZhsL4Z8SFiEGCjt8a1z3E71N65AhllpDQRE8/viewform
Syllabus and Tools

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

Prerequisites

Practical workshop sessions assume a basic usage of Unix/Linux command line. Familiarity with other software tools would be an advantage.

 

Course limitations
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.
For more information, please visit
Training material availability

Training materials for this course are available as a single downloadable archive here: https://doi.org/10.25375/uct.19105517. Should you re-use any of these materials, please ensure that both the author/s of the material AND H3ABioNet are clearly credited.