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Found 15 result(s)

Human Protein Reference Database

HPRD

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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.

Human Proteinpedia

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Human Proteinpedia is a community portal for sharing and integration of human protein data. This is a joint project between Pandey at Johns Hopkins University, and Institute of Bioinformatics, Bangalore. This portal allows research laboratories around the world to contribute and maintain protein annotations. Human Protein Reference Database (HPRD) integrates data, that is deposited in Human Proteinpedia along with the existing literature curated information in the context of an individual protein. All the public data contributed to Human Proteinpedia can be queried, viewed and downloaded. Data pertaining to post-translational modifications, protein interactions, tissue expression, expression in cell lines, subcellular localization and enzyme substrate relationships may be deposited.

EnvBase

EnvBase data catalogue

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<<<!!!<<<This is an archive of the old NEBC site from nebc.nerc.ac.uk and is no longer updated. For new information regarding NERC Environmental Omics and the Bio-Linux system please see the EOS site at http://environmentalomics.org. >>>!!!>>> Ongoing NEBC activities, including the development of Bio-Linux, are being moved into the new EOS programme http://environmentalomics.org/portfolio/big-data-infrastructure/ . Once the current material from this website has been moved into EOS, this NEBC site will remain on-line as an archive. EnvBase is the searchable index to the data deposited through the NEBC, as well as related NERC experimental data. At present this is chiefly from the grants funded by the NERC Environmental Genomics Science Programme and the subsequent Post-genomics and Proteomics Science Programme, but more data from ongoing projects continues to be added

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).

The European Genome-phenome Archive

EGA

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The European Genome-phenome Archive (EGA) is designed to be a repository for all types of sequence and genotype experiments, including case-control, population, and family studies. We will include SNP and CNV genotypes from array based methods and genotyping done with re-sequencing methods. The EGA will serve as a permanent archive that will archive several levels of data including the raw data (which could, for example, be re-analysed in the future by other algorithms) as well as the genotype calls provided by the submitters. We are developing data mining and access tools for the database. For controlled access data, the EGA will provide the necessary security required to control access, and maintain patient confidentiality, while providing access to those researchers and clinicians authorised to view the data. In all cases, data access decisions will be made by the appropriate data access-granting organisation (DAO) and not by the EGA. The DAO will normally be the same organisation that approved and monitored the initial study protocol or a designate of this approving organisation. The European Genome-phenome Archive (EGA) allows you to explore datasets from genomic studies, provided by a range of data providers. Access to datasets must be approved by the specified Data Access Committee (DAC).

OpenWorm

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OpenWorm aims to build the first comprehensive computational model of the Caenorhabditis elegans (C. elegans), a microscopic roundworm. With only a thousand cells, it solves basic problems such as feeding, mate-finding and predator avoidance. Despite being extremely well studied in biology, this organism still eludes a deep, principled understanding of its biology. We are using a bottom-up approach, aimed at observing the worm behaviour emerge from a simulation of data derived from scientific experiments carried out over the past decade. To do so we are incorporating the data available in the scientific community into software models. We are engineering Geppetto and Sibernetic, open-source simulation platforms, to be able to run these different models in concert. We are also forging new collaborations with universities and research institutes to collect data that fill in the gaps All the code we produce in the OpenWorm project is Open Source and available on GitHub.

KBase

KBase: The U.S. Department of Energy Systems Biology Knowledgebase

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The Department of Energy Systems Biology Knowledgebase (KBase) is a software and data platform designed to meet the grand challenge of systems biology: predicting and designing biological function. KBase integrates data and tools in a unified graphical interface so users do not need to access them from numerous sources or learn multiple systems in order to create and run sophisticated systems biology workflows. Users can perform large-scale analyses and combine multiple lines of evidence to model plant and microbial physiology and community dynamics. KBase is the first large-scale bioinformatics system that enables users to upload their own data, analyze it (along with collaborator and public data), build increasingly realistic models, and share and publish their workflows and conclusions. KBase aims to provide a knowledgebase: an integrated environment where knowledge and insights are created and multiplied.

Canadian Epigenetics, Environment and Health Research Consortium Network

CEEHRC Network

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CEEHRC represents a multi-stage funding commitment by the Canadian Institutes of Health Research (CIHR) and multiple Canadian and international partners. The overall aim is to position Canada at the forefront of international efforts to translate new discoveries in the field of epigenetics into improved human health. The two sites will focus on sequencing human reference epigenomes and developing new technologies and protocols; they will also serve as platforms for other CEEHRC funding initiatives, such as catalyst and team grants. The complementary reference epigenome mapping efforts of the two sites will focus on a range of common human diseases. The Vancouver group will focus on the role of epigenetics in the development of cancer, including lymphoma and cancers of the ovary, colon, breast, and thyroid. The Montreal team will focus on autoimmune / inflammatory, cardio-metabolic, and neuropsychiatric diseases, using studies of identical twins as well as animal models of human disease.

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).

Leiden Open Variation Database

LOVD

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LOVD portal provides LOVD software and access to a list of worldwide LOVD applications through Locus Specific Database list and List of Public LOVD installations. The LOVD installations that have indicated to be included in the global LOVD listing are included in the overall LOVD querying service, which is based on an API.

FlowRepository

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FlowRepository is a web-based application accessible from a web browser that serves as an online database of flow cytometry experiments where users can query and download data collected and annotated according to the MIFlowCyt standard. It is primarily used as a data deposition place for experimental findings published in peer-reviewed journals in the flow cytometry field. FlowRepository is funded by the International Society for Advancement of Cytometry (ISAC) and powered by the Cytobank engine specifically extended for the purposes of this repository. FlowRepository has been developed by forking and extending Cytobank in 2011.

Kinetic models of biological systems

KiMoSys

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KiMoSys, a web application for quantitative KInetic MOdels of biological SYStems. Kinetic models, with the aim to understand and subsequently design the metabolism of organism of interest are constructed iteratively and require accurate experimental data for both the generation and verification of hypotheses. Therefore, there is a growing requirement for exchanging experimental data and models between the systems biology community, and to automate as much as possible the kinetic model building, editing, simulation and analysis steps.

HONmedia

Health On The Net Foundation

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<<<!!!<<< HON is no longer updated and will be permanently discontinued on December 15, 2022 >>>!!!>>>

The Centre for Applied Genomics Databases

TCAG Databases

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The Centre for Applied Genomics hosts a variety of databases related to ongoing supported projects. Curation of these databases is performed in-house by TCAG Bioinformatics staff. The Autism Chromosome Rearrangement Database, The Cystic Fibrosis Mutation Database, TThe Lafora Progressive Myoclonus Epilepsy Mutation and Polymorphism Database are included. Large Scale Genomics Research resources include, the Database of Genomic Variants, The Chromosome 7 Annotation Project, The Human Genome Segmental Duplication Database, and the Non-Human Segmental Duplication Database

Cancer GenomeAtlas Data Portal

Cancer Genome Atlas Data Portal

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The Cancer Genome Atlas (TCGA) Data Portal provides a platform for researchers to search, download, and analyze data sets generated by TCGA. It contains clinical information, genomic characterization data, and high level sequence analysis of the tumor genomes. The Data Coordinating Center (DCC) is the central provider of TCGA data. The DCC standardizes data formats and validates submitted data.