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Found 30 result(s)

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

Project Data Sphere

PDS

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Project Data Sphere, LLC, operates a free digital library-laboratory where the research community can broadly share, integrate and analyze historical, de-identified, patient-level data from academic and industry cancer Phase II-III clinical trials. These patient-level datasets are available through the Project Data Sphere platform to researchers affiliated with life science companies, hospitals and institutions, as well as independent researchers, at no cost and without requiring a research proposal.

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.

CARMEN

Code analysis, repository & modelling for e-neuroscience

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

International Mouse Phenotyping Consortium

IMPC

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The IMPC is a confederation of international mouse phenotyping projects working towards the agreed goals of the consortium: To undertake the phenotyping of 20,000 mouse mutants over a ten year period, providing the first functional annotation of a mammalian genome. Maintain and expand a world-wide consortium of institutions with capacity and expertise to produce germ line transmission of targeted knockout mutations in embryonic stem cells for 20,000 known and predicted mouse genes. Test each mutant mouse line through a broad based primary phenotyping pipeline in all the major adult organ systems and most areas of major human disease. Through this activity and employing data annotation tools, systematically aim to discover and ascribe biological function to each gene, driving new ideas and underpinning future research into biological systems; Maintain and expand collaborative “networks” with specialist phenotyping consortia or laboratories, providing standardized secondary level phenotyping that enriches the primary dataset, and end-user, project specific tertiary level phenotyping that adds value to the mammalian gene functional annotation and fosters hypothesis driven research; and Provide a centralized data centre and portal for free, unrestricted access to primary and secondary data by the scientific community, promoting sharing of data, genotype-phenotype annotation, standard operating protocols, and the development of open source data analysis tools. Members of the IMPC may include research centers, funding organizations and corporations.

Brain-CODE

Brain-Centre for Ontario Data Exploration

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Brain-CODE is a large-scale informatics platform that manages the acquisition and storage of multidimensional data collected from participants with a variety of brain disorders.

Cardiovascular Research Grid

CVRG

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The CardioVascular Research Grid (CVRG) project is creating an infrastructure for secure seamless access to study data and analysis tools. CVRG tools are developed using the Software as a Service model, allowing users to access tools through their browser, thus eliminating the need to install and maintain complex software.

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.

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.

MiCroKitS

formerly: MiCroKit

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During cell cycle, numerous proteins temporally and spatially localized in distinct sub-cellular regions including centrosome (spindle pole in budding yeast), kinetochore/centromere, cleavage furrow/midbody (related or homolog structures in plants and budding yeast called as phragmoplast and bud neck, respectively), telomere and spindle spatially and temporally. These sub-cellular regions play important roles in various biological processes. In this work, we have collected all proteins identified to be localized on kinetochore, centrosome, midbody, telomere and spindle from two fungi (S. cerevisiae and S. pombe) and five animals, including C. elegans, D. melanogaster, X. laevis, M. musculus and H. sapiens based on the rationale of "Seeing is believing" (Bloom K et al., 2005). Through ortholog searches, the proteins potentially localized at these sub-cellular regions were detected in 144 eukaryotes. Then the integrated and searchable database MiCroKiTS - Midbody, Centrosome, Kinetochore, Telomere and Spindle has been established.

Spatial Data Repository

The DHS Program

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The Spatial Data Repository provides geographically-linked health and demographic data from the MEASURE Demographic and Health Surveys (DHS) project and the U.S. Census Bureau for mapping in a geographic information system (GIS).

The whole brain Atlas

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This is an information resource for central nervous system imaging which integrates clinical information with magnetic resonance (MR), x-ray computed tomography (CT), and nuclear medicine images.

Follicular Lymphoma Genome Data at Canada's Michael Smith Genome Sciences Centre (BCGSC)

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<<<!!!<<< Genome data generated by BC Genome Sciences Centre is no longer available through this site as it is regularly deposited into controlled data repositories such as the European Genome Phenome Archive (EGA); ICGC (International Cancer Genome Consortium) and the Genome Data Commons (GDC) >>>!!!>>> Mapping, copy number analysis, sequence and gene expression data generated by the High Resolution Analysis of Follicular Lymphoma Genomes project. The data will be available for 24 patients with follicular lymphoma. All data will be made as widely and freely available as possible while safeguarding the privacy of participants, and protecting confidential and proprietary data.The data from this project will be submitted to public genomic data sources. These sources will be listed on this web site as the data becomes available in these external data sources.

Mouse Atlas of Gene Expression

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

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

Clinical Proteomic Tumor Analysis Consortium Data Portal

CPTAC Data Portal

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The CPTAC Data Portal is the centralized repository for the dissemination of proteomic data collected by the Proteome Characterization Centers (PCCs) for the CPTAC program. The portal also hosts analyses of the mass spectrometry data (mapping of spectra to peptide sequences and protein identification) from the PCCs and from a CPTAC-sponsored common data analysis pipeline (CDAP).

Cancer Cell Line Encyclopedia

CCLE

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The Cancer Cell Line Encyclopedia project is a collaboration between the Broad Institute, and the Novartis Institutes for Biomedical Research and its Genomics Institute of the Novartis Research Foundation to conduct a detailed genetic and pharmacologic characterization of a large panel of human cancer models, to develop integrated computational analyses that link distinct pharmacologic vulnerabilities to genomic patterns and to translate cell line integrative genomics into cancer patient stratification. The CCLE provides public access to genomic data, analysis and visualization for about 1000 cell lines.

DATA.GOV.UK

Opening up Government

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The Government is releasing public data to help people understand how government works and how policies are made. Some of this data is already available, but data.gov.uk brings it together in one searchable website. Making this data easily available means it will be easier for people to make decisions and suggestions about government policies based on detailed information.

ComBase

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ComBase is a resource for quantitative and predictive food microbiology. ComBase includes a database of observed microbial responses to a variety of food-related environments and a collection of predictive models.

VecNet

Vector-Borne Disease Network

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<<<!!!<<< The repository is no longer available. 2019-09-06: no more access to VecNet >>>!!!>>>

The Global Proteome Machine

GPM

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The Global Proteome Machine (GPM) is a protein identification database. This data repository allows users to post and compare results. GPM's data is provided by contributors like The Informatics Factory, University of Michigan, and Pacific Northwestern National Laboratories. The GPM searchable databases are: GPMDB, pSYT, SNAP, MRM, PEPTIDE and HOT.

Motion Capture Database HDM05

Mocap database HDM05

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It is the objective of our motion capture database HDM05 to supply free motion capture data for research purposes. HDM05 contains more than three hours of systematically recorded and well-documented motion capture data in the C3D as well as in the ASF/AMC data format. Furthermore, HDM05 contains for more than 70 motion classes in 10 to 50 realizations executed by various actors.

PATRIC

Pathosystems Resource Integration Center

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<<<!!!<<< This repository is no longer available. >>>!!!>>> PATRIC will go offline by mid-December2022. Here is what you need to know. As announced previously, PATRIC, the bacterial BRC, and IRD / ViPR, the viral BRCs, are being merged into the new Bacterial and Viral Bioinformatics Resource Center (BV-BRC). BV-BRC combines the data, tools, and technologies from these BRCs to provide an integrated resource for bacterial and viral genomics-based infectious disease research.

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.