Suchergebnisse

This report summarizes the proceedings of the 9th workshop of the Genomic Standards Consortium (GSC), held at the J. Craig Venter Institute, Rockville, MD, USA. It was the first GSC workshop to have open registration and attracted over 90 participants. This workshop featured sessions that provided overviews of the full range of ongoing GSC projects. It included sessions on Standards in Genomic Sciences, the open access journal of the GSC, building standards for genome annotation, the M5 platform for next-generation collaborative computational infrastructures, building ties with the biodiversity research community and two discussion panels with government and industry participants. Progress was made on all fronts, and major outcomes included the completion of the MIENS specification for publication and the formation of the Biodiversity working group.

This report summarizes the proceedings of the 9th workshop of the Genomic Standards Consortium (GSC), held at the J. Craig Venter Institute, Rockville, MD, USA. It was the first GSC workshop to have open registration and attracted over 90 participants. This workshop featured sessions that provided overviews of the full range of ongoing GSC projects. It included sessions on Standards in Genomic Sciences, the open access journal of the GSC, building standards for genome annotation, the M5 platform for next-generation collaborative computational infrastructures, building ties with the biodiversity research community and two discussion panels with government and industry participants. Progress was made on all fronts, and major outcomes included the completion of the MIENS specification for publication and the formation of the Biodiversity working group.

© The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Standards in Genomic Sciences 9 (2014): 1236-1250, doi:10.4056/sigs.4319681. ; This report summarizes the proceedings of the 14th workshop of the Genomic Standards Consortium (GSC) held at the University of Oxford in September 2012. The workshop's primary goal was to work towards the launch of the Genomic Observatories (GOs) Network under the GSC. For the first time, it brought together potential GOs sites, GSC members, and a range of interested partner organizations. It thus represented the first meeting of the GOs Network (GOs1). Key outcomes include the formation of a core group of "champions" ready to take the GOs Network forward, as well as the formation of working groups. The workshop also served as the first meeting of a wide range of participants in the Ocean Sampling Day (OSD) initiative, a first GOs action. Three projects with complementary interests – COST Action ES1103, MG4U and Micro B3 – organized joint sessions at the workshop. A two-day GSC Hackathon followed the main three days of meetings. ; This work was supported in part by the US Na-tional Science Foundation through the research coordination network award RCN4GSC, DBI-0840989 and in part by a grant from the Gordon and Betty Moore Foundation, and travel grants of COST Action ES1103. The stakeholder session was supported by the European Union's Seventh Framework Programme (FP7 /2007-2013) under grant agreement no 266055, and the Marine Ge-nomics for Users EU FP7 project (Coordination and support action, call FP7-KBBE-2010-4) grant no. 266055. We thank Eppendorf and Biomatters Ltd. for their sponsorship of the meeting.

AbstractOne of the biggest challenges in molecular biology is bridging the gap between the known and the unknown coding sequence space. This challenge is especially extreme in microbial systems, where between 40% and 60% of the predicted genes are of unknown function. Discarding this uncharacterized fraction should not be an option anymore. Here, we present a conceptual framework and a computational workflow that bridges this gap and provides a powerful strategy to contextualize the investigations of genes of unknown function. Our approach partitions the coding sequence space removing the known-unknown dichotomy, unifies genomic and metagenomic data and provides a framework to expand those investigations across environments and organisms. By analyzing 415,971,742 genes predicted from 1,749 metagenomes and 28,941 bacterial and archaeal genomes we showcase our approach and its application in ecological, evolutionary and biotechnological investigations. As a result, we put into perspective the extent of the unknown fraction, its diversity, and its relevance in genomic and environmental contexts. By identifying a target gene of unknown function for antibiotic resistance, we demonstrate how a contextualized unknown coding sequence space enables the generation of hypotheses that can be used to augment experimental data. ; The authors thankfully acknowledge the computer resources at MareNostrum and the technical support provided by Barcelona Supercomputing Center (RES-AECT-2014-2-0085), the BMBF795 funded de.NBI Cloud within the German Network for Bioinformatics Infrastructure (de.NBI) (031A537B, 031A533A, 031A538A, 031A533B, 031A535A, 031A537C, 031A534A, 031A532B), the University of Oxford Advanced Research Computing (http://dx.doi.org/10.5281/zenodo.22558) and the MARBITS bioinformatics core at ICM-CSIC. CV was supported by the Max Planck Society. AFG received funding from the European Union's Horizon 2020 research and innovation program Blue Growth: Unlocking the potential of Seas and Oceans under grant agreement no. 634486 (project acronym INMARE). AM was supported by the Biotechnology and Biological Sciences Research Council [BB/M011755/1, BB/R015228/1] and RDF by the European Molecular Biology Laboratory core funds. EOC was supported by project INTERACTOMA RTI2018-101205-B-I00 from the Spanish Agency of Science MICIU/AEI. SGA and PS received additional funding by the project MAGGY (CTM2017-87736-R) from the Spanish Ministry of Economy and Competitiveness. The Malaspina 2010 Expedition was supported by the Spanish Ministry of Economy and Competitiveness (MINECO) through the Consolider-Ingenio program (ref. CSD2008-00077). The authors thank Johannes Söding and Alex Bateman for helpful discussions.

Ocean Sampling Day was initiated by the EU-funded Micro B3 (Marine Microbial Biodiversity, Bioinformatics, Biotechnology) project to obtain a snapshot of the marine microbial biodiversity and function of the world's oceans. It is a simultaneous global mega-sequencing campaign aiming to generate the largest standardized microbial data set in a single day. This will be achievable only through the coordinated efforts of an Ocean Sampling Day Consortium, supportive partnerships and networks between sites. This commentary outlines the establishment, function and aims of the Consortium and describes our vision for a sustainable study of marine microbial communities and their embedded functional traits. ; European Union

© The Author(s), 2015. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in GigaScience 4 (2015): 27, doi:10.1186/s13742-015-0066-5. ; Ocean Sampling Day was initiated by the EU-funded Micro B3 (Marine Microbial Biodiversity, Bioinformatics, Biotechnology) project to obtain a snapshot of the marine microbial biodiversity and function of the world's oceans. It is a simultaneous global mega-sequencing campaign aiming to generate the largest standardized microbial data set in a single day. This will be achievable only through the coordinated efforts of an Ocean Sampling Day Consortium, supportive partnerships and networks between sites. This commentary outlines the establishment, function and aims of the Consortium and describes our vision for a sustainable study of marine microbial communities and their embedded functional traits. ; This work was supported by the Micro B3 project, which is funded from the European Union's Seventh Framework Programme (FP7; Joint Call OCEAN.2011‐2: Marine microbial diversity – new insights into marine ecosystems functioning and its biotechnological potential) under the grant agreement no 287589.