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Found 32 result(s)
The goal of the Signaling Pathways Project knowledgebase is to allow bench researchers to routinely ask sophisticated questions of the universe of multi-omics data points generated by the cellular signaling community. SPP is dedicated to helping researchers to make sense of the often overwhelming volume of multi-omics information in the field of cellular signaling.
NIAID’s TB Portals Program is a multi-national collaboration for TB data sharing and analysis to advance TB research. As a global consortium of clinicians, scientists, and IT professionals from 40 sites in 16 countries throughout eastern Europe, Asia, and sub-Saharan Africa, the TB Portals Program is a web-based, open-access repository of multi-domain TB data and tools for its analysis. Researchers can find linked socioeconomic/geographic, clinical, laboratory, radiological, and genomic data from over 7,500 international published TB patient cases with an emphasis on drug-resistant tuberculosis.
The Paleobiology Database (PaleoBioDB) is a non-governmental, non-profit public resource for paleontological data. It has been organized and operated by a multi-disciplinary, multi-institutional, international group of paleobiological researchers. Its purpose is to provide global, collection-based occurrence and taxonomic data for organisms of all geological ages, as well data services to allow easy access to data for independent development of analytical tools, visualization software, and applications of all types. The Database’s broader goal is to encourage and enable data-driven collaborative efforts that address large-scale paleobiological questions.
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The IDR makes datasets that have never previously been accessible publicly available, allowing the community to search, view, mine and even process and analyze large, complex, multidimensional life sciences image data. Sharing data promotes the validation of experimental methods and scientific conclusions, the comparison with new data obtained by the global scientific community, and enables data reuse by developers of new analysis and processing tools.
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NODE (The National Omics Data Encyclopedia) provides an integrated, compatible, comparable, and scalable multi-omics resource platform that supports flexible data management and effective data release. NODE uses a hierarchical data architecture to support storage of muti-omics data including sequencing data, MS based proteomics data, MS or NMR based metabolomics data, and fluorescence imaging data. Launched in early 2017, NODE has collected and published over 900 terabytes of omics data for researchers from China and all over the world in last three years, 22% of which contains multiple omics data. NODE provides functions around the whole life cycle of omics data, from data archive, data requests/responses to data sharing, data analysis, data review and publish.
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The Center for Tropical Forest Science (CTFS) is a global network of forest research plots committed to the study of tropical and temperate forest function and diversity. The multi-institutional network comprises more than forty forest research plots across the Americas, Africa, Asia, and Europe, with a strong focus on tropical regions. CTFS monitors the growth and survival of about 6 million trees of approximately 10,000 species.
>>>!!!<<< 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.
The Conserved Domain Database is a resource for the annotation of functional units in proteins. Its collection of domain models includes a set curated by NCBI, which utilizes 3D structure to provide insights into sequence/structure/function relationships
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The Health Atlas is an alliance of medical ontologists, medical systems biologists and clinical trials groups to design and implement a multi-functional and quality-assured atlas. It provides models, data and metadata on specific use cases from medical research projects from the partner institutions.
The Plant Metabolic Network (PMN) provides a broad network of plant metabolic pathway databases that contain curated information from the literature and computational analyses about the genes, enzymes, compounds, reactions, and pathways involved in primary and secondary metabolism in plants. The PMN currently houses one multi-species reference database called PlantCyc and 22 species/taxon-specific databases.
The Basis Set Exchange (BSE) provides a web-based user interface for downloading and uploading Gaussian-type (GTO) basis sets, including effective core potentials (ECPs), from the EMSL Basis Set Library. It provides an improved user interface and capabilities over its predecessor, the EMSL Basis Set Order Form, for exploring the contents of the EMSL Basis Set Library. The popular Basis Set Order Form and underlying Basis Set Library were originally developed by Dr. David Feller and have been available from the EMSL webpages since 1994.
The PhenoGen website shares experimental data with a worldwide community of investigators and provides a flexible, integrated, multi-resolution repository of neuroscience transcriptomic genetic data for collaborative research on genomic disorders. The main development focus is on providing Hybrid Rat Diversity Panel transcriptomic data (sequencing, genome coverage, reconstructed totalRNA/smallRNA transcriptomes, quanification of the transcriptome, eQTLs, and WGCNA) and integrating additional tools to provide platform for visualization and analysis of HRDP transcriptome data.
The European Mouse Mutant Archive – EMMA is a non-profit repository for the collection, archiving (via cryopreservation) and distribution of relevant mutant mouse strains essential for basic biomedical research. The laboratory mouse is the most important mammalian model for studying genetic and multi-factorial diseases in man. The comprehensive physical and data resources of EMMA support basic biomedical and preclinical research, and the available research tools and mouse models of human disease offer the opportunity to develop a better understanding of molecular disease mechanisms and may provide the foundation for the development of diagnostic, prognostic and therapeutic strategies.
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<<<!!!<<< The repository is offline >>>!!!>>> Store.Synchrotron is a fully functional, cloud computing based solution to raw X-ray data archival and dissemination at the Australian Synchrotron, largest stand-alone piece of scientific infrastructure in the southern hemisphere. Store.Synchrotron represents the logical extension of a long-standing effort in the macromolecular crystallography community to ensure that satisfactory evidence is provided to support the interpretation of structural experiments.
The U.S. Antarctic Program Data Center (USAP-DC) provides the central Project Catalog for projects funded by the NSF for the U.S. Antarctic Program and Data Repository for multi-disciplinary investigator research datasets derived from these projects. Services provided support investigators in documenting, preserving, and disseminating their research results. All data are openly accessible to the international community for browse, search, and data download. Datasets are registered in the Antarctic Master Directory to comply with the Antarctic Treaty.
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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.
INDEPTH is a global network of research centres that conduct longitudinal health and demographic evaluation of populations in low- and middle-income countries (LMICs). INDEPTH aims to strengthen global capacity for Health and Demographic Surveillance Systems (HDSSs), and to mount multi-site research to guide health priorities and policies in LMICs, based on up-to-date scientific evidence. The data collected by the INDEPTH Network members constitute a valuable resource of population and health data for LMIC countries. This repository aims to make well documented anonymised longitudinal microdata from these Centres available to data users.
The National Sleep Research Resource (NSRR) is an NHLBI-supported repository for sharing large amounts of sleep data (polysomnography, actigraphy and questionnaire-based) from multiple cohorts, clinical trials, and other data sources. Launched in April 2014, the mission of the NSRR is to advance sleep and circadian science by supporting secondary data analysis, algorithmic development, and signal processing through the sharing of high-quality data sets.
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The China National GeneBank database (CNGBdb) is a unified platform for biological big data sharing and application services. CNGBdb has now integrated a large amount of internal and external biological data from resources such as CNGB, NCBI, and the EBI. There are several sub-databases in CNGBdb, including literature, variation, gene, genome, protein, sequence, organism, project, sample, experiment, run, and assembly. Based on underlying big data and cloud computing technologies, it provides various data services, including archive, analysis, knowledge search, and management authorization of biological data. CNGBdb adopts data structures and standards of international omics, health, and medicine, such as The International Nucleotide Sequence Database Collaboration (INSDC), The Global Alliance for Genomics and Health GA4GH (GA4GH), Global Genome Biodiversity Network (GGBN), American College of Medical Genetics and Genomics (ACMG), and constructs standardized data and structures with wide compatibility. All public data and services provided by CNGBdb are freely available to all users worldwide. CNGB Sequence Archive (CNSA) is the bionomics data repository of CNGBdb. CNGB Sequence Archive (CNSA) is a convenient and efficient archiving system of multi-omics data in life science, which provides archiving services for raw sequencing reads and further analyzed results. CNSA follows the international data standards for omics data, and supports online and batch submission of multiple data types such as Project, Sample, Experiment/Run, Assembly, Variation, Metabolism, Single cell, and Sequence. Moreover, CNSA has achieved the correlation of sample entities, sample information, and analyzed data on some projects. Its data submission service can be used as a supplement to the literature publishing process to support early data sharing.CNGB Sequence Archive (CNSA) is a convenient and efficient archiving system of multi-omics data in the life science of CNGBdb, which provides archiving services for raw sequencing reads and further analyzed results. CNSA follows the international data standards for omics data, and supports online and batch submission of multiple data types such as Project, Sample, Experiment/Run, Assembly, Variation, Metabolism, Single cell, Sequence. Its data submission service can be used as a supplement to the literature publishing process to support early data sharing.
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The CyberCell database (CCDB) is a comprehensive collection of detailed enzymatic, biological, chemical, genetic, and molecular biological data about E. coli (strain K12, MG1655). It is intended to provide sufficient information and querying capacity for biologists and computer scientists to use computers or detailed mathematical models to simulate all or part of a bacterial cell at a nanoscopic (10-9 m), mesoscopic (10-8 m).The CyberCell database CCDB actually consists of 4 browsable databases: 1) the main CyberCell database (CCDB - containing gene and protein information), 2) the 3D structure database (CC3D – containing information for structural proteomics), 3) the RNA database (CCRD – containing tRNA and rRNA information), and 4) the metabolite database (CCMD – containing metabolite information). Each of these databases is accessible through hyperlinked buttons located at the top of the CCDB homepage. All CCDB sub-databases are fully web enabled, permitting a wide variety of interactive browsing, search and display operations. and microscopic (10-6 m) level.
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.
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The public MorpheusML model repository collects, curates, documents and tests computational models for multi-scale and multicellular biological systems. Model must be encoded in the model description language MorpheusML. Subsections of the repository distinguish published models from contributed non-published and example models. New models are simulated in Morpheus or Artistoo independently from the authors and results are compared to published results. Successful reproduction is documented on the model's webpage. Models in this repository are included into the CI and test pipelines for each release of the model simulator Morpheus to check and guarantee reproducibility of results across future simulator updates. The model’s webpage provides a History-link to all past model versions and edits that are automatically tracked via Git. Each model is registered with a unique and persistent ID of the format M..... The model description page (incl. the biological context and key results of that model), the model’s XML file, the associated paper, and all further files (often simulation result videos) connected with that model can be retrieved via a persistent URL of the format https://identifiers.org/morpheus/M..... - for technical details on the citable ModelID please see https://registry.identifiers.org/registry/morpheus - for the model definition standard MorpheusML please see https://doi.org/10.25504/FAIRsharing.78b6a6 - for the model simulator Morpheus please see https://morpheus.gitlab.io - for the model simulator Artistoo please see https://artistoo.net/converter.html
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ISTA Research Explorer is an online digital repository of multi-disciplinary research datasets as well as publications produced at IST Austria, hosted by the Library. ISTA researchers who have produced research data associated with an existing or forthcoming publication, or which has potential use for other researches, are invited to upload their dataset for sharing and safekeeping. A persistent identifier and suggested citation will be provided.