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Found 548 result(s)

AlphaFold

AlphaFold Protein Structure Database

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AlphaFold DB provides open access to protein structure predictions for the human proteome and 20 other key organisms to accelerate scientific research.

Bacterial and Viral Bioinformatics Resource Center

BV-BRC

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The Bacterial and Viral Bioinformatics Resource Center (BV-BRC) is an information system designed to support research on bacterial and viral infectious diseases. BV-BRC combines two long-running BRCs: PATRIC, the bacterial system, and IRD/ViPR, the viral systems.

Mouse Models of Human Cancer database

MMHCdb

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The Mouse Tumor Biology (MTB) Database supports the use of the mouse as a model system of hereditary cancer by providing electronic access to: Information on endogenous spontaneous and induced tumors in mice, including tumor frequency & latency data, Information on genetically defined mice (inbred, hybrid, mutant, and genetically engineered strains of mice) in which tumors arise, Information on genetic factors associated with tumor susceptibility in mice and somatic genetic-mutations observed in the tumors, Tumor pathology reports and images, References, supporting MTB data and Links to other online resources for cancer.

Wellcome Trust Sanger Institute, Scientific resources

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The Wellcome Trust Sanger Institute is a charitably funded genomic research centre located in Hinxton, nine miles south of Cambridge in the UK. We study diseases that have an impact on health globally by investigating genomes. Building on our past achievements and based on priorities that exploit the unique expertise of our Faculty of researchers, we will lead global efforts to understand the biology of genomes. We are convinced of the importance of making this research available and accessible for all audiences. reduce global health burdens.

National Biodiversity Information System of Mexico

Sistema Nacional de Información sobre Biodiversidad de México

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The National Biodiversity Information System (SNIB) of Mexico by the National Commission for the Knowledge and Use of Biodiversity (CONABIO). The SNIB is of strategic importance in a megadiversity country like Mexico, making it clear to CONABIO from the beginning that the SNIB should rely on the work of the multiplicity of institutions and national and foreign experts that for years have been dedicated to the study of biodiversity of Mexico. The creation of this system was expressed as a mandate for CONABIO in the General Law of Ecological Balance and Environmental Protection (LGEEPA Art. 80 fraction V). The participation of specialists in the generation of data and information for the SNIB is one of the various ways in which they collaborate with this system, since having an information system that allows the country to make informed decisions regarding its biodiversity requires that it be made up of data and information supported by a broad network of experts.

Oral Cancer Gene Database

OrCGDB

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Oral Cancer Gene Database is an initiative of the Advanced Centre for Treatment, Research and Education in Cancer, Navi Mumbai. The present database, version II, consists of 374 genes. It is developed as a user friendly site that would provide the scientist, information and external links from one place. The database is accessed through a list of all genes, and Keyword Search using gene name or gene symbol, chromosomal location, CGH (in %), and molecular weight. Interaction Network shows the interaction between genes for particular biological processes and molecular functions.

The Cell Image Library

The Cell

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This library is a public and easily accessible resource database of images, videos, and animations of cells, capturing a wide diversity of organisms, cell types, and cellular processes. The Cell Image Library has been merged with "Cell Centered Database" in 2017. The purpose of the database is to advance research on cellular activity, with the ultimate goal of improving human health.

BIGG Database

Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions

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BiGG is a knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions. BiGG integrates several published genome-scale metabolic networks into one resource with standard nomenclature which allows components to be compared across different organisms. BiGG can be used to browse model content, visualize metabolic pathway maps, and export SBML files of the models for further analysis by external software packages. Users may follow links from BiGG to several external databases to obtain additional information on genes, proteins, reactions, metabolites and citations of interest.

GiardiaDB

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Giardia lamblia is a significant, environmentally transmitted, human pathogen and an amitochondriate protist. It is a major contributor to the enormous worldwide burden of human diarrheal diseases, yet the basic biology of this parasite is not well understood. No virulence factor has been identified. The Giardia lamblia genome contains only 12 million base pairs distributed onto five chromosomes. Its analysis promises to provide insights about the origins of nuclear genome organization, the metabolic pathways used by parasitic protists, and the cellular biology of host interaction and avoidance of host immune systems. Since the divergence of Giardia lamblia lies close to the transition between eukaryotes and prokaryotes in universal ribosomal RNA phylogenies, it is a valuable, if not unique, model for gaining basic insights into genetic innovations that led to formation of eukaryotic cells. In evolutionary terms, the divergence of this organism is at least twice as ancient as the common ancestor for yeast and man. A detailed study of its genome will provide insights into an early evolutionary stage of eukaryotic chromosome organization as well as other aspects of the prokaryotic / eukaryotic divergence.

MozAtlas

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MozAtlas provides gene expression data of adult male and female mosquitoes as tables, expressions, trees and models. MozAtlas also provides sequence orthology relationships with data provided by FlyBase, Vectorbase, Beetlebase, BeeBase, and WormBase.

RODARE

Rossendorf Data Repository

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Rodare is the institutional research data repository at HZDR (Helmholtz-Zentrum Dresden-Rossendorf). Rodare allows HZDR researchers to upload their research software and data and enrich those with metadata to make them findable, accessible, interoperable and retrievable (FAIR). By publishing all associated research software and data via Rodare research reproducibility can be improved. Uploads receive a Digital Object Identfier (DOI) and can be harvested via a OAI-PMH interface.

Edmond

The Open Research Data Repository of the Max Planck Society

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Edmond is the institutional repository of the Max Planck Society for public research data. It enables Max Planck scientists to create citable scientific assets by describing, enriching, sharing, exposing, linking, publishing and archiving research data of all kinds. Further on, all objects within Edmond have a unique identifier and therefore can be clearly referenced in publications or reused in other contexts.

GeneCards

The Human Gene Database

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GeneCards is a searchable, integrative database that provides comprehensive, user-friendly information on all annotated and predicted human genes. It automatically integrates gene-centric data from ~125 web sources, including genomic, transcriptomic, proteomic, genetic, clinical and functional information.

mentha

the interactome browser

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mentha archives evidence collected from different sources and presents these data in a complete and comprehensive way. Its data comes from manually curated protein-protein interaction databases that have adhered to the IMEx consortium. The aggregated data forms an interactome which includes many organisms. mentha is a resource that offers a series of tools to analyse selected proteins in the context of a network of interactions. Protein interaction databases archive protein-protein interaction (PPI) information from published articles. However, no database alone has sufficient literature coverage to offer a complete resource to investigate "the interactome". mentha's approach generates every week a consistent interactome (graph). Most importantly, the procedure assigns to each interaction a reliability score that takes into account all the supporting evidence. mentha offers eight interactomes (Homo sapiens, Arabidopsis thaliana, Caenorhabditis elegans, Drosophila melanogaster, Escherichia coli K12, Mus musculus, Rattus norvegicus, Saccharomyces cerevisiae) plus a global network that comprises every organism, including those not mentioned. The website and the graphical application are designed to make the data stored in mentha accessible and analysable to all users. Source databases are: MINT, IntAct, DIP, MatrixDB and BioGRID.

GENCODE

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GENCODE is a scientific project in genome research and part of the ENCODE (ENCyclopedia Of DNA Elements) scale-up project. The GENCODE consortium was initially formed as part of the pilot phase of the ENCODE project to identify and map all protein-coding genes within the ENCODE regions (approx. 1% of Human genome). Given the initial success of the project, GENCODE now aims to build an “Encyclopedia of genes and genes variants” by identifying all gene features in the human and mouse genome using a combination of computational analysis, manual annotation, and experimental validation, and annotating all evidence-based gene features in the entire human genome at a high accuracy.

WormBase

facilitating insights into nematode biology

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Launched in 2000, WormBase is an international consortium of biologists and computer scientists dedicated to providing the research community with accurate, current, accessible information concerning the genetics, genomics and biology of C. elegans and some related nematodes. In addition to their curation work, all sites have ongoing programs in bioinformatics research to develop the next generations of WormBase structure, content and accessibility

Candida Genome Database

CGD

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Candida Genome Database, a resource for genomic sequence data and gene and protein information for Candida albicans and related species. CGD is based on the Saccharomyces Genome Database. The Candida Genome Database (CGD) provides online access to genomic sequence data and manually curated functional information about genes and proteins of the human pathogen Candida albicans and related species. C. albicans is the best studied of the human fungal pathogens. It is a common commensal organism of healthy individuals, but can cause debilitating mucosal infections and life-threatening systemic infections, especially in immunocompromised patients. C. albicans also serves as a model organism for the study of other fungal pathogens.

Genomes OnLine Database

GOLD

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GOLD is currently the largest repository for genome project information world-wide. The accurate and efficient genome project tracking is a vital criterion for launching new genome sequencing projects, and for avoiding significant overlap between various sequencing efforts and centers.

cisRED

Databases of genome-wide regulatory module and element predictions

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

Mammalian Transcriptomic Database

MTD

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MTD is focused on mammalian transcriptomes with a current version that contains data from humans, mice, rats and pigs. Regarding the core features, the MTD browses genes based on their neighboring genomic coordinates or joint KEGG pathway and provides expression information on exons, transcripts, and genes by integrating them into a genome browser. We developed a novel nomenclature for each transcript that considers its genomic position and transcriptional features.

MorphoSource

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MorphoSource is a data repository specialized for 3D representing physical objects used in research in education (e.g., from museum or laboratory collections). It allows researchers and museum collection staff to store and organize, share, and distribute their own 3d data. Furthermore any registered user can immediately search for and download 3d morphological data sets that have been made accessible through the consent of data authors.

ErythronDB

Erythron Database

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<<<!!!<<< The original ErythronDB site is now retired! Code for generating the web site is available here https://github.com/ErythronDB/erythrondb-docker. >>>!!!>>>

Cornell Activity Datasets: CAD-60 & CAD-120

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

Genome Sequence Archive

GSA

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GSA is a data repository specialized for archiving raw sequence reads. It supports data generated from a variety of sequencing platforms ranging from Sanger sequencing machines to single-cell sequencing machines and provides data storing and sharing services free of charge for worldwide scientific communities. In addition to raw sequencing data, GSA also accommodates secondary analyzed files in acceptable formats (like BAM, VCF). Its user-friendly web interfaces simplify data entry and submitted data are roughly organized as two parts, viz., Metadata and File, where the former can be further assorted into BioProject, BioSample, Experiment and Run, and the latter contains raw sequence reads.

RADAM database portal

RADiation DAMage database

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RADAM portal is an interface to the network of RADAM (RADiation DAMage) Databases collecting data on interactions of ions, electrons, positrons and photons with biomolecular systems, on radiobiological effects and relevant phenomena occurring at different time, spatial and energy scales in irradiated targets during and after the irradiation. This networking system has been created by the Consortium of COST Action MP1002 (Nano-IBCT: Nano-scale insights into Ion Beam Cancer Therapy) during 2011-2014 using the Virtual Atomic and Molecular Data Center (VAMDC) standards.