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on page 1 showing 20 out of 22 results

Cite this (Berkeley Bioinformatics Open-Source Projects, RRID:SCR_006704)

URL: http://www.berkeleybop.org/

Resource Type: Resource, software resource, topical portal, portal, data or information resource

The BBOP, located at the Lawrence Berkeley National Labs, is a diverse group of scientific researchers and software engineers dedicated to developing tools and applying computational technologies to solve biological problems. Members of the group contribute to a number of projects, including the Gene Ontology, OBO Foundry, the Phenotypic Quality Ontology, modENCODE, and the Generic Model Organism Database Project. Our group is focused on the development, use, and integration of ontolgies into biological data analysis. Software written or maintained by BBOP is accessible through the site.

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Cite this (Berkeley Drosophila Genome Project, RRID:SCR_013094)

URL: http://www.fruitfly.org

Resource Type: Resource, topical portal, production service resource, analysis service resource, database, data analysis service, narrative resource, experimental protocol, portal, service resource, material resource, data or information resource

Database on the sequence of the euchromatic genome of Drosophila melanogaster In addition to genomic sequencing, the BDGP is 1) producing gene disruptions using P element-mediated mutagenesis on a scale unprecedented in metazoans; 2) characterizing the sequence and expression of cDNAs; and 3) developing informatics tools that support the experimental process, identify features of DNA sequence, and allow us to present up-to-date information about the annotated sequence to the research community. Resources * Universal Proteomics Resource: Search for clones for expression and tissue culture * Materials: Request genomic or cDNA clones, library filters or fly stocks * Download Sequence data sets and annotations in fasta or xml format by http or ftp * Publications: Browse or download BDGP papers * Methods: BDGP laboratory protocols and vector maps * Analysis Tools: Search sequences for CRMs, promoters, splice sites, and gene predictions * Apollo: Genome annotation viewer and editor September 15, 2009 Illumina RNA-Seq data from 30 developmental time points of D. melanogaster has been submitted to the Short Read Archive at NCBI as part of the modENCODE project. The data set currently contains 2.2 billion single-end and paired reads and over 201 billion base pairs.

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Cite this (BioModels Database, RRID:SCR_001993)

URL: http://www.ebi.ac.uk/biomodels-main/

Resource Type: Resource, topical portal, database, international standard specification, standard specification, narrative resource, service resource, portal, storage service resource, data repository, data or information resource

Repository of peer-reviewed, published, computational models that allows biologists to store, search and retrieve published mathematical models from the field of systems biology, but also more generally those of biological interest. Models in the database can be used to generate sub-models, can be simulated online, and can be converted between different representational formats. This resource also features programmatic access via Web Services. Each model is curated to verify that it corresponds to the reference publication and gives the proper numerical results. Curators also annotate the components of the models with terms from controlled vocabularies and links to other relevant data resources allowing users to search accurately for the models they need. The models can be retrieved in the SBML format and import/export facilities are being developed to extend the spectrum of formats supported by the resource.

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Cite this (BMAP - Brain Molecular Anatomy Project, RRID:SCR_008852)

URL: http://trans.nih.gov/bmap/index.htm

Resource Type: Resource, topical portal, portal, funding resource, data or information resource

The Brain Molecular Anatomy Project is a trans-NIH project aimed at understanding gene expression and function in the nervous system. BMAP has two major scientific goals: # Gene discovery: to catalog of all the genes expressed in the nervous system, under both normal and abnormal conditions. # Gene expression analysis: to monitor gene expression patterns in the nervous system as a function of cell type, anatomical location, developmental stage, and physiological state, and thus gain insight into gene function. In pursuit of these goals, BMAP has launched several initiatives to provide resources and funding opportunities for the scientific community. These include several Requests for Applications and Requests for Proposals, descriptions of which can be found in this Web site. BMAP is also in the process of establishing physical and electronic resources for the community, including repositories of cDNA clones for nervous system genes, and databases of gene expression information for the nervous system. Most of the BMAP initiatives so far have focused on the mouse as a model species because of the ease of experimental and genetic manipulation of this organism, and because many models of human disease are available in the mouse. However, research in humans, other mammalian species, non-mammalian vertebrates, and invertebrates is also being funded through BMAP. For the convenience of interested investigators, we have established this Web site as a central information resource, focusing on major NIH-sponsored funding opportunities, initiatives, genomic resources available to the research community, courses and scientific meetings related to BMAP initiatives, and selected reports and publications. When appropriate, we will also post initiatives not directly sponsored by BMAP, but which are deemed relevant to its goals. Posting decisions are made by the Trans-NIH BMAP Committee

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Cite this (Caenorhabditis elegans Natural Diversity Resource (CeNDR), RRID:SCR_014958)

URL: https://elegansvariation.org/

Resource Type: Resource, biomaterial supply resource, material resource, organism supplier, portal, data or information resource

Supplier and researcher of wild C. elegans strains. CeNDR supplies organisms, analyzes whole-genome sequences, and facilitates genetic mappings to aid researchers in gene discovery.

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Cite this (ChemHealthWeb, RRID:SCR_005851)

URL: http://publications.nigms.nih.gov/chemhealth/

Resource Type: Resource, topical portal, narrative resource, training material, portal, video resource, data or information resource

Visit ChemHealthWeb for research highlights, chemist profiles, games and videos and other Web extras. The NIGMS Chemistry of Health booklet describes basic chemistry and biochemistry research that spurs a better understanding of human health.

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Cite this (Drug Design Data Resource, RRID:SCR_000497)

URL: http://drugdesigndata.org

Resource Type: Resource, database, portal, data or information resource

Project portal's database of protein-ligand data sets provided by pharmaceutical partners that provide atomic details of drug mechanisms that will be used to improve computer-aided drug-design methods and thus accelerate drug discovery. The project aims to help companies release the high-quality data they have generated, which has incredible value to researchers working to improve methods of computer-aided drug discovery. Everyone stands to benefit from the ability to develop new medications more quickly and inexpensively. What computational chemists globally are trying to do is to make faster, more accurate, more predictive programs to speed up the process. Part of their mission is to engage the community in these challenges to test newly developed predictive algorithms.

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Cite this (EMDataBank.org: Unified Data Resource for Cryo Electron Microscopy, RRID:SCR_003207)

URL: http://www.emdatabank.org

Resource Type: Resource, service resource, portal, storage service resource, project portal, data repository, data or information resource

Portal for deposition and retrieval of cryo electron microscopy (3DEM) density maps, atomic models, and associated metadata. Global resource for 3 Dimensional Electron Microscopy structure data archiving and retrieval, news, events, software tools, data standards, validation methods.

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Cite this (eMERGE Network: electronic Medical Records and Genomics, RRID:SCR_007428)

URL: https://www.mc.vanderbilt.edu/victr/dcc/projects/acc/index.php/Main_Page

Resource Type: Resource, topical portal, portal, data or information resource

A national consortium formed to develop, disseminate, and apply approaches to research that combine DNA biorepositories with electronic medical record (EMR) systems for large-scale, high-throughput genetic research. The consortium is composed of seven member sites exploring the ability and feasibility of using EMR systems to investigate gene-disease relationships. Themes of bioinformatics, genomic medicine, privacy and community engagement are of particular relevance to eMERGE. The consortium uses data from the EMR clinical systems that represent actual health care events and focuses on ethical issues such as privacy, confidentiality, and interactions with the broader community.

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Cite this (exRNA Atlas, RRID:SCR_017221)

URL: https://exrna-atlas.org

Resource Type: Resource, expression atlas, organization portal, application programming interface, data access protocol, production service resource, analysis service resource, database, consortium, atlas, service resource, portal, data analysis service, software resource, ontology, controlled vocabulary, data or information resource

Software tool as data and metadata repository of Extracellular RNA Communication Consortium. Atlas includes small RNA sequencing and qPCR derived exRNA profiles from human and mouse biofluids. All RNAseq datasets are processed using version 4 of exceRpt small RNAseq pipeline. Atlas accepts submissions for RNAseq or qPCR data.

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Cite this (Function BIRN, RRID:SCR_007291)

URL: http://www.birncommunity.org/collaborators/function-birn/

Resource Type: Resource, topical portal, portal, data or information resource

The FBIRN Federated Informatics Research Environment (FIRE) includes tools and methods for multi-site functional neuroimaging. This includes resources for data collection, storage, sharing and management, tracking, and analysis of large fMRI datasets. fBIRN is a national initiative to advance biomedical research through data sharing and online collaboration. BIRN provides data-sharing infrastructure, software tools, strategies and advisory services - all from a single source.

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Cite this ( Hippocampal Slice Wave Animations , RRID:SCR_008372)

URL: http://www.jneurosci.org/supplemental/18/12/4570/

Resource Type: Resource, topical portal, animation software, resource, software application, data visualization software, portal, software resource, data processing software, simulation software, data or information resource

THIS RESOURCE IS NO LONGER IN SERVICE, documented on January 29, 2013. Supplemental data for the paper Changes in mitochondrial function resulting from synaptic activity in the rat hippocampal slice, by Vytautas P. Bindokas, Chong C. Lee, William F. Colmers, and Richard J. Miller that appears in the Journal of Neuroscience June 15, 1998. You can view digital movies of changes in fluorescence intensity by clicking on the title of interest.

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    KnowEnG

Cite this (KnowEnG, RRID:SCR_016875)

URL: https://knoweng.org

Resource Type: Resource, software resource, organization portal, training resource, portal, data or information resource

Part of the NIH Big Data to Knowledge (BD2K) Initiative. One of 11 Centers of Excellence in Big Data Computing. Platform for genomics data analysis where user-supplied data sets will be analyzed in the context of existing knowledge. E-science framework for genomics where biomedical scientists will have access to powerful methods of data mining, network mining, and machine learning to extract knowledge out of genomics data.

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    Leginon

Cite this (Leginon, RRID:SCR_016731)

URL: http://emg.nysbc.org/redmine/projects/leginon/wiki/Leginon_Homepage

Resource Type: Resource, data repository, data processing software, software application, service resource, portal, storage service resource, software resource, data acquisition software, data or information resource, image acquisition software

System designed for automated collection of images from a transmission electron microscope.

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Cite this (LIPID Metabolites And Pathways Strategy, RRID:SCR_006579)

URL: http://www.lipidmaps.org/

Resource Type: Resource, topical portal, database, standard specification, narrative resource, portal, data or information resource

A multi-institutional effort to identify and quantitate, using a systems biology approach and sophisticated mass spectrometers, all of the major - and many minor - lipid species in mammalian cells, as well as to quantitate the changes in these species in response to perturbation. The goal of their research is to better understand lipid metabolism and the active role lipids play in diabetes, stroke, cancer, arthritis, Alzheimer's and other lipid-based diseases in order to facilitate development of more effective treatments. Resources available include: LIPID MAPS publications, detailed biochemical pathways, improved protocols for lipid separation and quantification, analytical tools for determining lipid quantitation, structure drawing tools for automatically drawing lipid molecular structures in stereochemical detail, and experimental data. The LIPID MAPS organization includes six lipidomics core laboratories, each specialized in extracting, identifying, and quantifying one of the major categories of mammalian lipids: fatty acyls, glycerolipids, glycerophospholipids, sphingolipids, sterol lipids, and prenol lipids. Other core laboratories and bridge projects include bioinformatics, mass spectrometric imaging, lipid synthesis, oxidized lipids, and macrophage biology and genomics.

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    MODELLER

Cite this (MODELLER, RRID:SCR_008395)

URL: http://salilab.org/modeller/modeller.html

Resource Type: Resource, topical portal, software application, portal, software resource, simulation software, data or information resource

Software tool as Program for Comparative Protein Structure Modelling by Satisfaction of Spatial Restraints. Used for homology or comparative modeling of protein three dimensional structures. User provides alignment of sequence to be modeled with known related structures and MODELLER automatically calculates model containing all non hydrogen atoms.

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Cite this (National Resource for Translational and Developmental Proteomics, RRID:SCR_016907)

URL: http://nrtdp.northwestern.edu/

Resource Type: Organization, service resource, organization portal, training resource, portal, data or information resource

Organization dedicated to analysis of protein molecules by mass spectrometry, with a focus on intact protein measurements. Biomedical projects originated from clinical and basic research programs that utilize both targeted and untargeted analyses. Used for the development of new technology, training and dissemination of proteomics methods to laboratories and scientists.

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Cite this (Omics Discovery Index, RRID:SCR_010494)

URL: http://www.omicsdi.org/

Resource Type: Resource, database, portal, data or information resource

Portal for dataset discovery across a heterogeneous, distributed group of transcriptomics, genomics, proteomics and metabolomics data resources. These resources span eight repositories in three continents and six organisations, including both open and controlled access data resources.

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Cite this (PhosphoSitePlus: Protein Modification Site, RRID:SCR_001837)

URL: http://www.phosphosite.org

Resource Type: Resource, knowledge environment resource, portal, data or information resource

A freely accessible on-line systems biology resource devoted to all aspects of protein modification, as well as other post-translational modifications. It provides valuable and unique tools for both cell biologists and mass spectroscopists. PhosphoSite is a human- and mouse-centric database. It includes features such as: viewing the locations of modified residues on molecular models; browsing and searching MS2 records by disease, tissue, and cell line; submitting lists of peptides to identify previously reported genes; searching by sub-cellular localization, treatment, tissues, cell types, cell lines and diseases, and protein types and protein domains; searching for experimentally-verified kinase substrates and viewing preferred substrate motifs; and viewing MS2 spectra for peptides and sites not previously published.

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    Simbios

Cite this (Simbios, RRID:SCR_004320)

URL: http://simbios.stanford.edu/index.html

Resource Type: Resource, organization portal, training resource, journal article, portal, software resource, postdoctoral program resource, data or information resource

Simbios is the NIH Center for physics-based Simulation of Biological Structures. Simbios provides infrastructure, software, and training to help biomedical researchers understand biological form and function as they create novel drugs, synthetic tissues, medical devices, and surgical interventions. Simbios is investigating a wide scale of biological structures - from molecules to organisms. Driving biological problems include RNA folding, protein folding, myosin dynamics, cardiovascular dynamics, and neuromuscular biomechanics. Investigators interested in collaborating with Simbios can apply for NIH funding. To encourage collaboration in building accurate biological models and simulations, Simbios also provides the biomedical community with https://simtk.org, a free, secure, distributed, development system for projects. Projects may include models, software, data, documentation, publications, and graphics and have automatic backups and off-site storage. Projects may be public or private and have project-specific mailing lists, forums, bug & feature databases, news, blogs, and source-code repositories. Simbios is developing and disseminating the SimTK core simulation toolkit, (simtk.org/home/simtkcore). SimTK core is open-source software developed by experienced professionals. The software includes advanced capabilities for modeling the geometry and physics of biological systems. To ensure utility and accuracy, the software and training material is being developed and tested in close collaboration with biomedical scientists. Simbios has developed OpenSim, an application for advanced neuromuscular modeling that uses the SimTK toolkit, and is making it openly available at simtk.org/home/opensim. Simbios also publishes the Biomedical Computation Review, a magazine devoted to the science and tools in biocomputation, aimed at the community which encompasses the diverse biocomputation disciplines. To help researchers find high quality software and tools Simbios has also establishes the Simbiome an inventory of high-quality commercial and academic bio-simulation tools. Simbios has recurring openings for postdoctoral researchers.

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