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Found 89 result(s)

Network Data Exchange

NDEx

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The NDEx Project provides an open-source framework where scientists and organizations can share, store, manipulate, and publish biological network knowledge. The NDEx Project maintains a free, public website; alternatively, users can also decide to run their own copies of the NDEx Server software in cases where the stored networks must be kept in a highly secure environment (such as for HIPAA compliance) or where high application load is incompatible with a shared public resource.

PDBj

Protein Data Bank Japan

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PDBj (Protein Data Bank Japan) provides a centralized PDB archive of macromolecular structures, integrated tools for data retrieval, visualization, and functional characterization. PDBj is supported by JST-NBDC and Osaka University.

American Type Culture Collection

ATCC

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While focused on supporting the scientific community, ATCC activities range widely, from repository-related operations to providing specialized services, conducting in-house R&D and intellectual property management. ATCC serves U.S. and international researchers by characterizing cell lines, bacteria, viruses, fungi and protozoa, as well as developing and evaluating assays and techniques for validating research resources and preserving and distributing biological materials to the public and private sector research communities. Our management philosophy emphasizes customer satisfaction, value addition, cost-effective operations and competitive benchmarking for all areas of our enterprise.

IntAct

IntAct Molecular Interaction Database

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IntAct provides a freely available, open source database system and analysis tools for molecular interaction data. All interactions are derived from literature curation or direct user submissions and are freely available.

Ensembl

e!

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The Ensembl project produces genome databases for vertebrates and other eukaryotic species. Ensembl is a joint project between the European Bioinformatics Institute (EBI) and the Wellcome Trust Sanger Institute (WTSI) to develop a software system that produces and maintains automatic annotation on selected genomes.The Ensembl project was started in 1999, some years before the draft human genome was completed. Even at that early stage it was clear that manual annotation of 3 billion base pairs of sequence would not be able to offer researchers timely access to the latest data. The goal of Ensembl was therefore to automatically annotate the genome, integrate this annotation with other available biological data and make all this publicly available via the web. Since the website's launch in July 2000, many more genomes have been added to Ensembl and the range of available data has also expanded to include comparative genomics, variation and regulatory data. Ensembl is a joint project between European Bioinformatics Institute (EBI), an outstation of the European Molecular Biology Laboratory (EMBL), and the Wellcome Trust Sanger Institute (WTSI). Both institutes are located on the Wellcome Trust Genome Campus in Hinxton, south of the city of Cambridge, United Kingdom.

Genome-Scale Metabolic Network DataBase

GSMNDB

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<<<!!!<<< 2019-12-23: the repository is offline >>>!!!>>> Introduction of genome-scale metabolic network: The completion of genome sequencing and subsequent functional annotation for a great number of species enables the reconstruction of genome-scale metabolic networks. These networks, together with in silico network analysis methods such as the constraint based methods (CBM) and graph theory methods, can provide us systems level understanding of cellular metabolism. Further more, they can be applied to many predictions of real biological application such as: gene essentiality analysis, drug target discovery and metabolic engineering

UCSC Genome Browser

University of California Santa Cruz Genome Bioinformatics

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It is an interactive website offering access to genome sequence data from a variety of vertebrate and invertebrate species and major model organisms, integrated with a large collection of aligned annotations. The Browser is a graphical viewer optimized to support fast interactive performance and is an open-source, web-based tool suite built on top of a MySQL database for rapid visualization, examination, and querying of the data at many levels.

EcoCyc Database

EcoCyc E. coli Database

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EcoCyc is a scientific database for the bacterium Escherichia coli K-12 MG1655. The EcoCyc project performs literature-based curation of the entire genome, and of transcriptional regulation, transporters, and metabolic pathways.

Ensembl Genomes

e!EnsemblGenomes

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The Ensembl genome annotation system, developed jointly by the EBI and the Wellcome Trust Sanger Institute, has been used for the annotation, analysis and display of vertebrate genomes since 2000. Since 2009, the Ensembl site has been complemented by the creation of five new sites, for bacteria, protists, fungi, plants and invertebrate metazoa, enabling users to use a single collection of (interactive and programatic) interfaces for accessing and comparing genome-scale data from species of scientific interest from across the taxonomy. In each domain, we aim to bring the integrative power of Ensembl tools for comparative analysis, data mining and visualisation across genomes of scientific interest, working in collaboration with scientific communities to improve and deepen genome annotation and interpretation.

Ensembl Protists

e!EnsemblProtists

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EnsemblProtists is a genome-centric portal for protists species.

Ensembl Bacteria

e!EnsemblBacteria

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This site provides access to complete, annotated genomes from bacteria and archaea (present in the European Nucleotide Archive) through the Ensembl graphical user interface (genome browser). Ensembl Bacteria contains genomes from annotated INSDC records that are loaded into Ensembl multi-species databases, using the INSDC annotation import pipeline.

International Mouse Phenotyping Consortium

IMPC

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The IMPC is a confederation of international mouse phenotyping projects working towards the agreed goals of the consortium: To undertake the phenotyping of 20,000 mouse mutants over a ten year period, providing the first functional annotation of a mammalian genome. Maintain and expand a world-wide consortium of institutions with capacity and expertise to produce germ line transmission of targeted knockout mutations in embryonic stem cells for 20,000 known and predicted mouse genes. Test each mutant mouse line through a broad based primary phenotyping pipeline in all the major adult organ systems and most areas of major human disease. Through this activity and employing data annotation tools, systematically aim to discover and ascribe biological function to each gene, driving new ideas and underpinning future research into biological systems; Maintain and expand collaborative “networks” with specialist phenotyping consortia or laboratories, providing standardized secondary level phenotyping that enriches the primary dataset, and end-user, project specific tertiary level phenotyping that adds value to the mammalian gene functional annotation and fosters hypothesis driven research; and Provide a centralized data centre and portal for free, unrestricted access to primary and secondary data by the scientific community, promoting sharing of data, genotype-phenotype annotation, standard operating protocols, and the development of open source data analysis tools. Members of the IMPC may include research centers, funding organizations and corporations.

Ensembl Metazoa

e!EnsemblMetazoa

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Ensembl Metazoa is a genome-centric portal for metazoan species of scientific interest.

DRYAD

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Dryad is an open data publishing platform and a community committed to the open availability and routine re-use of all research data. We publish data in any format and any discipline. All Dryad data undergoes a curation process and is published under a CC0 waiver to promote reuse.

European Variation Archive

EVA

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The European Variation Archive is an open-access database of all types of genetic variation data from all species. The EVA provides access to highly detailed, granular, raw variant data from human, with other species to follow. As of September 2017, EMBL-EBI will maintain reliable accessions for non-human genetic variation data through the European Variation Archive (EVA). NCBI's dbSNP database will continue to maintain stable identifiers for human genetic variation data only. This change will enable a more rapid turnaround for data sharing in this burgeoning field.

MGnify

formerly: EBI Metagenomics

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MGnify (formerly: EBI Metagenomics) offers an automated pipeline for the analysis and archiving of microbiome data to help determine the taxonomic diversity and functional & metabolic potential of environmental samples. Users can submit their own data for analysis or freely browse all of the analysed public datasets held within the repository. In addition, users can request analysis of any appropriate dataset within the European Nucleotide Archive (ENA). User-submitted or ENA-derived datasets can also be assembled on request, prior to analysis.

NCBI Influenza Virus Resource

NCBI Flu

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This resource allows users to search for and compare influenza virus genomes and gene sequences taken from GenBank. It also provides a virus sequence annotation tool and links to other influenza resources: NIAID project, JCVI Flu, Influenza research database, CDC Flu, Vaccine Selection and WHO Flu. NOTE: The redirects that are planned for completion by May 2024 will NOT impact the Influenza Virus Resource in any way. The Influenza Virus Resource will continue to be available, serving up data to support our Flu-research community.

NCBI Virus Variation

Influenza Virus Database

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<<<!!!<<< Effective May 2024, Virus Variation will no longer be available and will be redirected to NCBI Virus https://www.ncbi.nlm.nih.gov/labs/virus/vssi/#/ >>>!!!>>> NCBI Virus Variation is a specialized database which collects tools to provide searchable resources in the fields of Influenza virus, Dengue virus, and West Nile virus. Specific BLAST databases are listed. Their new publications are also available in their site. Rotavirus database will be added in their site soon.

NCBI Protein Clusters

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The Entrez Protein Clusters database contains annotation information, publications, structures and analysis tools for related protein sequences encoded by complete genomes. The data available in the Protein Clusters Database is generated from prokaryotic genomic studies and is intended to assist researchers studying micro-organism evolution as well as other biological sciences. Available genomes include plants and viruses as well as organelles and microbial genomes.

Yeast Resource Center Public Image Repository

YRC Public Image Repository

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The Yeast Resource Center Public Image Repository is a database of fluorescent microscopy images and their associated metadata/experimental parameters. The images depict the localization, co-localization and FRET (fluorescence energy transfer) of proteins in cells, particularly in the budding yeast Saccharomyces cerevisiae as a model organism. Users may download the entire datasets to improve their research.

ORegAnno

Open regulatory annotation database

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<<<!!!<<< 2017-06-02: We recently suffered a server failure and are working to bring the full ORegAnno website back online. In the meantime, you may download the complete database here: http://www.oreganno.org/dump/ ; Data are also available through UCSC Genome Browser (e.g., hg38 -> Regulation -> ORegAnno) https://genome.ucsc.edu/cgi-bin/hgTrackUi?hgsid=686342163_2it3aVMQVoXWn0wuCjkNOVX39wxy&c=chr1&g=oreganno >>>!!!>>> The Open REGulatory ANNOtation database (ORegAnno) is an open database for the curation of known regulatory elements from scientific literature. Annotation is collected from users worldwide for various biological assays and is automatically cross-referenced against PubMED, Entrez Gene, EnsEMBL, dbSNP, the eVOC: Cell type ontology, and the Taxonomy database, where appropriate, with information regarding the original experimentation performed (evidence). ORegAnno further provides an open validation process for all regulatory annotation in the public domain. Assigned validators receive notification of new records in the database and are able to cross-reference the citation to ensure record integrity. Validators have the ability to modify any record (deprecating the old record and creating a new one) if an error is found. Further, any contributor to the database can comment on any annotation by marking errors, or adding special reports into function as they see fit. These features of ORegAnno ensure that the collection is of the highest quality and uniquely provides a dynamic view of our changing understanding of gene regulation in the various genomes.

NCBI dbGaP

DataBase of Genotypes And Phenotypes

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The NCBI database of Genotypes and Phenotypes archives and distributes the results of studies that have investigated the interaction of genotype and phenotype, including genome-wide association studies, medical sequencing, molecular diagnostic assays, and association between genotype and non-clinical traits. The database provides summaries of studies, the contents of measured variables, and original study document text. dbGaP provides two types of access for users, open and controlled. Through the controlled access, users may access individual-level data such as phenotypic data tables and genotypes.

Bioconductor

Open Source Software for Bioinformatics

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Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images.

Hymenoptera Genome Database

HGD

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The Hymenoptera Genome Database is a genome informatics resource that supports the research of insects of the order Hymenoptera (e.g. bees, wasps, ants). HGD provides tools for data mining (HymenopteraMine), sequence searching (BLAST), genome browsing (JBrowse), genome annotation (Apollo) and data download. Available through the navigation bar on the HGD Home page are the archives Ant Genomes Portal, BeeBase, and NasoniaBase which will not be updated.

PANDIT

Protein and Associated Nucleotide Domains with Inferred Trees

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<<<!!!<<< Efforts to obtain renewed funding after 2008 were unfortunately not successful. PANDIT has therefore been frozen since November 2008, and its data are not updated since September 2005 when version 17.0 was released (corresponding to Pfam 17.0). The existing data and website remain available from these pages, and should remain stable and, we hope, useful. >>>!!!>>> PANDIT is a collection of multiple sequence alignments and phylogenetic trees. It contains corresponding amino acid and nucleotide sequence alignments, with trees inferred from each alignment. PANDIT is based on the Pfam database (Protein families database of alignments and HMMs), and includes the seed amino acid alignments of most families in the Pfam-A database. DNA sequences for as many members of each family as possible are extracted from the EMBL Nucleotide Sequence Database and aligned according to the amino acid alignment. PANDIT also contains a further copy of the amino acid alignments, restricted to the sequences for which DNA sequences were found.