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Found 134 result(s)
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>>>!!!<<< The repository is inactive, please use SciLifeLab Data Repository >>>!!!<<< This DOI repository provides permanent identifiers to data sets generated by Life Science researchers active in Sweden, and for which no other suitable public repository is available. BILS is a distributed national research infrastructure supported by the Swedish Research Council (Vetenskapsrådet) providing bioinformatics support to life science researchers in Sweden.
Swiss Institute of Bioinformatics (SIB) coordinates research and education in bioinformatics throughout Switzerland and provides bioinformatics services to the national and international research community. ExPASy gives access to numerous repositories and databases of SIB. For example: array map, MetaNetX, SWISS-MODEL and World-2DPAGE, and many others see a list here http://www.expasy.org/resources
Pathogen Portal is a repository linking to the Bioinformatics Resource Centers (BRCs) sponsored by the National Institute of Allergy and Infectious Diseases (NIAID) and maintained by The Virginia Bioinformatics Institute. The BRCs are providing web-based resources to scientific community conducting basic and applied research on organisms considered potential agents of biowarfare or bioterrorism or causing emerging or re-emerging diseases. The Pathogen Portal supports and links to five Bioinformatics Resource Centers (BRCs). Each BRC specializes in a different group of pathogens, focusing on, but not limited to, pathogens causing (Re-)Emerging Infectious Diseases, and those in the NIAID Category A-C Priority Pathogen lists for biodefense research. The scope of the BRCs also includes Invertebrate Vectors of Human Disease. Pathogen Portal covers EuPathDB, IRD, PATRIC, VectorBase and ViPR.
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CORUM is a manually curated dataset of mammalian protein complexes. Annotation of protein complexes includes protein complex composition and other valuable information such as method of purification, cellular function of complexes or involvement in diseases.
Human Protein Reference Database (HPRD) has been established by a team of biologists, bioinformaticists and software engineers. This is a joint project between the PandeyLab at Johns Hopkins University, and Institute of Bioinformatics, Bangalore. HPRD is a definitive repository of human proteins. This database should serve as a ready reckoner for researchers in their quest for drug discovery, identification of disease markers and promote biomedical research in general. Human Proteinpedia (www.humanproteinpedia.org) is its associated data portal.
CryptoDB is an integrated genomic and functional genomic database for the parasite Cryptosporidium and other related genera. CryptoDB integrates whole genome sequence and annotation along with experimental data and environmental isolate sequences provided by community researchers. The database includes supplemental bioinformatics analyses and a web interface for data-mining.
AmoebaDB belongs to the EuPathDB family of databases and is an integrated genomic and functional genomic database for Entamoeba and Acanthamoeba parasites. In its first iteration (released in early 2010), AmoebaDB contains the genomes of three Entamoeba species (see below). AmoebaDB integrates whole genome sequence and annotation and will rapidly expand to include experimental data and environmental isolate sequences provided by community researchers . The database includes supplemental bioinformatics analyses and a web interface for data-mining.
The RESID Database of Protein Modifications is a comprehensive collection of annotations and structures for protein modifications including amino-terminal, carboxyl-terminal and peptide chain cross-link post-translational modifications.
The European Bioinformatics Institute (EBI) has a long-standing mission to collect, organise and make available databases for biomolecular science. It makes available a collection of databases along with tools to search, download and analyse their content. These databases include DNA and protein sequences and structures, genome annotation, gene expression information, molecular interactions and pathways. Connected to these are linking and descriptive data resources such as protein motifs, ontologies and many others. In many of these efforts, the EBI is a European node in global data-sharing agreements involving, for example, the USA and Japan.
ALSoD is a freely available database that has been transformed from a single gene storage facility recording mutations in the SOD1 gene to a multigene ALS bioinformatics repository and analytical instrument combining genotype, phenotype, and geographical information with associated analysis tools. These include a comparison tool to evaluate genes side by side or jointly with user configurable features, a pathogenicity prediction tool using a combination of computational approaches to distinguish variants with nonfunctional characteristics from disease-associated mutations with more dangerous consequences, and a credibility tool to enable ALS researchers to objectively assess the evidence for gene causation in ALS. Furthermore, integration of external tools, systems for feedback, annotation by users, and two-way links to collaborators hosting complementary databases further enhance the functionality of ALSoD.
PSnpBind is a large database of protein–ligand complexes covering a wide range of binding pocket mutations and small molecules’ landscape. This database can be used as a source of data for different types of studies, for example, developing machine learning algorithms to predict protein–ligand affinity or mutation's effect on it which requires an extensive amount of data with a wide coverage of mutation types and small molecules. Also, studies of protein-ligand interactions and conformer orientation changes across different mutated versions of a protein can be established using data from PSnpBind.
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VirHostNet is a bioinformatic information system dedidacted to the biocuration, data integration, reproducible systems-level analysis and visualisation of Virus / Host protein-protein interactions Network based on graph theory. VirHostNet is an open and gold standard knowledgebase shared in PSI MITAB 2.5 format using the PSICQUIC webservice and distributed through the NDEx platform. VirHostNet is FAIR and is recognized as a COVID-19 ressource by Elixir bio.tools, the European Virus Bioinformatics Center and FAIRsharing.org.
Established by the HLA Informatics Group of the Anthony Nolan Research Institute, IPD provides a centralized system for studying the immune system's polymorphism in genes. The IPD maintains databases concerning the sequences of human Killer-cell Immunoglobulin-like Receptors (KIR), sequences of the major histocompatibility complex in a number of species, human platelet antigens (HPA), and tumor cell lines. Each subject has related, credible news, current research and publications, and a searchable database for highly specific, research grade genetic information.
The Cancer Immunome Database (TCIA) provides results of comprehensive immunogenomic analyses of next generation sequencing data (NGS) data for 20 solid cancers from The Cancer Genome Atlas (TCGA) and other datasource. The Cancer Immunome Atlas (TCIA) was developed and is maintained at the Division of Bioinformatics (ICBI). The database can be queried for the gene expression of specific immune-related gene sets, cellular composition of immune infiltrates (characterized using gene set enrichment analyses and deconvolution), neoantigens and cancer-germline antigens, HLA types, and tumor heterogeneity (estimated from cancer cell fractions). Moreover it provides survival analyses for different types immunological parameters. TCIA will be constantly updated with new data and results.
EuPathDB (formerly ApiDB) is an integrated database covering the eukaryotic pathogens in the genera Acanthamoeba, Annacaliia, Babesia, Crithidia, Cryptosporidium, Edhazardia, Eimeria, Encephalitozoon, Endotrypanum, Entamoeba, Enterocytozoon, Giardia, Gregarina, Hamiltosporidium, Leishmania, Nematocida, Neospora, Nosema, Plasmodium, Theileria, Toxoplasma, Trichomonas, Trypanosoma and Vavraia, Vittaforma). While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all of these resources, and the opportunity to leverage orthology for searches across genera.
NetSlim is a resource of high-confidence signaling pathway maps derived from NetPath pathway reactions. 40-60% of the molecules and their reactions in NetPath pathways are available in NetSlim.
ViralZone is a SIB Swiss Institute of Bioinformatics web-resource for all viral genus and families, providing general molecular and epidemiological information, along with virion and genome figures. Each virus or family page gives an easy access to UniProtKB/Swiss-Prot viral protein entries.
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.
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bio.tools is a software registry for bioinformatics and the life sciences.
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DEG hosts records of currently available essential genomic elements, such as protein-coding genes and non-coding RNAs, among bacteria, archaea and eukaryotes. Essential genes in a bacterium constitute a minimal genome, forming a set of functional modules, which play key roles in the emerging field, synthetic biology.