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Genomic Standards Consortium
The Genomic Standards Consortium (GSC) is an initiative working towards richer descriptions of our collection of genomes, metagenomes and marker genes. Established in September 2005, this international community includes representatives from a range of major sequencing and bioinformatics centres (including NCBI, EMBL, DDBJ, JCVI, JGI, EBI, Sanger, FIG) and research institutions. The goal of the GSC is to promote mechanisms for standardizing the description of (meta)genomes, including the exchange and integration of (meta)genomic data. The number and pace of genomic and metagenomic sequencing projects will only increase as the use of ultra-high-throughput methods becomes common place and standards are vital to scientific progress and data sharing. Mission Community-driven standards have the best chance of success if developed within the auspices of international working groups. Participants in the GSC include biologists, computer scientists, those building genomic databases and ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Genomic Standards Consortium (GSC) Milestones
The Genomic Standards Consortium (GSC) is an initiative working towards richer descriptions of our collection of genomes, Metagenomics, metagenomes and marker genes. Established in September 2005, this international community includes representatives from a range of major DNA sequencing, sequencing and bioinformatics centres (including National Center for Biotechnology Information, NCBI, EMBL, DDBJ, J. Craig Venter Institute, JCVI, Joint Genome Institute, JGI, European Bioinformatics Institute, EBI, Wellcome Trust Sanger Institute, Sanger, FIG) and research institutions. The goal of the GSC is to promote mechanisms for standardizing the description of (meta)genomes, including the exchange and integration of (meta)genomic data. The number and pace of genomic and metagenomic sequencing projects will only increase as the use of ultra-high-throughput methods becomes common place and standards are vital to scientific progress and data sharing. Mission Community-driven standards have the ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Wellcome Trust Sanger Institute
The Wellcome Sanger Institute, previously known as The Sanger Centre and Wellcome Trust Sanger Institute, is a non-profit British genomics and genetics research institute, primarily funded by the Wellcome Trust. It is located on the Wellcome Genome Campus by the village of Hinxton, outside Cambridge. It shares this location with the European Bioinformatics Institute. It was established in 1992 and named after double Nobel Laureate Frederick Sanger. It was conceived as a large scale DNA sequencing centre to participate in the Human Genome Project, and went on to make the largest single contribution to the gold standard sequence of the human genome. From its inception the institute established and has maintained a policy of data sharing, and does much of its research in collaboration. Since 2000, the institute expanded its mission to understand "the role of genetics in health and disease". The institute now employs around 900 people and engages in five main areas of research ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Genomics Organizations
Genomics is an interdisciplinary field of biology focusing on the structure, function, evolution, mapping, and editing of genomes. A genome is an organism's complete set of DNA, including all of its genes as well as its hierarchical, three-dimensional structural configuration. In contrast to genetics, which refers to the study of ''individual'' genes and their roles in inheritance, genomics aims at the collective characterization and quantification of ''all'' of an organism's genes, their interrelations and influence on the organism. Genes may direct the production of proteins with the assistance of enzymes and messenger molecules. In turn, proteins make up body structures such as organs and tissues as well as control chemical reactions and carry signals between cells. Genomics also involves the sequencing and analysis of genomes through uses of high throughput DNA sequencing and bioinformatics to assemble and analyze the function and structure of entire genomes. Advances in gen ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
GigaScience
''GigaScience'' is a peer-reviewed scientific journal that was established in 2012. It covers research and large data-sets that result from work in the biomedical and life sciences. The editor-in-chief is Scott Edmunds. Originally, the journal was co-published by BioMed Central and the Beijing Genomics Institute (BGI). In 2016, it left BioMed Central to form a new partnership between the GigaScience Press department of BGI and Oxford University Press. In 2018, ''GigaScience'' won the Association of American Publishers' PROSE Award for Innovation in journal publishing in the multidisciplinary category. GigaDB and GigaGalaxy In order to host the large data-sets the journal covers, ''GigaScience'' has built and integrated its own disciplinary repository: GigaDB. The journal also provides a Galaxy-based platform to analyze data, ''GigaGalaxy''. The journal has tried to promote the use of Galaxy pipelines as publishable research outputs through its 'Galaxy Series' of articles. Abstr ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
JSON
JSON (JavaScript Object Notation, pronounced ; also ) is an open standard file format and data interchange format that uses human-readable text to store and transmit data objects consisting of attribute–value pairs and arrays (or other serializable values). It is a common data format with diverse uses in electronic data interchange, including that of web applications with servers. JSON is a language-independent data format. It was derived from JavaScript, but many modern programming languages include code to generate and parse JSON-format data. JSON filenames use the extension .json. Any valid JSON file is a valid JavaScript (.js) file, even though it makes no changes to a web page on its own. Douglas Crockford originally specified the JSON format in the early 2000s. He and Chip Morningstar sent the first JSON message in April 2001. Naming and pronunciation The 2017 international standard (ECMA-404 and ISO/IEC 21778:2017) specifies "Pronounced , as in 'Jason and The ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Earth Microbiome Project
The 'Earth Microbiome Project'' (EMP) is an initiative founded by Janet Jansson, Jack Gilbert and Rob Knight in 2010 to collect natural samples and to analyze the microbial community around the globe. Microbes are highly abundant, diverse, and have an important role in the ecological system. For example, the ocean contains an estimated 1.3 × 1028 archaeal cells, 3.1 × 1028 bacterial cells, and 1 × 1030 virus particles. The bacterial diversity, a measure of the number of ''types'' of bacteria in a community, is estimated to be about 160 for a mL of ocean water, 6,400–38,000 for a g of soil, and 70 for a mL of sewage works. Yet , it was estimated that the total global environmental DNA sequencing effort had produced less than 1 percent of the total DNA found in a liter of seawater or a gram of soil, and the specific interactions between microbes are largely unknown. The EMP aims to process as many as 200,000 samples in different biomes, genera ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Minimum Information Standards
Minimum information standards are sets of guidelines and formats for reporting data derived by specific high-throughput methods. Their purpose is to ensure the data generated by these methods can be easily verified, analysed and interpreted by the wider scientific community. Ultimately, they facilitate the transfer of data from journal articles (unstructured data) into databases (structured data) in a form that enables data to be mined across multiple data sets. Minimal information standards are available for a vast variety of experiment types including microarray (MIAME), RNAseq ( MINSEQE), metabolomics (MSI) and proteomics (MIAPE). Minimum information standards typically have two parts. Firstly, there is a set of reporting requirements – typically presented as a table or a checklist. Secondly, there is a data format. Information about an experiment needs to be converted into the appropriate data format for it to be submitted to the relevant database. In the case of MIAME, the ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Data Sharing
Data sharing is the practice of making data used for scholarly research available to other investigators. Many funding agencies, institutions, and publication venues have policies regarding data sharing because transparency and openness are considered by many to be part of the scientific method. A number of funding agencies and science journals require authors of peer-reviewed papers to share any supplemental information (raw data, statistical methods or source code) necessary to understand, develop or reproduce published research. A great deal of scientific research is not subject to data sharing requirements, and many of these policies have liberal exceptions. In the absence of any binding requirement, data sharing is at the discretion of the scientists themselves. In addition, in certain situations governments and institutions prohibit or severely limit data sharing to protect proprietary interests, national security, and subject/patient/victim confidentiality. Data sharing may ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
European Bioinformatics Institute
The European Bioinformatics Institute (EMBL-EBI) is an Intergovernmental Organization (IGO) which, as part of the European Molecular Biology Laboratory (EMBL) family, focuses on research and services in bioinformatics. It is located on the Wellcome Genome Campus in Hinxton near Cambridge, and employs over 600 full-time equivalent (FTE) staff. Institute leaders such as Rolf Apweiler, Alex Bateman, Ewan Birney, and Guy Cochrane, an adviser on the National Genomics Data Center Scientific Advisory Board, serve as part of the international research network of the BIG Data Center at the Beijing Institute of Genomics. Additionally, the EMBL-EBI hosts training programs that teach scientists the fundamentals of the work with biological data and promote the plethora of bioinformatic tools available for their research, both EMBL-EBI and non-EMBL-EBI-based. Bioinformatic services One of the roles of the EMBL-EBI is to index and maintain biological data in a set of databases, including E ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Metagenomics
Metagenomics is the study of genetic material recovered directly from environmental or clinical samples by a method called sequencing. The broad field may also be referred to as environmental genomics, ecogenomics, community genomics or microbiomics. While traditional microbiology and microbial genome sequencing and genomics rely upon cultivated clonal cultures, early environmental gene sequencing cloned specific genes (often the 16S rRNA gene) to produce a profile of diversity in a natural sample. Such work revealed that the vast majority of microbial biodiversity had been missed by cultivation-based methods. Because of its ability to reveal the previously hidden diversity of microscopic life, metagenomics offers a powerful lens for viewing the microbial world that has the potential to revolutionize understanding of the entire living world. As the price of DNA sequencing continues to fall, metagenomics now allows microbial ecology to be investigated at a much greater scale ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Joint Genome Institute
The U.S. Department of Energy (DOE) Joint Genome Institute (JGI), first located in Walnut Creek then Berkeley, California, was created in 1997 to unite the expertise and resources in genome mapping, DNA sequencing, technology development, and information sciences pioneered at the DOE genome centers at Lawrence Berkeley National Laboratory (Berkeley Lab), Lawrence Livermore National Laboratory (LLNL) and Los Alamos National Laboratory (LANL). As a DOE Office of Science User Facility of Berkeley Lab, the JGI staff is composed of employees from Berkeley Lab, LLNL and the HudsonAlpha Institute for Biotechnology. The JGI also collaborates with other DOE-supported programs and facilities, such as the Environmental Molecular Sciences Laboratory at Pacific Northwest National Laboratory (PNNL), the National Energy Research Scientific Computing Center, or NERSC, and the DOE Bioenergy Research Centers. History In 1999, the University of California, which manages the three national labs for ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
DDBJ
The DNA Data Bank of Japan (DDBJ) is a biological database that collects DNA sequences. It is located at the National Institute of Genetics (NIG) in the Shizuoka prefecture of Japan. It is also a member of the International Nucleotide Sequence Database Collaboration or INSDC. It exchanges its data with European Molecular Biology Laboratory at the European Bioinformatics Institute and with GenBank at the National Center for Biotechnology Information on a daily basis. Thus these three databanks contain the same data at any given time. History DDBJ began data bank activities in 1987 at NIG and remains the only nucleotide sequence data bank in Asia.Sagar AryaNucleotide sequences database22 February 2019 ''microbenotes.com'' accessed 26 March 2021 Organisation Although DDBJ mainly receives its data from Japanese researchers, it can accept data from contributors from any other country. DDBJ is primarily funded by the Japanese Ministry of Education, Culture, Sports, Science and Technolo ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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