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Found 17 result(s)

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.

FAIRDOMHub

The SEEK datafiles

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The FAIRDOMHub is built upon the SEEK software suite, which is an open source web platform for sharing scientific research assets, processes and outcomes. FAIRDOM (Web Site) will establish a support and service network for European Systems Biology. It will serve projects in standardizing, managing and disseminating data and models in a FAIR manner: Findable, Accessible, Interoperable and Reusable. FAIRDOM is an initiative to develop a community, and establish an internationally sustained Data and Model Management service to the European Systems Biology community. FAIRDOM is a joint action of ERA-Net EraSysAPP and European Research Infrastructure ISBE.

WorldWide Antimalarial Resistance Network

WWARN

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The WorldWide Antimalarial Resistance Network (WWARN) is a collaborative platform generating innovative resources and reliable evidence to inform the malaria community on the factors affecting the efficacy of antimalarial medicines. Access to data is provided through diverse Tools and Resources: WWARN Explorer, Molecular Surveyor K13 Methodology, Molecular Surveyor pfmdr1 & pfcrt, Molecular Surveyor dhfr & dhps.

InnateDB

A Knowlede Resource for Innate Immunity Interactions & Pathways

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InnateDB is a publicly available database of the genes, proteins, experimentally-verified interactions and signaling pathways involved in the innate immune response of humans, mice and bovines to microbial infection. The database captures an improved coverage of the innate immunity interactome by integrating known interactions and pathways from major public databases together with manually-curated data into a centralised resource. The database can be mined as a knowledgebase or used with our integrated bioinformatics and visualization tools for the systems level analysis of the innate immune response.

Pathway Commons

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Pathway Commons is a convenient point of access to biological pathway information collected from public pathway databases. Information is sourced from public pathway databases and is readily searched, visualized, and downloaded. The data is freely available under the license terms of each contributing database.

ArachnoServer

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ArachnoServer is a manually curated database containing information on the sequence, three-dimensional structure, and biological activity of protein toxins derived from spider venom. Spiders are the largest group of venomous animals and they are predicted to contain by far the largest number of pharmacologically active peptide toxins (Escoubas et al., 2006). ArachnoServer has been custom-built so that a wide range of biological scientists, including neuroscientists, pharmacologists, and toxinologists, can readily access key data relevant to their discipline without being overwhelmed by extraneous information.

European Nucleotide Archive

ENA

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The European Nucleotide Archive (ENA) captures and presents information relating to experimental workflows that are based around nucleotide sequencing. A typical workflow includes the isolation and preparation of material for sequencing, a run of a sequencing machine in which sequencing data are produced and a subsequent bioinformatic analysis pipeline. ENA records this information in a data model that covers input information (sample, experimental setup, machine configuration), output machine data (sequence traces, reads and quality scores) and interpreted information (assembly, mapping, functional annotation). Data arrive at ENA from a variety of sources. These include submissions of raw data, assembled sequences and annotation from small-scale sequencing efforts, data provision from the major European sequencing centres and routine and comprehensive exchange with our partners in the International Nucleotide Sequence Database Collaboration (INSDC). Provision of nucleotide sequence data to ENA or its INSDC partners has become a central and mandatory step in the dissemination of research findings to the scientific community. ENA works with publishers of scientific literature and funding bodies to ensure compliance with these principles and to provide optimal submission systems and data access tools that work seamlessly with the published literature.

PRoteomics IDEntifications Database

PRIDE

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The PRIDE PRoteomics IDEntifications database is a centralized, standards compliant, public data repository for proteomics data, including protein and peptide identifications, post-translational modifications and supporting spectral evidence. PRIDE encourages and welcomes direct user submissions of mass spectrometry data to be published in peer-reviewed publications.

Berkeley Drosophila Genome Project

BDGP

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The goals of the Drosophila Genome Center are to finish the sequence of the euchromatic genome of Drosophila melanogaster to high quality and to generate and maintain biological annotations of this sequence. In addition to genomic sequencing, the BDGP is 1) producing gene disruptions using P element-mediated mutagenesis on a scale unprecedented in metazoans; 2) characterizing the sequence and expression of cDNAs; and 3) developing informatics tools that support the experimental process, identify features of DNA sequence, and allow us to present up-to-date information about the annotated sequence to the research community.

Birdbase

A database of avian genes & genomes

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<<<!!!<<< This repository is no longer available. >>>!!!>>> The sequencing of several bird genomes and the anticipated sequencing of many more provided the impetus to develop a model organism database devoted to the taxonomic class: Aves. Birds provide model organisms important to the study of neurobiology, immunology, genetics, development, oncology, virology, cardiovascular biology, evolution and a variety of other life sciences. Many bird species are also important to agriculture, providing an enormous worldwide food source worldwide. Genomic approaches are proving invaluable to studying traits that affect meat yield, disease resistance, behavior, and bone development along with many other factors affecting productivity. In this context, BirdBase will serve both biomedical and agricultural researchers.

LIPID MAPS

LIPID Metabolites And Pathways Strategy

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Tthe Lipidomics Gateway - a free, comprehensive website for researchers interested in lipid biology, provided by the LIPID MAPS (Lipid Metabolites and Pathways Strategy) Consortium. The LIPID MAPS Lipidomics Gateway provides a rich collection of information and resources to help you stay abreast of the latest developments in this rapidly expanding field. LIPID Metabolites And Pathways Strategy (LIPID MAPS®) is a multi-institutional effort created in 2003 to identify and quantitate, using a systems biology approach and sophisticated mass spectrometers, all of the major — and many minor — lipid species in mammalian cells, as well as to quantitate the changes in these species in response to perturbation. The ultimate goal of our research is to better understand lipid metabolism and the active role lipids play in diabetes, stroke, cancer, arthritis, Alzheimer's and other lipid-based diseases in order to facilitate development of more effective treatments. Since our inception, we have made great strides toward defining the "lipidome" (an inventory of the thousands of individual lipid molecular species) in the mouse macrophage. We have also worked to make lipid analysis easier and more accessible for the broader scientific community and to advance a robust research infrastructure for the international research community. We share new lipidomics findings and methods, hold annual meetings open to all interested investigators, and are exploring joint efforts to extend the use of these powerful new methods to new applications

The Arabidopsis Information Resource

TAIR

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The Arabidopsis Information Resource (TAIR) maintains a database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana . Data available from TAIR includes the complete genome sequence along with gene structure, gene product information, metabolism, gene expression, DNA and seed stocks, genome maps, genetic and physical markers, publications, and information about the Arabidopsis research community. Gene product function data is updated every two weeks from the latest published research literature and community data submissions. Gene structures are updated 1-2 times per year using computational and manual methods as well as community submissions of new and updated genes. TAIR also provides extensive linkouts from our data pages to other Arabidopsis resources.

Scotland's Rural College Research Data Repository

SRUC research data

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SRUC is currently on a transformational journey as we move towards becoming a unique, market-led and mission diverse 21st Century rural university, driving the future needs of a dynamic, innovative and competitive rural sector in Scotland, and working with our collaborators and partners worldwide to solve the biggest global agrifood challenges. Our researchers already carry out strategic and applied research on global and local food security issues, and actively support the translation of research results into practice. Our research ethos is strongly collaborative, and we have a long history of industrial, NGO and academic partnerships locally and internationally. As well as having longstanding disciplinary strengths in several key areas, we actively promote interdisciplinary research, especially linking natural and social sciences. We have a particular interest in research that helps inform policy, with Scottish and UK Government rural affairs and environment departments and the EU as key research clients.

GenBank

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GenBank® is a comprehensive database that contains publicly available nucleotide sequences for almost 260 000 formally described species. These sequences are obtained primarily through submissions from individual laboratories and batch submissions from large-scale sequencing projects, including whole-genome shotgun (WGS) and environmental sampling projects. Most submissions are made using the web-based BankIt or standalone Sequin programs, and GenBank staff assigns accession numbers upon data receipt. Daily data exchange with the European Nucleotide Archive (ENA) and the DNA Data Bank of Japan (DDBJ) ensures worldwide coverage. GenBank is accessible through the NCBI Entrez retrieval system, which integrates data from the major DNA and protein sequence databases along with taxonomy, genome, mapping, protein structure and domain information, and the biomedical journal literature via PubMed. BLAST provides sequence similarity searches of GenBank and other sequence databases. Complete bimonthly releases and daily updates of the GenBank database are available by FTP.

Berkeley Drosophila Genome Project insitu

BDGP insitu homepage

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In early 2010 we updated the site to facilitate more rapid transfer of our data to the public database and focus our efforts on the core mission of providing expression pattern images to the research community. The original database https://www.fruitfly.org/index.html reproduced functions available on FlyBase, complicating our updates by the requirement to re-synchronize with FlyBase updates. Our expression reports on the new site still link to FlyBase gene reports, but we no longer reproduce FlyBase functions and therefore can update expression data on an ongoing basis instead of more infrequent major releases. All the functions relating to the expression patterns remain and we soon will add an option to search expression patterns by image similarity, in addition to annotation term searches. In a transitional phase we will leave both the old and the new sites up, but the newer data (post Release 2) will appear only on the new website. We welcome any feedback or requests for additional features. - The goals of the Drosophila Genome Center are to finish the sequence of the euchromatic genome of Drosophila melanogaster to high quality and to generate and maintain biological annotations of this sequence. In addition to genomic sequencing, the BDGP is 1) producing gene disruptions using P element-mediated mutagenesis on a scale unprecedented in metazoans; 2) characterizing the sequence and expression of cDNAs; and 3) developing informatics tools that support the experimental process, identify features of DNA sequence, and allow us to present up-to-date information about the annotated sequence to the research community.

The Microbial Protein Interaction Database

MPIDB

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>>>!!!<<< as stated 2017-06-09 MPIDB is no longer available under URL http://www.jcvi.org/mpidb/about.php >>>!!!<<< The microbial protein interaction database (MPIDB) aims to collect and provide all known physical microbial interactions. Currently, 24,295 experimentally determined interactions among proteins of 250 bacterial species/strains can be browsed and downloaded. These microbial interactions have been manually curated from the literature or imported from other databases (IntAct, DIP, BIND, MINT) and are linked to 26,578 experimental evidences (PubMed ID, PSI-MI methods). In contrast to these databases, interactions in MPIDB are further supported by 68,346 additional evidences based on interaction conservation, protein complex membership, and 3D domain contacts (iPfam, 3did). We do not include (spoke/matrix) binary interactions infered from pull-down experiments.

RCSB Protein Data Bank

RCSB PDB

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The Protein Data Bank (PDB) archive is the single worldwide repository of information about the 3D structures of large biological molecules, including proteins and nucleic acids. These are the molecules of life that are found in all organisms including bacteria, yeast, plants, flies, other animals, and humans. Understanding the shape of a molecule helps to understand how it works. This knowledge can be used to help deduce a structure's role in human health and disease, and in drug development. The structures in the archive range from tiny proteins and bits of DNA to complex molecular machines like the ribosome.