DOE JGI releases new version of metagenome data management & analysis system
Targeting its ever-expanding user community, the U.S. Department of Energy Joint Genome Institute (DOE JGI) has released an upgraded version of the IMG/M metagenome data management and analysis system, accessible to the public here. The JGI is a key international research effort analysing genomes from organisms for use in the production of next-generation bioenergy and biofuels.
IMG/M provides tools for analyzing the functional capability of microbial communities based on their metagenome DNA sequence in the context of reference isolate genomes. The new version of IMG/M includes five additional metagenome datasets generated from microbial community samples that were the subject of recently published studies. These include the metagenomic and functional analysis of termite hindgut microbiota (Nature 450, 560-565, 22 November 2007 - previous post) and the single cell genetic analysis of TM7, a rare and uncultivated microbe from the human mouth (PNAS, July 17, 2007, vol. 104, no. 29, 11889-11894).
"IMG/M is a fantastic tool that is incredibly helpful in understanding our data," said Stephen Quake, Co-Chair, Department of Bioengineering at Stanford University, Investigator, Howard Hughes Medical Institute, and senior author on the PNAS study. "We used IMG/M in numerous ways, both to analyze our data and to understand general properties of other relevant bacterial genomes. I look forward to analyzing our new datasets with IMG/M."
IMG/M will be demonstrated at a workshop on March 26 as part of the DOE JGI Third Annual User Meeting. IMG/M contains all isolate genomes in version 2.4 of DOE JGI’s Integrated Microbial Genomes (IMG) system, which represents an increase of 1,339 reference genomes from the previous version of IMG/M. Now, IMG/M contains 2,953 isolate genomes consisting of 819 bacterial, 50 archaeal, 40 eukaryotic genomes, and 2,044 viruses.
IMG/M provides new tools for analyzing metagenome datasets in the context of reference isolate genomes, such as the Reference Genome Context Viewer and Protein Recruitment Plot that allow the examination of metagenomes in the context of individual reference isolate genomes. New Abundance Comparison and Functional Category Comparison tools enable pairwise function analysis (COG, Pfam, Enzyme, TIGRfam) and functional category (e.g., COG category) abundance comparisons, respectively, between a metagenome dataset and one or several reference metagenomes or genomes, and test whether the differences in abundance are statistically significant:
energy :: sustainability :: biomass :: bioenergy :: biofuels :: lignocellulose :: genomics :: microbes :: bioconversion :: biotechnology :: microbiology :: Joint Genome Institute ::
IMG/M has been developed jointly by the DOE JGI’s Genome Biology Program (GBP) and Lawrence Berkeley National Laboratory (LBNL) Biological Data Management and Technology Center (BDMTC). The large-scale pairwise gene similarity computations for all the genomes included in IMG/M have been carried out using ScalaBLAST by the Computational Biology and Bioinformatics Group of the Computational Sciences and Mathematics Division at Pacific Northwest National Laboratory, using the William R. Wiley Environmental Molecular Sciences Laboratory (EMSL) Molecular Sciences Computing Facility supercomputer.
The U.S. Department of Energy Joint Genome Institute, supported by the DOE Office of Science, unites the expertise of five national laboratories - Lawrence Berkeley, Lawrence Livermore, Los Alamos, Oak Ridge, and Pacific Northwest - along with the Stanford Human Genome Center to advance genomics in support of the DOE missions related to clean energy generation and environmental characterization and cleanup. DOE JGI’s Walnut Creek, CA, Production Genomics Facility provides integrated high-throughput sequencing and computational analysis that enable systems-based scientific approaches to these challenges.
References:
U.S. Department of Energy, Joint Genome Institute: DOE JGI Releases a New Version of its Metagenome Data Management & Analysis System - February 7, 2007.
Biopact: Scientists sequence and analyse genomes of termite gut microbes to yield novel enzymes for cellulosic biofuel production - November 22, 2007
Article continues
IMG/M provides tools for analyzing the functional capability of microbial communities based on their metagenome DNA sequence in the context of reference isolate genomes. The new version of IMG/M includes five additional metagenome datasets generated from microbial community samples that were the subject of recently published studies. These include the metagenomic and functional analysis of termite hindgut microbiota (Nature 450, 560-565, 22 November 2007 - previous post) and the single cell genetic analysis of TM7, a rare and uncultivated microbe from the human mouth (PNAS, July 17, 2007, vol. 104, no. 29, 11889-11894).
"IMG/M is a fantastic tool that is incredibly helpful in understanding our data," said Stephen Quake, Co-Chair, Department of Bioengineering at Stanford University, Investigator, Howard Hughes Medical Institute, and senior author on the PNAS study. "We used IMG/M in numerous ways, both to analyze our data and to understand general properties of other relevant bacterial genomes. I look forward to analyzing our new datasets with IMG/M."
IMG/M will be demonstrated at a workshop on March 26 as part of the DOE JGI Third Annual User Meeting. IMG/M contains all isolate genomes in version 2.4 of DOE JGI’s Integrated Microbial Genomes (IMG) system, which represents an increase of 1,339 reference genomes from the previous version of IMG/M. Now, IMG/M contains 2,953 isolate genomes consisting of 819 bacterial, 50 archaeal, 40 eukaryotic genomes, and 2,044 viruses.
IMG/M provides new tools for analyzing metagenome datasets in the context of reference isolate genomes, such as the Reference Genome Context Viewer and Protein Recruitment Plot that allow the examination of metagenomes in the context of individual reference isolate genomes. New Abundance Comparison and Functional Category Comparison tools enable pairwise function analysis (COG, Pfam, Enzyme, TIGRfam) and functional category (e.g., COG category) abundance comparisons, respectively, between a metagenome dataset and one or several reference metagenomes or genomes, and test whether the differences in abundance are statistically significant:
energy :: sustainability :: biomass :: bioenergy :: biofuels :: lignocellulose :: genomics :: microbes :: bioconversion :: biotechnology :: microbiology :: Joint Genome Institute ::
IMG/M has been developed jointly by the DOE JGI’s Genome Biology Program (GBP) and Lawrence Berkeley National Laboratory (LBNL) Biological Data Management and Technology Center (BDMTC). The large-scale pairwise gene similarity computations for all the genomes included in IMG/M have been carried out using ScalaBLAST by the Computational Biology and Bioinformatics Group of the Computational Sciences and Mathematics Division at Pacific Northwest National Laboratory, using the William R. Wiley Environmental Molecular Sciences Laboratory (EMSL) Molecular Sciences Computing Facility supercomputer.
The U.S. Department of Energy Joint Genome Institute, supported by the DOE Office of Science, unites the expertise of five national laboratories - Lawrence Berkeley, Lawrence Livermore, Los Alamos, Oak Ridge, and Pacific Northwest - along with the Stanford Human Genome Center to advance genomics in support of the DOE missions related to clean energy generation and environmental characterization and cleanup. DOE JGI’s Walnut Creek, CA, Production Genomics Facility provides integrated high-throughput sequencing and computational analysis that enable systems-based scientific approaches to these challenges.
References:
U.S. Department of Energy, Joint Genome Institute: DOE JGI Releases a New Version of its Metagenome Data Management & Analysis System - February 7, 2007.
Biopact: Scientists sequence and analyse genomes of termite gut microbes to yield novel enzymes for cellulosic biofuel production - November 22, 2007
Article continues
Friday, February 08, 2008
Biogas from vast amounts of food waste: new Food Bank/Industry partnership launched in Ontario
The Ontario Association of Food Banks (OAFB) and StormFisher Biogas, an Ontario-based renewable energy utility, have joined forces to launch Plan Zero, a province-wide social enterprise that will generate renewable electricity from food industry surplus and by-products that are destined for landfills.
Plan Zero will work with food industry producers, growers and manufacturers to direct organic by-products to StormFisher's biogas production facilities - called anaerobic digesters - which accelerate the decomposition of organic matter to create biogas for use in producing electricity, renewable natural gas and heat. Plan Zero will direct a portion of the proceeds from the sale of energy to Ontario's electricity grid to the OAFB.
StormFisher's anaerobic digesters can produce energy using a wide range of organic materials, from used cooking oils to cow manure. The company also formed relationships with farms, food processing facilities, universities and technology providers. Its first three biogas facilities are currently in early development in London, Drayton and Port Colborne (Ontario) and will be operational by 2009.
Plan Zero also provides a way for food industry producers, growers and manufacturers to direct surplus food products to the provincial food bank network. This surplus product will be distributed to food banks in over 100 communities throughout Ontario. Under Plan Zero, StormFisher and the OAFB will secure long-term agreements with food industry producers, growers and manufacturers that are looking for an environmental and economically beneficial alternative for disposing of their organic by-products:
energy :: sustainability ::biomass :: bioenergy :: biofuels :: biogas :: biomethane :: anaerobic digestion :: food waste ::
Generating electricity from biogas involves capturing the gas produced by the decomposition of organic matter such as food by-products in anaerobic digesters - large holding tanks deprived of oxygen. The decomposition creates a mix of methane and carbon dioxide ("biogas") with the methane subsequently captured and burned to power an electricity generator. The energy created by the generator can then be fed directly into the electrical grid and sold to the Ontario Power Authority (OPA) to supply the province's electricity demand.
As a company that works both with the OAFB and StormFisher, we know the value of putting food that won't be sold to a good use. This is a program that just makes sense. - Chris Swartz, Director of Warehousing, Gordon Food Service Canada
StormFisher has announced agreements to create renewable electricity in partnership with a number of food processing companies in Ontario. One such partnership, with Inniskillin Wines, will create renewable electricity from the winery's grape by-products. About 1,000 to 2,000 tonnes of winery by-products previously destined to a landfill will be given a new use as a fuel. Methane gas produced by the decomposition of grape pomace will be captured and used to generate power for homes in the Niagara region.
References:
StormFischer Biogas: New Food Bank/Industry Partnership to Market Renewable Energy From Food Industry By-Products - January 31, 2008.
Article continues
posted by Biopact team at 7:19 PM 0 comments links to this post