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Archive for January, 2009

The GSC proposal to host a SIG this year at ISMB 2009 in Sweden has been successful. Further details will follow soon but the one day meeting will be held Saturday June 27th before the start of the main ISMB / ECCB 2009 meeting in Stockholm.

The official title of the SIG is “Metagenomics, Metadata and Metaanalysis (M3)“. There will a set of invited speakers along with a call for papers and posters.

Some further background about the spirit of the meeting below. The “M3” Hompage will appear here in time

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ISMB SIG: Metagenomics, Metadata and Metaanalysis (M3), June 27th, Stockholm

There are now thousands of genomes and metagenomes available for study (see the Genomes Online Database. Interest in improved sampling of diverse environments (e.g. ocean, soil, sediment, and a range of hosts) combined with advances in the development and application of ultra-high throughput sequence methodologies is set to vastly accelerate the pace at which new metagenomes are generated. For example, in 2007, the Global Ocean Survey published scientific analyses of 41 metagenomes, and as of October 2008, the submission of user-generated metagenomes to the public MG-Rast Annotation server surpassed 1300. We have also entered an era of ‘mega-sequencing projects’ that now include funded projects like the Genomic Encyclopedia of Bacteria and Archaea (GEBA) project and the Human Microbiome Initiative (e.g. HMP), with many more visionary projects on the horizon.

While genomes represent the full genetic (DNA) complement of a single organism, metagenomes represent the DNA of an entire community of organisms. Metagenomes are partial samples of complex and largely unknown communities that can only be poorly assembled. Genome and metagenomes are now also being complemented with studies of metatranscriptomes (community transcript profiles) and metaproteomes (community protein profiles). The comparative study of these datasets, including multi-omic data sets from the same community, bring with them the need for new computational approaches.
These data hold the promise of unparalleled insights into fundamental questions across a range of fields including evolution, ecology, environment biology, health and medicine. Advances stem from improved understandings of the combinations, abundances and functions of the organisms in these communities and their genes and pathways. We are just starting to exploit these technologies to understand the microbial world and have only scratched the surface in terms of sampling natural microbial diversity in terms of space and time.

This SIG will explore the latest concepts, algorithms, tools, informatics pipelines, databases and standards being developed to cope with the analysis of vast quantities of metagenomic data. Through a series of invited and contributed talks, a panel discussion, and flash talks associated with a poster session, we aim to highlight scientific advances in the field and identify core computational challenges facing the wider community.

We aim to bring together researchers collecting samples for metagenomic analysis with those building the computational infrastructure required to fully exploit them with those thinking about the implementation of standards. In particular, we aim to encourage the participation of researchers already using metadata to detect patterns of biological interest. For example, those that are detecting trends in collections of genomes or metagenomes based on habitat or geographic location, or by analogy for microbiome studies by host or anatomical location, or studies that integrate substantial environmental, phenotypic, or epidemiology data.

This SIG will be hosted by the Genomic Standards Consortium (GSC). It will place emphasis on understanding the community’s needs for the complementary standards required to drive metagenomic science forward and support comparative studies. A SIG report will be published in the GSC’s online, open access journal “Standards in Genomic Sciences”. Contributed submissions based on talks and posters that describe studies that demonstrate the power of using curated (e.g. habitat or host) and measured (e.g. geographic location, salinity, temperature, or pH) contextual data in comparative metagenomic studies of large numbers of samples are encouraged. Likewise, papers describing new approaches, tools, databases, standards, ontologies or substantial new sets of curated metadata that aid in the integration and inter-operablility of disparate datasets are welcomed.

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