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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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GenePaint Resource Report Resource Website 100+ mentions |
GenePaint (RRID:SCR_003015) | GenePaint.org | atlas, reference atlas, data or information resource, database, expression atlas | Digital atlas of gene expression patterns in developing and adult mouse. Several reference atlases are also available through this site. Expression patterns are determined by non-radioactive in situ hybridization on serial tissue sections. Sections are available from several developmental ages: E10.5, E14.5 (whole embryos), E15.5, P7 and P56 (brains only). To retrieve expression patterns, search by gene name, site of expression, GenBank accession number or sequence homology. For viewing expression patterns, GenePaint.org features virtual microscope tool that enables zooming into images down to cellular resolution. | gene expression, adult mouse, annotated, c57bl6, mouse, mouse embryo, mrna, non radioactive in situ hybridization, light microscopy, molecular neuroanatomy resource, in situ hybridization, embryonic, postnatal, adult, brain, head, annotation, rna probe, sequence, anatomical structure, FASEB list |
has parent organization: Max Planck Institute for Biophysical Chemistry; Gottingen; Germany is parent organization of: GenePaint E15 Atlas is parent organization of: GenePaint P7 Atlas is parent organization of: GenePaint P56 Mouse Atlas is parent organization of: GenePaint Interactive Anatomy Atlas |
Burroughs Wellcome Fund ; European Union ; Max Planck Society ; Merck Genome Research Institute ; Romansky Endowment ; NINDS ; BMBF |
PMID:14681479 PMID:22936000 |
nif-0000-00009, SCR_017526 | SCR_003015 | Atlas of Gene Expression Patterns in Mouse Embryo | 2026-08-11 09:40:48 | 164 | ||||||
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GreenPhylDB Resource Report Resource Website 10+ mentions |
GreenPhylDB (RRID:SCR_002834) | GreenPhylDB | service resource, analysis service resource, data or information resource, database, data analysis service, production service resource | A database designed for plant comparative and functional genomics based on complete genomes. It comprises complete proteome sequences from the major phylum of plant evolution. The clustering of these proteomes was performed to define a consistent and extensive set of homeomorphic plant families. Based on this, lists of gene families such as plant or species specific families and several tools are provided to facilitate comparative genomics within plant genomes. The analyses follow two main steps: gene family clustering and phylogenomic analysis of the generated families. Once a group of sequences (cluster) is validated, phylogenetic analyses are performed to predict homolog relationships such as orthologs and ultraparalogs. | comparative genomics, genome, functional genomics, genomics, gene family, homolog, bio.tools |
uses: Gene Ontology is listed by: bio.tools is listed by: Debian has parent organization: CIRAD |
PMID:20864446 | Free, Freely available, Available for download | biotools:greenphyldb, nif-0000-02928 | http://greenphyl.cirad.fr, http://www.greenphyl.org/v3/, https://bio.tools/greenphyldb | SCR_002834 | 2026-08-11 09:40:38 | 20 | ||||||
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Mutant Mouse Resource and Research Center Resource Report Resource Website 1000+ mentions |
Mutant Mouse Resource and Research Center (RRID:SCR_002953) | MMRRC | biomaterial supply resource, organism supplier, material resource | National public repository system for mutant mice. Archives and distributes scientifically valuable spontaneous and induced mutant mouse strains and ES cell lines for use by biomedical research community. Includes breeding/distribution facilities and information coordinating center. Mice strains are cryopreserved, unless live colony must be established. Live mice are supplied from production colony, from colony recovered from cryopreservation, or via micro-injection of cell line into host blastocysts. MMRRC member facilities also develop technologies to improve handling of mutant mice, including advances in assisted reproductive techniques, cryobiology, genetic analysis, phenotyping and infectious disease diagnostics. | RIN, Resource Information Network, stem cell, mouse strain, embryonic stem cell, embryonic stem cell line, cryopreserved, mutant mouse strain, mutant, transgenic, database, FASEB list, RRID Community Authority |
is used by: Integrated Animals is listed by: One Mind Biospecimen Bank Listing is listed by: Biositemaps is listed by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: NIDDK Research Resources is listed by: NIDDK Information Network (dkNET) is listed by: Resource Information Network is affiliated with: MUGA is affiliated with: MegaMUGA is related to: Federation of International Mouse Resources is related to: Mouse Mutagenesis Center for Developmental Defects is related to: MGI strains has parent organization: Jackson Laboratory has parent organization: University of California at Davis; California; USA has parent organization: University of Missouri; Missouri; USA has parent organization: University of North Carolina at Chapel Hill; North Carolina; USA has parent organization: National Institutes of Health is parent organization of: Deltagen and Lexicon Knockout Mice and Phenotypic Data Resource provides: Knockout Mouse Project Repository has organization facet: University of California at Davis Mutant Mouse Resource and Research Center has organization facet: Mutant Mouse Resource and Research Center - University of North Carolina has organization facet: Mutant Mouse Resource and Research Center - University of Missouri has organization facet: Mutant Mouse Resource and Research Center - Jackson Laboratory |
NIH Office of the Director U42 OD012210; NIH Office of the Director U42 OD010918; NIH Office of the Director U42 OD010924; NIH Office of the Director U42 OD010921; NCRR RR026296; NIH Blueprint for Neuroscience Research |
Restricted | nif-0000-00045 | SCR_002953 | Mutant Mouse Regional Resource Center | 2026-08-11 09:40:39 | 1079 | ||||||
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I2D Resource Report Resource Website 10+ mentions |
I2D (RRID:SCR_002957) | I2D | service resource, analysis service resource, data or information resource, database, data analysis service, production service resource | Database of known and predicted mammalian and eukaryotic protein-protein interactions, it is designed to be both a resource for the laboratory scientist to explore known and predicted protein-protein interactions, and to facilitate bioinformatics initiatives exploring protein interaction networks. 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. It contains 490,600 Source Interactions, 370,002 Predicted Interactions, for a total of 846,116 interactions, and continues to expand as new protein-protein interaction data becomes available. | interaction, prediction, protein-protein interaction, high-throughput, model organism, mammal, eukaryote, visualization, interolog, protein |
is related to: Interaction Reference Index is related to: IMEx - The International Molecular Exchange Consortium is related to: PSICQUIC Registry is related to: IntAct has parent organization: University of Toronto; Ontario; Canada |
National Science and Engineering Research Council RGPIN 203833-02; NIGMS P50-GM62413 |
PMID:17535438 PMID:15657099 |
Free, Available for download, Freely available | nif-0000-03005, r3d100010675 | https://doi.org/10.17616/R3BG8R | SCR_002957 | Interologous Interaction Database, OPHID, I2D - Interologous Interaction Database | 2026-08-11 09:40:46 | 23 | ||||
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Diseasome Resource Report Resource Website 1+ mentions |
Diseasome (RRID:SCR_002792) | Diseasome | service resource, map, data or information resource, book, narrative resource, image, data set | A disease / disorder relationships explorer and a sample of a map-oriented scientific work. It uses the Human Disease Network dataset and allows intuitive knowledge discovery by mapping its complexity. The Human Disease Network (official) dataset, a poster of the data and related book (Biology - The digital era, ISBN: 978-2-271-06779-1) are available. This kind of data has a network-like organization, and relations between elements are at least as important as the elements themselves. More data could be integrated to this prototype and could eventually bring closer phenotype and genotype. Results should be visual, but also printable. Creating posters can enhance collaborative work. It facilitates discussion and sharing of ideas about the data. This website initiative is an invitation to think about the benefits of networks exploration but above all it tries to outline future designs of scientific information systems. | disease, disorder, genotype, phenotype, poster, network |
is related to: Allen Institute Neurowiki has parent organization: Gephi |
Dana-Farber Cancer Institute ; W. M. Keck Foundation ; NHGRI ; NIGMS |
PMID:17502601 | Free, Freely Available | nif-0000-24580 | SCR_002792 | Diseaseome | 2026-08-11 09:40:44 | 1 | |||||
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BLOCK-iT RNAi Designer Resource Report Resource Website 10+ mentions |
BLOCK-iT RNAi Designer (RRID:SCR_002794) | BLOCK-iT RNAi Designer | service resource, analysis service resource, data analysis service, production service resource, commercial organization | A free tool to design effective RNAi molecules that includes the following target design options: Stealth RNAi siRNA, siRNA, miR RNAi, shRNA, siRNA to Stealth RNAi siRNA, and siRNA to shRNA. | rnai, design, sirna, blast, molecule, rnai design | has parent organization: Life Technologies | Free, Freely Available | rid_000099 | SCR_002794 | 2026-08-11 09:40:37 | 10 | ||||||||
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Primate Resource Referral Service Resource Report Resource Website 1+ mentions |
Primate Resource Referral Service (RRID:SCR_002828) | PRRS | service resource, data or information resource, database, production service resource, material service resource | It provides the communications/database network needed for efficient acquisition and sharing of existing captive primates and primate-related resources by investigators and institutions both nationally and internationally. The overall goal of this service is to maximize the use of existing captive primates, thereby reducing the total number of primates needed for research, and in turn, helping to promote the conservation of primate populations in the wild. Services Provided PRRS services include 1) Referral Service, an immediate, staff-operated service designed to match investigator inquiries/requests to the available resource listings maintained in the PRRS master database; 2) CURRENT LISTINGS, a twice-monthly newsletter listing current availability of, as well as needs for, primates, tissues, equipment, and services; 3) ANNUAL RESOURCE GUIDE (ARG), an annual publication that lists subscribing suppliers of primates, laboratories, equipment, and commercial services such as transportation and quarantine facilities; and 4) Web site, an interactive site that includes the full text of CURRENT LISTINGS as well as online forms for posting resource availabilities/needs and listing updates, the current ARG, a diagram of primate taxonomy with illustrative photographs, online renewal and feedback forms, general service information, and links to other sites of interest to the primate research community. The PRRS also maintains a database of colonies, primates, and primate materials to which notices of availability and need can be referred. Services are available without charge to government-supported researchers and other scientists in the United States and abroad using primates in their work. Sponsors: The PRRS is made possible by grant RR-01240 from the National Center for Research Resources, National Institutes of Health. | equipment, colony, communication, institution, investigator, network, primate, research, tissue | has parent organization: University of Washington; Seattle; USA | Free | nif-0000-24969 | http://www.wanprc.org/prrs/ | SCR_002828 | Primate Resource Referral Service | 2026-08-11 09:40:38 | 3 | ||||||
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FSL Resource Report Resource Website 5000+ mentions |
FSL (RRID:SCR_002823) | software toolkit, software resource, software library | Software library of image analysis and statistical tools for fMRI, MRI and DTI brain imaging data. Include registration, atlases, diffusion MRI tools for parameter reconstruction and probabilistic taractography, and viewer. Several brain atlases, integrated into FSLView and Featquery, allow viewing of structural and cytoarchitectonic standard space labels and probability maps for cortical and subcortical structures and white matter tracts. Includes Harvard-Oxford cortical and subcortical structural atlases, Julich histological atlas, JHU DTI-based white-matter atlases, Oxford thalamic connectivity atlas, Talairach atlas, MNI structural atlas, and Cerebellum atlas. | dti, brain, imaging, data, structural, mri, diffusion, function, preprocessing, analysis, statistical, tractography, atlas, neuroimaging, parameter, reconstruction, volumetric, segmentation, independent, component, temporal, transformation |
uses: Neuroimaging Data Model is used by: Spinal Cord Toolbox is used by: Functional Real-time Interactive Endogenous Neuromodulation and Decoding (FRIEND) is used by: XFSL: An FSL toolbox is used by: CMIND PY lists: SUSAN lists: FUGUE lists: Miscvis lists: BayCEST lists: ICA-PNM is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Debian is listed by: SoftCite is related to: Rodent Brain Extraction Tool is related to: Human Connectome Coordination Facility is related to: BASH4RfMRI is related to: DW-MRI registration in FSL is related to: FSL extensions is related to: Diffusion MRI of Traumatic Brain Injury is related to: Segmentation of Hippocampus Subfields is related to: masked ICA (mICA) Toolbox has parent organization: University of Oxford; Oxford; United Kingdom has plug in: Multivariate Exploratory Linear Optimized Decomposition into Independent Components has plug in: FMRI Expert Analysis Tool has plug in: FABBER has plug in: BASIL has plug in: VERBENA has plug in: Brain Extraction Tool has plug in: FMRIB's Automated Segmentation Tool has plug in: FMRIB’s Integrated Registration and Segmentation Tool has plug in: Harvard - Oxford Cortical Structural Atlas has plug in: FMRIB's Linear Image Registration Tool has plug in: FNIRT has plug in: FSLVBM has plug in: SIENA has plug in: SIENAX has plug in: Multimodal Image Segmentation Tool has plug in: Brain Intensity AbNormality Classification Algorithm has plug in: Multimodal Surface Matching has plug in: fsl_anat has plug in: FMRIB's Diffusion Toolbox has plug in: Tract Based Spatial Statistics has plug in: XTRACT has plug in: eddy has plug in: topup has plug in: eddyqc has plug in: randomise has plug in: PALM has plug in: fsl-cluster has plug in: FDR has plug in: DualRegression has plug in: FLOBS has plug in: FSLeyes has plug in: Fslutils has plug in: Atlasquery has plug in: MCFLIRT has plug in: POSSUM has plug in: FSL-MRS |
EPSRC ; MRC ; BBSRC ; GlaxoSmithKline ; Pfizer |
PMID:21979382 PMID:19059349 PMID:15501092 |
Free, Available for download, Freely available | nif-0000-00305, birnlex_2067, SCR_007368 | http://www.nitrc.org/projects/fsl, http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/, https://sources.debian.org/src/fsl/ | SCR_002823 | , FMRIB Software Library, fMRIB Software Library, Functional Magnetic Resonance Imaging of the Brain Software Library | 2026-08-11 09:40:38 | 5015 | |||||
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Dana Foundation Resource Report Resource Website 10+ mentions |
Dana Foundation (RRID:SCR_002789) | service resource, funding resource, data or information resource, outreach program, podcast, book, blog, narrative resource, training resource, training material, journal article, training service resource | A private philanthropy with principal interests in brain science, immunology, and education. The portal provides general information about the brain and current brain research, links to validated sites related brain disorders, education resources and lesson plans, and support for the training of in-school arts specialists. The Dana Foundation science and health grants support brain research in neuroscience and immunology and their interrelationship in human health and disease. The grant sections include brain and immuno-imaging, clinical neuroscience research, human immunology and neuroimmunology. The Foundation also occasionally sponsors workshops and forums for working scientists, as well as offering funding for selected young researchers to continue their education or to attend seminars and workshops elsewhere. | education, foundation, funding resource, human brain, clinical, development, disease, disorder, grant, neruroimmunology, neuroethics, neuroscience, philanthropy, podcast, research | is parent organization of: Dana Foundation: BrainWeb | Free | nif-0000-24463 | SCR_002789 | The Dana Foundation | 2026-08-11 09:40:38 | 23 | ||||||||
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Human Proteinpedia Resource Report Resource Website 10+ mentions |
Human Proteinpedia (RRID:SCR_002948) | Human Proteinpedia | service resource, data or information resource, storage service resource, database, data repository | A community portal for sharing and integration of human protein data that allows research laboratories to contribute and maintain protein annotations. The Human Protein Reference Database (HPRD) integrates data that is deposited along with the existing literature curated information in the context of an individual protein. Data pertaining to post-translational modifications, protein-protein interactions, tissue expression, expression in cell lines, subcellular localization and enzyme substrate relationships can be submitted. | enzyme, protein expression, post-translational modification, protein-protein interaction, subcellular localization, enzyme substrate, tissue expression, protein, protein binding, peptide, mass spectrometry, mass spectrometry spectra, immunohistochemistry, western blotting, microarray, co-immunoprecipitation, fluorescence, annotation, cell line expression, disease tissue expression, FASEB list |
is listed by: re3data.org is related to: HPRD - Human Protein Reference Database has parent organization: Johns Hopkins University; Maryland; USA has parent organization: Institute of Bioinformatics; Bangalore; India |
PMID:18259167 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-02999, r3d100010985 | https://doi.org/10.17616/R3V62C | SCR_002948 | 2026-08-11 09:40:39 | 32 | ||||||
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Virtual Physiological Human Network of Excellence Resource Report Resource Website 10+ mentions |
Virtual Physiological Human Network of Excellence (RRID:SCR_002855) | portal, topical portal, research forum portal, data or information resource, job resource, disease-related portal | The VPH NoE is a project which aims to help support and progress European research in biomedical modeling and simulation of the human body. This project will improve our ability to predict, diagnose and treat disease, and have a dramatic impact on the future of healthcare, the pharmaceutical and medical device industries. The VPH Network of Excellence (VPH NoE) is designed to foster, harmonize and integrate pan-European research in the field of i) patient-specific computer models for personalised and predictive healthcare and ii) ICT-based tools for modeling and simulation of human physiology and disease-related processes. The main objectives of the VPH Network of Excellence are to support the: :- Coordination of research portfolios of VPH NoE partners through initiation of Exemplar integrative research projects that encourage inter-institution and interdisciplinary VPH research; :- Integration of research infrastructures of VPH NoE partners through development of the VPH ToolKit: a shared and mutually accessible source of research equipment, managerial and research infrastructures, facilities and services; :- Development of a portfolio of interdisciplinary training activities including a formal consultation on, and assessment of, VPH careers; :- Establishment of a core set of VPH-related dissemination and networking activities which will engage everyone from partners within the VPH NoE/other VPH projects, to national policy makers, to the public at large; :- Creation of Industrial, Clinical and Scientific Advisory Boards that will jointly guide the direction of the VPH NoE and, through consultation, explore the practical and legal options for real and durable integration within the VPH research community; :- Implementation of key working groups that will pursue specific issues relating to VPH, notably integrating VPH research worldwide through international physiome initiatives. Finally, by involving clinical and industrial stakeholders, VPH NoE also plans to lay a reliable ground to support sustainable interactions and collaboration between research and healthcare communities. Virtual Physiological Human lists, as its main target outcome, patient-specific computer models for personalized and predictive healthcare and ICT-based tools for modeling and simulation of human physiology and disease-related processes. Collaborative projects (IPs and STREPs) within the call will meet specific objectives, addressing: patient-specific computational modeling and simulation of organs or systems data integration and new knowledge extraction and clinical applications and demonstration of tangible benefits of patient-specific computational models. The networking action outlined within the call - the VPH NoE - should serve to connect these efforts, and lay the foundations for the methodological and technical framework to support such research. It should also build on previous EC investment in this field, including the outcomes of VPH type' projects funded within the EU Sixth Framework Programme, and through other National and International initiatives. The Virtual Physiological Human Network of Excellence (VPH NoE) has been designed with "service to the community" of VPH researchers as its primary purpose. Its aims range from the development of a VPH ToolKit and associated infrastructural resources, through integration of models and data across the various relevant levels of physiological structure and functional organization, to VPH community building and support. The VPH NoE aims to foster the development of new and sustainable educational, training and career structures for those involved in VPH related science, technology and medicine. The VPH NoE constitutes a leading group of universities, institutes and organizations who will, by integrating their experience and ongoing activities in VPH research, promote the creation of an environment that actively supports and nurtures interdisciplinary research, education, training and strategic development. The VPH NoE will lead the coordination of diverse activities within the VPH Initiative to help deliver: new environments for predictive, patient-specific, evidence-based, more effective and safer healthcare; improved semantic interoperability of biomedical information and contribution to a common health information infrastructure; facile, on-demand access to distributed European computational infrastructure to support clinical decision making; and increased European multidisciplinary research excellence in biomedical informatics and molecular medicine by fostering closer cooperation between ICT, medical device, medical imaging, pharmaceutical and biotech companies. The VPH NoE will connect the diverse VPH Initiative projects, including not only those funded as part of the VPH initiative but also those of previous EC frameworks and national funding schemes, together with industry, healthcare providers, and international organizations, thereby ensuring that these impacts will be realized. VPH NoE work packages and project structure The VPH NoE activities are divided between five main work packages (follow the links at the top of the page for more information on each). In brief, the focus of each work package is as follows: -Work package 1: Network Management -Work package 2: VPH NoE Exemplar Projects -Work package 3: VPH NoE ToolKit development -Work package 4: VPH NoE Training and Career Development -Work package 5: Spreading Excellence within the VPH NoE and VPH-I In view of its role as the networking action for the VPH Initiative, all VPH NoE activities have been designed to serve and interconnect not only the VPH NoE core members, but also the projects funded within the VPH call (VPH-I) and the wider research community. Key activities which the VPH NoE will pursue, in support of the development of a research environment which facilitates integrative, interdisciplinary and multilevel VPH research, are: -Support for integrative research -Training and dissemination activities -Networking activities Sponsors: VPH NoE is supported by The Directorate-General Research (DG RTD) and The Directorate-General Information Society and Media (DG INFSO). | education, environment, european, biomedical, biotechnology, body, computational, development, device, diagnosis, disease, healthcare, human, imaging, industry, medical, model, molecular, patient, pharmaceutical, physiology, research, science, simulation, technology, treatment | Free, Freely available | nif-0000-25315 | SCR_002855 | VPH NoE | 2026-08-11 09:40:45 | 11 | |||||||||
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MicroArray and Gene Expression Markup Language Resource Report Resource Website 1+ mentions |
MicroArray and Gene Expression Markup Language (RRID:SCR_003023) | MAGE-ML | markup language, data or information resource, narrative resource, standard specification, interchange format | A language / data exchange format designed to describe and communicate information about microarray based experiments that is based on XML and can describe microarray designs, microarray manufacturing information, microarray experiment setup and execution information, gene expression data and data analysis results. MAGE-ML has been automatically derived from Microarray Gene Expression Object Model (MAGE-OM), which is developed and described using the Unified Modelling Language (UML) -- a standard language for describing object models. Descriptions using UML have an advantage over direct XML document type definitions (DTDs), in many respects. First they use graphical representation depicting the relationships between different entities in a way which is much easier to follow than DTDs. Second, the UML diagrams are primarily meant for humans, while DTDs are meant for computers. Therefore MAGE-OM should be considered as the primary model, and MAGE-ML will be explained by providing simplified fragments of MAGE-OM, rather then XML DTD or XML Schema. (from the description by Ugis Sarkans) The field of gene expression experiments has several distinct technologies that a standard must include. These include single vs. dual channel experiments, cDNA vs. oligonucleotides. Because of these different technologies and different types of gene expression experiments, it is not expected that all aspects of the standard will be used by all organizations. Given the massive amount of data associated with a single set of experiments, it is felt that Extensible Markup Language (XML) is the best way to describe the data. The use of a Document Type Definition (DTD) allows a well-defined tag set, a vocabulary, to describe the domain of gene expression experiments. It also has the virtue of compressing very well so that files in an XML format compress to ten percent of their original size. XML is now widely accepted as a data exchange format across multiple platforms. | microarray, gene expression, bioinformatics |
is listed by: 3DVC is related to: MADAM is related to: MIAME is related to: RNA Abundance Database has parent organization: European Bioinformatics Institute has parent organization: MAGE |
European Union ; TEMBLOR project |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-30390 | SCR_003023 | MicroArray and Gene Expression Markup Language | 2026-08-11 09:40:40 | 5 | ||||||
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Sal-Site Resource Report Resource Website 50+ mentions |
Sal-Site (RRID:SCR_002850) | Sal-Site | service resource, topical portal, portal, image collection, analysis service resource, data or information resource, organism-related portal, database, data analysis service, production service resource | Portal that supports Ambystoma-related research and educational efforts. It is composed of several resources: Salamander Genome Project, Ambystoma EST Database, Ambystoma Gene Collection, Ambystoma Map and Marker Collection, Ambystoma Genetic Stock Center, and Ambystoma Research Coordination Network. | gene, genomic, expressed sequence tag, blast, model organism, genome, salamander, animal model, genetic map, genetic marker, gene expression, limb regeneration, microarray, quantitative-pcr, rna-seq, nanostring, husbandry, embryo, limb, mutant, strain, neural, olfaction, phentotype, regeneration, renal, retina, sequence, vision, human, chicken, xenopus tropicalis, FASEB list | has parent organization: University of Kentucky; Kentucky; USA | NSF OB0242833; NSF DBI0443496; NCRR R24 RR016344; NIH Office of the Director R24 OD010435 |
PMID:16359543 | Free, Freely available | nif-0000-25309 | https://orip.nih.gov/comparative-medicine/programs/vertebrate-models | SCR_002850 | Ambystoma Resources for Model Amphibians Database | 2026-08-11 09:40:38 | 92 | ||||
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ArrayExpress Resource Report Resource Website 5000+ mentions |
ArrayExpress (RRID:SCR_002964) | ArrayExpress | service resource, data or information resource, storage service resource, database, catalog, data repository | International functional genomics data collection generated from microarray or next-generation sequencing (NGS) platforms. Repository of functional genomics data supporting publications. Provides genes expression data for reuse to the research community where they can be queried and downloaded. Integrated with the Gene Expression Atlas and the sequence databases at the European Bioinformatics Institute. Contains a subset of curated and re-annotated Archive data which can be queried for individual gene expression under different biological conditions across experiments. Data collected to MIAME and MINSEQE standards. Data are submitted by users or are imported directly from the NCBI Gene Expression Omnibus. | gold, standard, functional, genomics, data, collection, microarray, next, generation, sequencing, NGS, repository |
uses: MIAME uses: MINSEQE uses: Gene Expression Omnibus is used by: NIF Data Federation is used by: BioSample Database at EBI is used by: Integrated Datasets is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: DataCite is listed by: OMICtools is listed by: re3data.org is related to: DDBJ Omics Archive is related to: MIAME is related to: Gene Expression Atlas is related to: Experimental Factor Ontology is related to: Bgee: dataBase for Gene Expression Evolution is related to: ISA Infrastructure for Managing Experimental Metadata is related to: FlyMine is related to: MAGE-TAB is related to: Experimental Factor Ontology is related to: Magic is related to: ArrayExpress (R) is related to: CancerMIRNome has parent organization: European Bioinformatics Institute |
European Union ; SLING 226073; European Commission ; Gen2Phen 200754; NHGRI P41 HG003619 |
PMID:23193272 PMID:21071405 |
Available Public or Private, Free, Available for download, The community can contribute to this resource, Acknowledgement requested, to access private data registration required | OMICS_01023, nif-0000-30123, r3d100010222 | http://www.ebi.ac.uk/microarray-as/ae, https://doi.org/10.17616/R3302G | SCR_002964 | , ArrayExpress, ArrayExpress - functional genomics data, ArrayExpress Archive | 2026-08-11 09:40:39 | 7814 | ||||
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Developmental Therapeutics Program Resource Report Resource Website 500+ mentions |
Developmental Therapeutics Program (RRID:SCR_003057) | DTP | portal, topical portal, service resource, funding resource, data or information resource | Portal for preclinical information and research materials, including web-accessible data and tools, NCI-60 Tumor Cell Line Screen, compounds in vials and plates, tumor cells, animals, and bulk drugs for investigational new drug (IND)-directed studies. DTP has been involved in the discovery or development of more than 70 percent of the anticancer therapeutics on the market today, and will continue helping the academic and private sectors to overcome various therapeutic development barriers, particularly through supporting high-risk projects and therapeutic development for rare cancers. Initially DTP made its drug discovery and development services and the results from the human tumor cell line assay publicly accessible to researchers worldwide. At first, the site offered in vitro human cell line data for a few thousand compounds and in vitro anti-HIV screening data for roughly 42,000 compounds. Today, visitors can find: * Downloadable in vitro human tumor cell line data for some 43,500 compounds and 15,000 natural product extracts * Results for 60,000 compounds evaluated in the yeast assay * In vivo animal model results for 30,000 compounds * 2-D and 3-D chemical structures for more than 200,000 compounds * Molecular target data, including characterizations for at least 1,200 targets, plus data from multiple cDNA microarray projects In addition to browsing DTP's databases and downloading data, researchers can request individual samples or sets of compounds on 96-well plates for research, or they can submit their own compounds for consideration for screening via DTP's online submission form. Once a compound is submitted for screening, researchers can follow its progress and retrieve data using a secure web interface. The NCI has collected information on almost half a million chemical structures in the past 50 years. DTP has made this information accessible and useful for investigators through its 3-D database, a collection of three-dimensional structures for more than 200,000 drugs. Investigators use the 3-D database to screen compounds for anticancer therapeutic activity. Also available on DTP's website are 127,000 connection tables for anticancer agents. A connection table is a convenient way of depicting molecular structures without relying on drawn chemical structures. As unique lists of atoms and their connections, the connection tables can be indexed and stored in computer databases where they can be used for patent searches, toxicology studies, and precursor searching, for example., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | cell line, drug discovery, drug development, drug, treatment, therapy, biopharmaceutical, bortezomib, paclitaxel, romidepsin, eribulin, sipuleucel-t, anticancer therapeutic, compound, natural product extract, animal model, in vivo, in vitro, chemical structure, chemical, structure, anti-hiv, anticancer, molecular structure, database, chemotherapeutic agent, testing, drug synthesis, chemistry, grant, contract, information technology, molecular pharmacology, natural product, pharmaceutical, screening technology, toxicology, pharmacology, screening, FASEB list |
is used by: NIF Data Federation is related to: Integrated Cell Lines has parent organization: National Cancer Institute |
Cancer, Tumor | NCI | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-30447 | https://medschool.cuanschutz.edu/colorado-cancer-center/research/research-programs/developmental-therapeutics | SCR_003057 | Developmental Therapeutics Program NCI/NIH | 2026-08-11 09:40:49 | 571 | ||||
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Computational Biology Center Resource Report Resource Website 50+ mentions |
Computational Biology Center (RRID:SCR_002877) | portal, topical portal, data or information resource, training resource, disease-related portal | Computational biology research at Memorial Sloan-Kettering Cancer Center (MSKCC) pursues computational biology research projects and the development of bioinformatics resources in the areas of: sequence-structure analysis; gene regulation; molecular pathways and networks, and diagnostic and prognostic indicators. The mission of cBio is to move the theoretical methods and genome-scale data resources of computational biology into everyday laboratory practice and use, and is reflected in the organization of cBio into research and service components ~ the intention being that new computational methods created through the process of scientific inquiry should be generalized and supported as open-source and shared community resources. Faculty from cBio participate in graduate training provided through the following graduate programs: * Gerstner Sloan-Kettering Graduate School of Biomedical Sciences * Graduate Training Program in Computational Biology and Medicine Integral to much of the research and service work performed by cBio is the creation and use of software tools and data resources. The tools that we have created and utilize provide evidence of our involvement in the following areas: * Cancer Genomics * Data Repositories * iPhone & iPod Touch * microRNAs * Pathways * Protein Function * Text Analysis * Transcription Profiling | drug, evolution, experiment, gene, algorithm, bioinformatics, biology, cancer, clinical, computational, diagnostic, genome, human, initiation, kinetics, laboratory, leukemia, ligand, metastasis, microrna, mirna, model, molecular, network, pathway, phenotype, prognostic, progression, protein, regulation, research, resistance, rna, sequence, stem cell, structure, t cell, therapy, treatment, tumor | is parent organization of: TMBETA-GENOME- Annotation of Beta-Barrel Membrane Proteins in Genomic Sequences | Free, Freely available | nif-0000-25560 | SCR_002877 | cBio | 2026-08-11 09:40:38 | 71 | ||||||||
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Brian Simulator Resource Report Resource Website 10+ mentions |
Brian Simulator (RRID:SCR_002998) | Brian | software application, simulation software, software resource | Software Python package for simulating spiking neural networks. Useful for neuroscientific modelling at systems level, and for teaching computational neuroscience. Intuitive and efficient neural simulator. | simulation, spiking, neuron, brain, communication, modelling, computational neuroscience, python, spiking neuron, neural network |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Ecole Normale Superieure; Paris; France |
European Union ; French National Research Agency ; CNRS ; Ecole Normale Superieure; Paris; France |
DOI:10.7554/eLife.47314 DOI:10.3389/neuro.01.026.2009 DOI:10.7554/eLife.47314 |
Free, Available for download, Freely available | nif-0000-30223 | http://www.nitrc.org/projects/brian | SCR_002998 | Brian 2, Brian spiking neural network simulator, Brian2 | 2026-08-11 09:40:40 | 29 | ||||
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Allen Developing Mouse Brain Atlas Resource Report Resource Website 100+ mentions |
Allen Developing Mouse Brain Atlas (RRID:SCR_002990) | atlas, reference atlas, data or information resource, database, expression atlas | Map of gene expression in developing mouse brain revealing gene expression patterns from embryonic through postnatal stages. Provides information about spatial and temporal regulation of gene expression with database. Feature include seven sagittal reference atlases created with a developmental ontology. These anatomic atlases may be viewed alongside in situ hybridization (ISH) data as well as by itself. | gene, expression, developing, mouse, brain, pattern, embryonic, postnatal, stage, data, database, reference, atlas, ontology, anatomy, ISH |
is related to: Allen Brain Atlas API is related to: Allen Human Brain Atlas: BrainSpan (Atlas of the Developing Brain) has parent organization: Allen Institute for Brain Science has parent organization: Allen Brain Atlas |
PMID:22832508 | Free, Public | nif-0000-00509 | SCR_002990 | Allen Brain Atlas Developing Mouse Brain | 2026-08-11 09:40:40 | 217 | |||||||
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DIALIGN Resource Report Resource Website 10+ mentions |
DIALIGN (RRID:SCR_003041) | DIALIGN | service resource, analysis service resource, web service, software resource, data analysis service, production service resource, data access protocol | Tool for multiple sequence alignment using various sources of external information that is particularly useful to detect local homologies in sequences with low overall similarity. While standard alignment methods rely on comparing single residues and imposing gap penalties, DIALIGN constructs pairwise and multiple alignments by comparing entire segments of the sequences. No gap penalty is used. This approach can be used for both global and local alignment, but it is particularly successful in situations where sequences share only local homologies. Several versions of DIALIGN are available online at GOBICS, http://dialign.gobics.de/ | dna, protein, sequence alignment, sequence, alignment, fasta, genome, genomic sequence, homology, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite has parent organization: Bielefeld University; North Rhine-Westphalia; Germany |
PMID:15215344 PMID:23620293 DOI:10.1186/1748-7188-3-6 |
Free, Available for download, Freely available | nif-0000-30417, OMICS_24606, OMICS_00973, biotools:dialign-tx | http://dialign.gobics.de/, https://bio.tools/dialign-tx | https://sources.debian.org/src/dialign-tx/ | SCR_003041 | DIALIGN at GOBICS | 2026-08-11 09:40:48 | 44 | ||||
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Lowes Syndrome Mutation Database Resource Report Resource Website 1+ mentions |
Lowes Syndrome Mutation Database (RRID:SCR_002907) | service resource, data or information resource, storage service resource, database, data repository | The Lowe Syndrome Mutation Database is now being maintained by the National Center for Biotechnology Information (NCBI) at the National Institutes of Health. A database of mutations causing Lowe syndrome. Information on new mutations may be submitted online. Lowe oculocerebrorenal syndrome is an X-linked disorder caused by mutations in the OCRL1 gene, which encodes a 105-kDa Golgi protein with phosphatidylinositol (4,5) bisphosphate 5-phosphatase activity. genetics | mutation | has parent organization: NCBI | Lowe syndrome | NHGRI | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-00155 | http://research.nhgri.nih.gov/lowe/ | SCR_002907 | Lowe Syndrome Mutation Database | 2026-08-11 09:40:39 | 1 |
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