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Found 20 result(s)

GESDB

Genetic Epidemiology Simulation Database

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

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.

Ensembl Metazoa

e!EnsemblMetazoa

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

GISAID

GISAID EpiFlu database

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The GISAID Initiative promotes the international sharing of all influenza virus sequences, related clinical and epidemiological data associated with human viruses, and geographical as well as species-specific data associated with avian and other animal viruses, to help researchers understand how the viruses evolve, spread and potentially become pandemics. *** GISAID does so by overcoming disincentives/hurdles or restrictions, which discourage or prevented sharing of influenza data prior to formal publication. *** The Initiative ensures that open access to data in GISAID is provided free-of-charge and to everyone, provided individuals identify themselves and agree to uphold the GISAID sharing mechanism governed through its Database Access Agreement. GISAID calls on all users to agree to the basic premise of upholding scientific etiquette, by acknowledging the originating laboratories providing the specimen and the submitting laboratories who generate the sequence data, ensuring fair exploitation of results derived from the data, and that all users agree that no restrictions shall be attached to data submitted to GISAID, to promote collaboration among researchers on the basis of open sharing of data and respect for all rights and interests.

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.

VIPERdb

Virus Particle Explorer database

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VIPERdb is a database for icosahedral virus capsid structures . The emphasis of the resource is on providing data from structural and computational analyses on these systems, as well as high quality renderings for visual exploration. In addition, all virus capsids are placed in a single icosahedral orientation convention, facilitating comparison between different structures. The web site includes powerful search utilities , links to other relevant databases, background information on virus capsid structure, and useful database interface tools.

GeneWeaver.org

The Ontological Discovery Environment

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GeneWeaver combines cross-species data and gene entity integration, scalable hierarchical analysis of user data with a community-built and curated data archive of gene sets and gene networks, and tools for data driven comparison of user-defined biological, behavioral and disease concepts. Gene Weaver allows users to integrate gene sets across species, tissue and experimental platform. It differs from conventional gene set over-representation analysis tools in that it allows users to evaluate intersections among all combinations of a collection of gene sets, including, but not limited to annotations to controlled vocabularies. There are numerous applications of this approach. Sets can be stored, shared and compared privately, among user defined groups of investigators, and across all users.

Triticeae Toolbox

T3

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A database for plant breeders and researchers to combine, visualize, and interrogate the wealth of phenotype and genotype data generated by the Triticeae Coordinated Agricultural Project (TCAP).

IMGT/3Dstructure-DB and IMGT/2Dstructure-DB

International ImMunoGeneTics information system/3Dstructure-DB and IMGT/2Dstructure-DB

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IMGT/3Dstructure-DB is the IMGT three-dimensional (3D) structure database.

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.

Ensembl Protists

e!EnsemblProtists

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EnsemblProtists is a genome-centric portal for protists species.

HumanCyc

Encyclopedia of Human Genes and Metabolism

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HumanCyc provides an encyclopedic reference on human metabolic pathways. It provides a zoomable human metabolic map diagram, and it has been used to generate a steady-state quantitative model of human metabolism. 2016: Subscriptions are now required to access HumanCyc. For more information on obtaining a subscription, click here: http://www.phoenixbioinformatics.org/biocyc#product-biocyc-subscription

HAGR

Human Ageing Genomic Resources

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The Human Ageing Genomic Resources (HAGR) is a collection of databases and tools designed to help researchers study the genetics of human ageing using modern approaches such as functional genomics, network analyses, systems biology and evolutionary analyses.

ImmPort

Immunology Database and Analysis Portal

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The Immunology Database and Analysis Portal (ImmPort) archives clinical study and trial data generated by NIAID/DAIT-funded investigators. Data types housed in ImmPort include subject assessments i.e., medical history, concomitant medications and adverse events as well as mechanistic assay data such as flow cytometry, ELISA, ELISPOT, etc. --- You won't need an ImmPort account to search for compelling studies, peruse study demographics, interventions and mechanistic assays. But why stop there? What you really want to do is download the study, look at each experiment in detail including individual ELISA results and flow cytometry files. Perhaps you want to take those flow cytometry files for a test drive using FLOCK in the ImmPort flow cytometry module. To download all that interesting data you will need to register for ImmPort access.

EchoBase

an integrated post-genomic database for E.coli

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EchoBase is a database that curates new experimental and bioinformatic information about the genes and gene products of the model bacterium Escherichia coli K-12 strain MG1655.

Vega

Vertebrate Genome Annotation database

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A repository for high-quality gene models produced by the manual annotation of vertebrate genomes. The final update of Vega, version 68, was released in February 2017 and is now archived at vega.archive.ensembl.org. We plan to maintain this resource until Feb 2020.

Population Health Data Archive

PHDA

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The National Population Health Data Center (NPHDC) is one of the 20 national science data center approved by the Ministry of Science and Technology and the Ministry of Finance. The Population Health Data Archive (PHDA) is developed by NPHDC relying on the Institute of Medical Information, Chinese Academy of Medical Sciences. PHDA mainly receives scientific data from science and technology projects supported by the national budget, and also collects data from other multiple sources such as medical and health institutions, research institutions and social individuals, which is oriented to the national big data strategy and the healthy China strategy. The data resources cover basic medicine, clinical medicine, public health, traditional Chinese medicine and pharmacy, pharmacy, population and reproduction. PHDA supports data collection, archiving, processing, storage, curation, verification, certification and release in the field of population health. Provide multiple types of data sharing and application services for different hierarchy users and help them find, access, interoperate and reuse the data in a safe and controlled environment. PHDA provides important support for promoting the open sharing of scientific data of population health and domestic and foreign cooperation.

ALEXA

ALEXA-A

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ALEXA is a microarray design platform for 'alternative expression analysis'. This platform facilitates the design of expression arrays for analysis of mRNA isoforms generated from a single locus by the use of alternative transcription initiation, splicing and polyadenylation sites. We use the term 'ALEXA' to describe a collection of novel genomic methods for 'alternative expression' analysis. 'Alternative expression' refers to the identification and quantification of alternative mRNA transcripts produced by alternative transcript initiation, alternative splicing and alternative polyadenylation. This website provides supplementary materials, source code and other downloads for recent publications describing our studies of alternative expression (AE). Most recently we have developed a method, 'ALEXA-Seq' and associated resources for alternative expression analysis by massively parallel RNA sequencing.

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

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.