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Found 205 result(s)

BioSample

BioSample at the NCBI

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The BioSample database contains descriptions of biological source materials used in experimental assays.

BioSimulations

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BioSimulations is a web application for sharing and re-using biomodels, simulations, and visualizations of simulations results. BioSimulations supports a wide range of modeling frameworks (e.g., kinetic, constraint-based, and logical modeling), model formats (e.g., BNGL, CellML, SBML), and simulation tools (e.g., COPASI, libRoadRunner/tellurium, NFSim, VCell). BioSimulations aims to help researchers discover published models that might be useful for their research and quickly try them via a simple web-based interface.

STITCH

Search Tool for Interactions of Chemicals

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The Database explores the interactions of chemicals and proteins. It integrates information about interactions from metabolic pathways, crystal structures, binding experiments and drug-target relationships. Inferred information from phenotypic effects, text mining and chemical structure similarity is used to predict relations between chemicals. STITCH further allows exploring the network of chemical relations, also in the context of associated binding proteins.

Stemformatics

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Stemformatics is a collaboration between the stem cell and bioinformatics community. We were motivated by the plethora of exciting cell models in the public and private domains, and the realisation that for many biologists these were mostly inaccessible. We wanted a fast way to find and visualise interesting genes in these exemplar stem cell datasets. We'd like you to explore. You'll find data from leading stem cell laboratories in a format that is easy to search, easy to visualise and easy to export.

FAIRDOMHub

The SEEK datafiles

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The FAIRDOMHub is built upon the SEEK software suite, which is an open source web platform for sharing scientific research assets, processes and outcomes. FAIRDOM (Web Site) will establish a support and service network for European Systems Biology. It will serve projects in standardizing, managing and disseminating data and models in a FAIR manner: Findable, Accessible, Interoperable and Reusable. FAIRDOM is an initiative to develop a community, and establish an internationally sustained Data and Model Management service to the European Systems Biology community. FAIRDOM is a joint action of ERA-Net EraSysAPP and European Research Infrastructure ISBE.

DEPOD

DEPhOsphorylation Database

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DEPOD - the human DEPhOsphorylation Database (version 1.1) is a manually curated database collecting human active phosphatases, their experimentally verified protein and non-protein substrates and dephosphorylation site information, and pathways in which they are involved. It also provides links to popular kinase databases and protein-protein interaction databases for these phosphatases and substrates. DEPOD aims to be a valuable resource for studying human phosphatases and their substrate specificities and molecular mechanisms; phosphatase-targeted drug discovery and development; connecting phosphatases with kinases through their common substrates; completing the human phosphorylation/dephosphorylation network.

Pathogen Portal

the Bioinformatics Resource Centers Portal

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Pathogen Portal is a repository linking to the Bioinformatics Resource Centers (BRCs) sponsored by the National Institute of Allergy and Infectious Diseases (NIAID) and maintained by The Virginia Bioinformatics Institute. The BRCs are providing web-based resources to scientific community conducting basic and applied research on organisms considered potential agents of biowarfare or bioterrorism or causing emerging or re-emerging diseases. The Pathogen Portal supports and links to five Bioinformatics Resource Centers (BRCs). Each BRC specializes in a different group of pathogens, focusing on, but not limited to, pathogens causing (Re-)Emerging Infectious Diseases, and those in the NIAID Category A-C Priority Pathogen lists for biodefense research. The scope of the BRCs also includes Invertebrate Vectors of Human Disease. Pathogen Portal covers EuPathDB, IRD, PATRIC, VectorBase and ViPR.

MassBank Europe

MassBank

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Database of mass spectra of known, unknown and provisionally identified substances. MassBank is the first public repository of mass spectral data for sharing them among scientific research community. MassBank data are useful for the chemical identification and structure elucidation of chemical compounds detected by mass spectrometry.

European Zebrafish Resource Center

EZRC

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The EZRC at KIT houses the largest experimental fish facility in Europe with a capacity of more than 300,000 fish. Zebrafish stocks are maintained mostly as frozen sperm. Frequently requested lines are also kept alive as well as a selection of wildtype strains. Several thousand mutations in protein coding genes generated by TILLING in the Stemple lab of the Sanger Centre, Hinxton, UK and lines generated by ENU mutagenesis by the Nüsslein-Volhard lab in addition to transgenic lines and mutants generated by KIT groups or brought in through collaborations. We also accept submissions on an individual basis and ship fish upon request to PIs in Europe and elsewhere. EZRC also provides screening services and technologies such as imaging and high-throughput sequencing. Key areas include automation of embryo handling and automated image acquisition and processing. Our platform also involves the development of novel microscopy techniques (e.g. SPIM, DSLM, robotic macroscope) to permit high-resolution, real-time imaging in 4D. By association with the ComPlat platform, we can support also chemical screens and offer libraries with up to 20,000 compounds in total for external users. As another service to the community the EZRC provides plasmids (cDNAs, transgenes, Talen, Crispr/cas9) maintained by the Helmholtz repository of Bioparts (HERBI) to the scientific community. In addition the fish facility keeps a range of medaka stocks, maintained by the Loosli group.

AspGD

Aspergillus Genome Database

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<<<!!!!<<<< AspGD data are being integrated into FungiDB. Please click here for additional details https://fungidb.org/>>>>!!!!>>>

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.

4TU.ResearchData | science.engineering.design

formerly: 4TU.Centre for Research Data

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4TU.ResearchData, previously known as 4TU.Centre for Research Data, is a research data repository dedicated to the science, engineering and design disciplines. It offers the knowledge, experience and the tools to manage, publish and find scientific research data in a standardized, secure and well-documented manner. 4TU.ResearchData provides the research community with: Customised advice and support on research data management; A long-term repository for scientific research data; Support for current research projects; Tools to enhance reuse of research data.

Beta Cell Biology Consortium Reagent and Data Resources

BCBC Reagent and Data Resources

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>>>!!!<<< Sorry.we are no longer in operation >>>!!!<<< The Beta Cell Biology Consortium (BCBC) was a team science initiative that was established by the National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK). It was initially funded in 2001 (RFA DK-01-014), and competitively continued both in 2005 (RFAs DK-01-17, DK-01-18) and in 2009 (RFA DK-09-011). Funding for the BCBC came to an end on August 1, 2015, and with it so did our ability to maintain active websites.!!! One of the many goals of the BCBC was to develop and maintain databases of useful research resources. A total of 813 different scientific resources were generated and submitted by BCBC investigators over the 14 years it existed. Information pertaining to 495 selected resources, judged to be the most scientifically-useful, has been converted into a static catalog, as shown below. In addition, the metadata for these 495 resources have been transferred to dkNET in the form of RDF descriptors, and all genomics data have been deposited to either ArrayExpress or GEO. Please direct questions or comments to the NIDDK Division of Diabetes, Endocrinology & Metabolic Diseases (DEM).

Mouse Phenome Database

MPD

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The Mouse Phenome Database (MPD; phenome.jax.org) has characterizations of hundreds of strains of laboratory mice to facilitate translational discoveries and to assist in selection of strains for experimental studies.

CanGEM

Cancer GEnome Mine

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>>>!!!<<<As stated 2017-05-23 Cancer GEnome Mine is no longer available >>>!!!<<< Cancer GEnome Mine is a public database for storing clinical information about tumor samples and microarray data, with emphasis on array comparative genomic hybridization (aCGH) and data mining of gene copy number changes.

miRBase

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The miRBase database is a searchable database of published miRNA sequences and annotation. Each entry in the miRBase Sequence database represents a predicted hairpin portion of a miRNA transcript (termed mir in the database), with information on the location and sequence of the mature miRNA sequence (termed miR). Both hairpin and mature sequences are available for searching and browsing, and entries can also be retrieved by name, keyword, references and annotation. All sequence and annotation data are also available for download. The miRBase Registry provides miRNA gene hunters with unique names for novel miRNA genes prior to publication of results.

caArray

Array Data Management System

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>>>!!!<<< caArray Retirement Announcement >>>!!!<<< The National Cancer Institute (NCI) Center for Biomedical Informatics and Information Technology (CBIIT) instance of the caArray database was retired on March 31st, 2015. All publicly-accessible caArray data and annotations will be archived and will remain available via FTP download https://wiki.nci.nih.gov/x/UYHeDQ and is also available at GEO http://www.ncbi.nlm.nih.gov/geo/ . >>>!!!<<< While NCI will not be able to provide technical support for the caArray software after the retirement, the source code is available on GitHub https://github.com/NCIP/caarray , and we encourage continued community development. Molecular Analysis of Brain Neoplasia (Rembrandt fine-00037) gene expression data has been loaded into ArrayExpress: http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-3073 >>>!!!<<< caArray is an open-source, web and programmatically accessible microarray data management system that supports the annotation of microarray data using MAGE-TAB and web-based forms. Data and annotations may be kept private to the owner, shared with user-defined collaboration groups, or made public. The NCI instance of caArray hosts many cancer-related public datasets available for download.

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.

SimTK

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SimTK is a free project-hosting platform for the biomedical computation community that enables researchers to easily share their software, data, and models and provides the infrastructure so they can support and grow a community around their projects. It has over 126.656 members, hosts 1.648 projects from researchers around the world, and has had more than 2.095.783 files downloaded from it. Individuals have created SimTK projects to meet publisher and funding agencies’ software and data sharing requirements, run scientific challenges, create a collection of their community’s resources, and much more.

e!DAL - electronic Data Archive Library

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!!! <<< this record is no longer maintained, please use https://www.re3data.org/repository/r3d100011876 or https://www.re3data.org/repository/r3d100011647 >>> !!!: e!DAL stands for electronic Data Archive Library. It is a lightweight open source software software framework for publishing and sharing research data. e!DAL was developed based on experiences coming from decades of research data management and has grown towards being a general data archiving and publication infrastructure [https://doi.org/10.1186/1471-2105-15-214]. First research data repository is "Plant Genomics and Phenomics Research Data Repository" [https://doi.org/10.1093/database/baw033].

QTL Archive

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This site provides access to raw data from various QTL (quantitative trait loci) studies using rodent inbred line crosses. Data are available in the .csv format used by R/qtl and pseudomarker programs. In some cases analysis scripts and/or results are posted to accompany the data.

ZFMK Biodiversity Data Center

ZFMK Natural History Collections - occurrence data

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The ZFMK Biodiversity Data Center is aimed at hosting, archiving, publishing and distributing data from biodiversity research and zoological collections. The Biodiversity Data Center handles and curates data on: - The specimens of the institutes collection, including provenance, distribution, habitat, and taxonomic data. - Observations, recordings and measurements from field research, monitoring and ecological inventories. - Morphological measurements, descriptions on specimens, as well as - Genetic barcode libraries, and - Genetic and molecular research data associated with specimens or environmental samples. For this purpose, suitable software and hardware systems are operated and the required infrastructure is further developed. Core components of the software architecture are: The DiversityWorkbench suite for managing all collection-related information. The Digital Asset Management system easyDB for multimedia assets. The description database Morph·D·Base for morphological data sets and character matrices.

GeneLab

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GeneLab is an interactive, open-access resource where scientists can upload, download, store, search, share, transfer, and analyze omics data from spaceflight and corresponding analogue experiments. Users can explore GeneLab datasets in the Data Repository, analyze data using the Analysis Platform, and create collaborative projects using the Collaborative Workspace. GeneLab promises to facilitate and improve information sharing, foster innovation, and increase the pace of scientific discovery from extremely rare and valuable space biology experiments. Discoveries made using GeneLab have begun and will continue to deepen our understanding of biology, advance the field of genomics, and help to discover cures for diseases, create better diagnostic tools, and ultimately allow astronauts to better withstand the rigors of long-duration spaceflight. GeneLab helps scientists understand how the fundamental building blocks of life itself – DNA, RNA, proteins, and metabolites – change from exposure to microgravity, radiation, and other aspects of the space environment. GeneLab does so by providing fully coordinated epigenomics, genomics, transcriptomics, proteomics, and metabolomics data alongside essential metadata describing each spaceflight and space-relevant experiment. By carefully curating and implementing best practices for data standards, users can combine individual GeneLab datasets to gain new, comprehensive insights about the effects of spaceflight on biology. In this way, GeneLab extends the scientific knowledge gained from each biological experiment conducted in space, allowing scientists from around the world to make novel discoveries and develop new hypotheses from these priceless data.

PhenoGen Informatics

PhenoGen

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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.

Interologous Interaction Database

I2D

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I2D (Interologous Interaction Database) is an on-line database of known and predicted mammalian and eukaryotic protein-protein interactions. It has been built by mapping high-throughput (HTP) data between species. Thus, until experimentally verified, these interactions should be considered "predictions". It remains one of the most comprehensive sources of known and predicted eukaryotic PPI. I2D includes data for S. cerevisiae, C. elegans, D. melonogaster, R. norvegicus, M. musculus, and H. sapiens.