Sep 8-10 Course. Extracting ecological signal from noise: an introduction to tools for the analysis of high throughput sequencing data from microbial communities
This participatory workshop will provide an overview of tools for the analysis of high throughput sequencing data from microbial communities.
Main content
Bioinformatics has become a bottleneck for scientists applying molecular methods in microbial ecology. For high throughput sequencing, technologies have advanced more quickly than our ability to analyse the data.
Now, for the very first time, we see the emergence of technical and mathematical tools which are powerful enough to permit meaningful examination of the biological diversity of various environments using molecular methods. The new generation of massive parallel sequencing technology and a new generation of mathematical tools allow the rational exploration of the diversity of the microbial world
This participatory workshop will provide an overview of tools for the analysis of high throughput sequencing data from microbial communities. The topics covered will include:
- Noise removal from pyrosequenced amplicons – Pyronoise
- Taxonomic classification of reads – RDP and Megan classifiers
- Estimates of total diversity and sampling efforts
- Metrics and multivariate statistics for community comparison – Unifrac
- Integrated pipelines – Qiime and Mothur
Participants will be encouraged to bring data sets for analysis during the course of the workshop. Larger data sets (up to one full 454 run) should be sent to us at least a week prior to the workshop so that we can start de-noising the data. For smaller data sets (up to ¼ 454 run) this will not be necessary. We would also recommend that each group bring a laptop running some version of Unix (e.g. Linux or Mac Os X) for installation of software and/or have access to a Linux computer remotely through a windows laptop running ssh or equivalent.
Programme - updated September 6th 2010
Applications
Application deadline: August 20th
Please send the application by e-mail to contact@mcb.uib.no
Please include name, place of work, the title of your current PhD/research project and what previous (if any) MCB activities you have participated in.
The course is open to all interested, but MCB-members will have priority, and PhD-students will have priority over other groups.
Speakers and Organisers
Chris Quince’s research is focusing on development of novel tools for the analysis of genomics data from microbial communities with the integration of the resulting information into predictive mathematical models. This will build on our existing research into noise removal from pyrosequencing data and statistics for determining microbial diversity, extending the results to new sequencing platforms and shotgun metagenomics sequences.
Bill Sloan’s research interests are in mathematical modelling of both biological and physical environmental systems. Recently his research has concentrated on modeling the ecology of engineered and natural microbial communities. In particular on interpreting the output from new molecular methods for characterising microbial communities in situ to estimate biodiversity and describe community assembly.
Tom Curtis core interest is the engineering of real open microbial systems and his abiding belief is that these systems obey a suite of fundamental rules and that engineers will only unlock the power of such systems when they grasp those rules. Working with colleagues in Glasgow and Newcastle he has developed tools, concepts and theories that support this end. He has become particularly well known for his work on the engineering of the diversity and community assembly of microbial communities. This work is central to all open biological systems, engineered or otherwise and could be an essential pre-requisite for the application of synthetic biological methods in such systems.
Anders Lanzen has a background in bioinformatics and genomics with several years experience from the National Bioifnformatics Service group hosted by the Computational Biology Unit of the Bergen Center for Computational Science at the University of Bergen. The focus of Anders’s PhD project is bioinformatic methodology for high throughput sequencing in environmental genomics, with a special emphasis on 454 pyrosequencing data.
Greg Caporaso is a computational biologist based in the Knight Laboratory at the University of Colorado at Boulder. He is the lead software developer on the Quantitative Insights Into Microbial Ecology (QIIME) project, and is
generally interested in microbial ecology in both free-living and host-associated environments. Greg spends a considerable amount of his timedeveloping bioinformatics software. In addition to QIIME, he is also the
primary developer on the Python Nearest Alignment Search Tool (PyNAST), and a contributor to the Python Comparative Genomics Toolkit (PyCogent). Recent work includes development and publication of a protocol for using theIllumina GAII platform to study microbial communities, and analyses of bacterial, archaeal and fungal communities in soil.
Lise Øvreås has been an active member in a research group that has pioneered whole community analysis in soil, water and sediment ecosystems. She has a solid research experience in environmental microbiology, and in developing and applying holistic molecular techniques for use in natural ecosystems. She has further experience in using high throughput sequencing analyses to gain knowledge about the biodiversity and ecology of microorganisms from various environments.
