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Found 36 result(s)

BioModels

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BioModels is a repository of mathematical models of biological and biomedical systems. It hosts a vast selection of existing literature-based physiologically and pharmaceutically relevant mechanistic models in standard formats. Our mission is to provide the systems modelling community with reproducible, high-quality, freely-accessible models published in the scientific literature.

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.

doRiNA

database of RNA interactions in post-transcriptional regulation

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doRiNA is a database of transcriptome-wide binding site data for RNA binding proteins and microRNAs

Screening Unit Berlin-Buch

Screening Unit Jens Peter von Kries

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The mission of the platform is to enable access for academic projects towards experiments in high-throughput without loss of IP and on a cost basis, which does not restrict access towards HTS usage. The FMP hosts the central open access technology platform of EU-OPENSCREEN, the ChemBioNet and theHelmholtz-Initiative für Wirkstoffforschung, the Screening Unit. The Unit serves for systematic screening of large compound or genome-wide RNAi libraries with state-of-the-art equipment like automated microscopes and microfluidic systems. The Screening Unit is part of the Chemical Biology Platform of the FMP also supported by the MDC. See also: https://www.mdc-berlin.de/screening-unit

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.

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.

Biomedical Informatics Research Network

BIRN

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>>>!!!<<< As stated 2017-05-16 The BIRN project was finished a few years ago. The web portal is no longer live.>>>!!!<<< BIRN is a national initiative to advance biomedical research through data sharing and online collaboration. It supports multi-site, and/or multi-institutional, teams by enabling researchers to share significant quantities of data across geographic distance and/or incompatible computing systems. BIRN offers a library of data-sharing software tools specific to biomedical research, best practice references, expert advice and other resources.

NetPath

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<<<!!!<<< This repository is no longer available. >>>!!!>>> NetPath is currently one of the largest open-source repository of human signaling pathways that is all set to become a community standard to meet the challenges in functional genomics and systems biology. Signaling networks are the key to deciphering many of the complex networks that govern the machinery inside the cell. Several signaling molecules play an important role in disease processes that are a direct result of their altered functioning and are now recognized as potential therapeutic targets. Understanding how to restore the proper functioning of these pathways that have become deregulated in disease, is needed for accelerating biomedical research. This resource is aimed at demystifying the biological pathways and highlights the key relationships and connections between them. Apart from this, pathways provide a way of reducing the dimensionality of high throughput data, by grouping thousands of genes, proteins and metabolites at functional level into just several hundreds of pathways for an experiment. Identifying the active pathways that differ between two conditions can have more explanatory power than just a simple list of differentially expressed genes and proteins.

IUCN Red List of Threatened Species

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The IUCN Red List of Threatened Species provides taxonomic, conservation status and distribution data on plants and animals that are critically endangered, endangered and vulnerable. Data are available in Esri File Geodatabase format, Esri Shapefile format, and Excel format.

Cancer Genome Anatomy Project

CGAP

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>>>!!!<<< Noticed 26.08.2020: The NCI CBIIT instance of the CGAP no longer exist on this website. The Mitelman Database of Chromosome Aberrations and Gene Fusions in Cancer has a new home at the NCI-funded Institute for Systems Biology Cancer Genomics Cloud available at the following location: https://mitelmandatabase.isb-cgc.org >>>!!!<<<

Woods Hole Oceanographic Institution - Data & Repositories

WHOI

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WHOI is the world's leading non-profit oceanographic research organization. WHOI maintains unparalleled depth and breadth of expertise across a range of oceanographic research areas. Institution scientists and engineers work collaboratively within and across six research departments to advance knowledge of the global ocean and its fundamental importance to other planetary systems. At the same time, they also train future generations of ocean scientists and address problems that have a direct impact in efforts to understand and manage critical marine resources.

CoRIS

Coral Reef Information System

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NOAA's Coral Reef Information System (CoRIS) is a web-based information portal that provides access to NOAA coral reef information and data products with emphasis on the U.S. states, territories and remote island areas. NOAA Coral Reef activities include coral reef mapping, monitoring and assessment; natural and socioeconomic research and modeling; outreach and education; and management and stewardship.

MetaCyc

Metabolic Pathway Database

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MetaCyc is a curated database of experimentally elucidated metabolic pathways from all domains of life. MetaCyc contains pathways involved in both primary and secondary metabolism, as well as associated metabolites, reactions, enzymes, and genes. The goal of MetaCyc is to catalog the universe of metabolism by storing a representative sample of each experimentally elucidated pathway. MetaCyc applications include: Online encyclopedia of metabolism, Prediction of metabolic pathways in sequenced genomes, Support metabolic engineering via enzyme database, Metabolite database aids. metabolomics research.

Yeast Resource Center

Yeast Resource Center Public Data Repository

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The Yeast Resource Center provides access to data about mass spectrometry, yeast two-hybrid arrays, deconvolution florescence microscopy, protein structure prediction and computational biology. These services are provided to further the goal of a complete understanding of the chemical interactions required for the maintenance and faithful reproduction of a living cell. The observation that the fundamental biological processes of yeast are conserved among all eukaryotes ensures that this knowledge will shape and advance our understanding of living systems.

TB Database

Tuberculosis Database

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The repository is no longer available. >>>!!!<<< 2018-08-29: no more access to TB Database >>>!!!<<<

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.

4DGenome

Chromatin Interaction Database

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4DGenome is a public database that archives and disseminates chromatin interaction data. Currently, 4DGenome contains over 8,038,247 interactions curated from both experimental studies (high throughput and individual studies) and computational predictions. It covers five organisms, Homo sapiens, Mus musculus, Drosophila melanogaster, Plasmodium falciparum, and Saccharomyces cerevisiae.

COVID-19 Interactive Map

Johns Hopkins Coronavirus Resource Center

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JHU has stopped collecting data as of 03/10/2023 After three years of around-the-clock tracking of COVID-19 data from around the world, Johns Hopkins has discontinued the Coronavirus Resource Center’s operations. The site’s two raw data repositories will remain accessible for information collected from 1/22/20 to 3/10/23 on cases, deaths, vaccines, testing and demographics. Coronavirus COVID-19 Global Cases by the Center for Systems Science and Engineering (CSSE) at Johns Hopkins University (JHU). Johns Hopkins experts in global public health, infectious disease, and emergency preparedness have been at the forefront of the international response to COVID-19. This website is a resource to help advance the understanding of the virus, inform the public, and brief policymakers in order to guide a response, improve care, and save lives. All data collected and displayed are made freely available through a GitHub repository https://github.com/CSSEGISandData/COVID-19, along with the feature layers of the dashboard, which are now included in the ESRI Living Atlas: https://livingatlas.arcgis.com/en/home/

NCBI Gene

Gene

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The Gene database provides detailed information for known and predicted genes defined by nucleotide sequence or map position. Gene supplies gene-specific connections in the nexus of map, sequence, expression, structure, function, citation, and homology data. Unique identifiers are assigned to genes with defining sequences, genes with known map positions, and genes inferred from phenotypic information. These gene identifiers are used throughout NCBI's databases and tracked through updates of annotation. Gene includes genomes represented by NCBI Reference Sequences (or RefSeqs) and is integrated for indexing and query and retrieval from NCBI's Entrez and E-Utilities systems.

Ocean Networks Canada

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Ocean Networks Canada maintains several observatories installed in three different regions in the world's oceans. All three observatories are cabled systems that can provide power and high bandwidth communiction paths to sensors in the ocean. The infrastructure supports near real-time observations from multiple instruments and locations distributed across the Arctic, NEPTUNE and VENUS observatory networks. These observatories collect data on physical, chemical, biological, and geological aspects of the ocean over long time periods, supporting research on complex Earth processes in ways not previously possible.

NCBI Trace Archive

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<<<!!!<<< This repository is no longer available. (Trace Archive is scheduled to retire on June 17, 2022) >>>!!!>>>

European Nucleotide Archive

ENA

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The European Nucleotide Archive (ENA) captures and presents information relating to experimental workflows that are based around nucleotide sequencing. A typical workflow includes the isolation and preparation of material for sequencing, a run of a sequencing machine in which sequencing data are produced and a subsequent bioinformatic analysis pipeline. ENA records this information in a data model that covers input information (sample, experimental setup, machine configuration), output machine data (sequence traces, reads and quality scores) and interpreted information (assembly, mapping, functional annotation). Data arrive at ENA from a variety of sources. These include submissions of raw data, assembled sequences and annotation from small-scale sequencing efforts, data provision from the major European sequencing centres and routine and comprehensive exchange with our partners in the International Nucleotide Sequence Database Collaboration (INSDC). Provision of nucleotide sequence data to ENA or its INSDC partners has become a central and mandatory step in the dissemination of research findings to the scientific community. ENA works with publishers of scientific literature and funding bodies to ensure compliance with these principles and to provide optimal submission systems and data access tools that work seamlessly with the published literature.

JaLTER MetaCat Service

JaLTER Database Systems

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The vision of the JaLTER is to provide scientific knowledge which contributes to conservation, advancement and sustainability of environment, ecosystem services, productivity and biodiversity for a society by conducting long-term and interdisciplinary research in ecological science including human dimensions. The JaLTER is closely linked with the International Long-Term Ecological Research Network (ILTER Network).

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.

Global Genome Biodiversity Network

DNA Bank Network (formerly)

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The DNA Bank Network was established in spring 2007 and was funded until 2011 by the German Research Foundation (DFG). The network was initiated by GBIF Germany (Global Biodiversity Information Facility). It offers a worldwide unique concept. DNA bank databases of all partners are linked and are accessible via a central web portal, providing DNA samples of complementary collections (microorganisms, protists, plants, algae, fungi and animals). The DNA Bank Network was one of the founders of the Global Genome Biodiversity Network (GGBN) and is fully merged with GGBN today. GGBN agreed on using the data model proposed by the DNA Bank Network. The Botanic Garden and Botanical Museum Berlin-Dahlem (BGBM) hosts the technical secretariat of GGBN and its virtual infrastructure. The main focus of the DNA Bank Network is to enhance taxonomic, systematic, genetic, conservation and evolutionary studies by providing: • high quality, long-term storage of DNA material on which molecular studies have been performed, so that results can be verified, extended, and complemented, • complete on-line documentation of each sample, including the provenance of the original material, the place of voucher deposit, information about DNA quality and extraction methodology, digital images of vouchers and links to published molecular data if available.