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Found 60 result(s)

ExPASy Bioinformatics Resource Portal

SIB Bioinformatics Resource Portal

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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

SilkPathDB

Silkworm Pathogen Database

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Silkworm Pathogen Database (SilkPathDB) is a comprehensive resource for studying on pathogens of silkworm, including microsporidia, fungi, bacteria and virus. SilkPathDB provides access to not only genomic data including functional annotation of genes and gene products, but also extensive biological information for gene expression data and corresponding researches. SilkPathDB will be help with researches on pathogens of silkworm as well as other Lepidoptera insects.

Protist EST Program Database

PEP Database

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<<<!!!<<< The PEP database (TBestDB)--Defunct as of 2017-04 >>>!!!>>> https://megasun.bch.umontreal.ca/pepdb/pepdb.html

Kikapu

University of the Western Cape Institutional Research Data Respository

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The University of the Western Cape (UWC) uses Figshare for Institutions for their institutional research data repository. It is called Kikapu, and serves as a repository for storing and disseminating research data.

NCAA Student-Athlete Experiences Data Archive

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<<<!!!<<< This website will no longer be supported after September 30, 2020. Study data and documentation that you access from this website will continue to be available through ICPSR https://web.archive.org/web/20200813092858/https://www.icpsr.umich.edu/. >>>!!!>>>

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.

Vivli

A global clinical research data sharing platform

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Vivli is a non-profit organization working to advance human health through the insights and discoveries gained by sharing and analyzing data. It is home to an independent global data-sharing and analytics platform which serves all elements of the international research community. The platform includes a data repository, in-depth search engine and cloud-based analytics, and harmonizes governance, policy and processes to make sharing data easier. Vivli acts as a neutral broker between data contributor and data user and the wider data sharing community.

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.

International Mouse Strain Resource

IMSR

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The IMSR is a searchable online database of mouse strains, stocks, and mutant ES cell lines available worldwide, including inbred, mutant, and genetically engineered strains. The goal of the IMSR is to assist the international scientific community in locating and obtaining mouse resources for research. Note that the data content found in the IMSR is as supplied by strain repository holders. For each strain or cell line listed in the IMSR, users can obtain information about: Where that resource is available (Repository Site); What state(s) the resource is available as (e.g. live, cryopreserved embryo or germplasm, ES cells); Links to descriptive information about a strain or ES cell line; Links to mutant alleles carried by a strain or ES cell line; Links for ordering a strain or ES cell line from a Repository; Links for contacting the Repository to send a query

Reactome

a curated pathway database

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Reactome is a manually curated, peer-reviewed pathway database, annotated by expert biologists and cross-referenced to bioinformatics databases. Its aim is to share information in the visual representations of biological pathways in a computationally accessible format. Pathway annotations are authored by expert biologists, in collaboration with Reactome editorial staff and cross-referenced to many bioinformatics databases. These include NCBI Gene, Ensembl and UniProt databases, the UCSC and HapMap Genome Browsers, the KEGG Compound and ChEBI small molecule databases, PubMed, and Gene Ontology.

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.

datastore by Universität Münster

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datastore is the cross-domain research data repository of the University Münster (Germany). In datastore, scientific members of the University Münster can publish their research data following the FAIR principles, including the assignment of a DOI for each dataset as a persistent identifier.

Mouse Genome Informatics

MGI

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MGI is the international database resource for the laboratory mouse, providing integrated genetic, genomic, and biological data to facilitate the study of human health and disease. The projects contributing to this resource are: Mouse Genome Database (MGD) Project, Gene Expression Database (GXD) Project, Mouse Tumor Biology (MTB) Database Project, Gene Ontology (GO) Project at MGI, MouseMine Project, MouseCyc Project at MGI

Viral Bioinformatics Resource Center

VBRC

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Databases of viral genomic information (genes, gene families, and genomes), and software to perform comparative genomics analyses

DataverseNO

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DataverseNO (https://dataverse.no) is a curated, FAIR-aligned national generic repository for open research data from all academic disciplines. DataverseNO commits to facilitate that published data remain accessible and (re)usable in a long-term perspective. The repository is owned and operated by UiT The Arctic University of Norway. DataverseNO accepts submissions from researchers primarily from Norwegian research institutions. Datasets in DataverseNO are grouped into institutional collections as well as special collections. The technical infrastructure of the repository is based on the open source application Dataverse (https://dataverse.org), which is developed by an international developer and user community led by Harvard University.

TriTrypDB

kinetoplastid genomics resource

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TriTrypDB is an integrated genomic and functional genomic database for pathogens of the family Trypanosomatidae, including organisms in both Leishmania and Trypanosoma genera. TriTrypDB and its continued development are possible through the collaborative efforts between EuPathDB, GeneDB and colleagues at the Seattle Biomedical Research Institute (SBRI).

Chesapeake Bay Data Hub

Chesapeake Bay Program

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This interface provides access to several types of data related to the Chesapeake Bay. Bay Program databases can be queried based upon user-defined inputs such as geographic region and date range. Each query results in a downloadable, tab- or comma-delimited text file that can be imported to any program (e.g., SAS, Excel, Access) for further analysis. Comments regarding the interface are encouraged. Questions in reference to the data should be addressed to the contact provided on subsequent pages.

cisRED

Databases of genome-wide regulatory module and element predictions

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<<<!!!<<< This repository is no longer available. >>>!!!>>>

University of Manchester figshare

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The University selected figshare as a general purpose research data repository to enable researchers to share research data, facilitate open research practices and meet the evolving requirements of research funders and academic publishers. This is a public-facing platform for researchers to share their data and build, over time, a comprehensive representation of the research done at the University across all faculties and disciplines.

MG-RAST

Metagenomics analysis server

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The MG-RAST server is an open source system for annotation and comparative analysis of metagenomes. Users can upload raw sequence data in fasta format; the sequences will be normalized and processed and summaries automatically generated. The server provides several methods to access the different data types, including phylogenetic and metabolic reconstructions, and the ability to compare the metabolism and annotations of one or more metagenomes and genomes. In addition, the server offers a comprehensive search capability. Access to the data is password protected, and all data generated by the automated pipeline is available for download in a variety of common formats. MG-RAST has become an unofficial repository for metagenomic data, providing a means to make your data public so that it is available for download and viewing of the analysis without registration, as well as a static link that you can use in publications. It also requires that you include experimental metadata about your sample when it is made public to increase the usefulness to the community.

NCBI Genome

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<<<!!!<<< Effective May 2024, NCBI's Genome resource will no longer be available. NCBI Genome data can now be found on the NCBI Datasets taxonomy pages. https://www.re3data.org/repository/r3d100014298 >>>!!!>>> The Genome database contains annotations and analysis of eukaryotic and prokaryotic genomes, as well as tools that allow users to compare genomes and gene sequences from humans, microbes, plants, viruses and organelles. Users can browse by organism, and view genome maps and protein clusters.

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.

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.

SILVA

A comprehensive on-line resource for quality checked and aligned ribosomal RNA sequence data.

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SILVA is a comprehensive, quality-controlled web resource for up-to-date aligned ribosomal RNA (rRNA) gene sequences from the Bacteria, Archaea and Eukaryota domains alongside supplementary online services. In addition to data products, SILVA provides various online tools such as alignment and classification, phylogenetic tree calculation and viewer, probe/primer matching, and an amplicon analysis pipeline. With every full release a curated guide tree is provided that contains the latest taxonomy and nomenclature based on multiple references. SILVA is an ELIXIR Core Data Resource.

Academic Torrents

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Academic Torrents is a distributed data repository. The academic torrents network is built for researchers, by researchers. Its distributed peer-to-peer library system automatically replicates your datasets on many servers, so you don't have to worry about managing your own servers or file availability. Everyone who has data becomes a mirror for those data so the system is fault-tolerant.