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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Yogo Data Management System Resource Report Resource Website |
Yogo Data Management System (RRID:SCR_004239) | software application, software resource, software toolkit, source code | A set of software tools created to rapidly build scientific data-management applications. These applications will enhance the process of data annotation, analysis, and web publication. The system provides a set of easy-to-use software tools for data sharing by the scientific community. It enables researchers to build their own custom-designed data management systems. The problem of scientific data management rests on several challenges. These include flexible data storage, a way to share the stored data, tools to curate the data, and history of the data to show provenance. The Yogo Framework gives you the ability to build scientific data management applications that address all of these challenges. The Yogo software is being developed as part of the NeuroSys project. All tools created as part of the Yogo Data Management Framework are open source and released under an OSI approved license. | has parent organization: Montana State University | The Michael J. Fox Foundation for Parkinsons Research ; Lumina Foundation ; NSF ; EPSCoR Program ; Montana State University; Montana; USA ; NIMH MH0441-07 |
Open unspecified license | nlx_25179 | SCR_004239 | Yogo Framework, Yogo Data Management Framework, Yogo | 2026-09-05 06:25:16 | 0 | ||||||||
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Open Connectome Project Resource Report Resource Website 1+ mentions |
Open Connectome Project (RRID:SCR_004232) | Open Connectome Project | analysis service resource, data access protocol, data analysis service, data or information resource, data repository, data set, image repository, production service resource, service resource, software resource, source code, storage service resource, web service | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 9, 2023. Connectomes repository to facilitate the analysis of connectome data by providing a unified front for connectomics research. With a focus on Electron Microscopy (EM) data and various forms of Magnetic Resonance (MR) data, the project aims to make state-of-the-art neuroscience open to anybody with computer access, regardless of knowledge, training, background, etc. Open science means open to view, play, analyze, contribute, anything. Access to high resolution neuroanatomical images that can be used to explore connectomes and programmatic access to this data for human and machine annotation are provided, with a long-term goal of reconstructing the neural circuits comprising an entire brain. This project aims to bring the most state-of-the-art scientific data in the world to the hands of anybody with internet access, so collectively, we can begin to unravel connectomes. Services: * Data Hosting - Their Bruster (brain-cluster) is large enough to store nearly any modern connectome data set. Contact them to make your data available to others for any purpose, including gaining access to state-of-the-art analysis and machine vision pipelines. * Web Viewing - Collaborative Annotation Toolkit for Massive Amounts of Image Data (CATMAID) is designed to navigate, share and collaboratively annotate massive image data sets of biological specimens. The interface is inspired by Google Maps, enhanced to allow the exploration of 3D image data. View the fork of the code or go directly to view the data. * Volume Cutout Service - RESTful API that enables you to select any arbitrary volume of the 3d database (3ddb), and receive a link to download an HDF5 file (for matlab, C, C++, or C#) or a NumPy pickle (for python). Use some other programming language? Just let them know. * Annotation Database - Spatially co-registered volumetric annotations are compactly stored for efficient queries such as: find all synapses, or which neurons synapse onto this one. Create your own annotations or browse others. *Sample Downloads - In addition to being able to select arbitrary downloads from the datasets, they have also collected a few choice volumes of interest. * Volume Viewer - A web and GPU enabled stand-alone app for viewing volumes at arbitrary cutting planes and zoom levels. The code and program can be downloaded. * Machine Vision Pipeline - They are building a machine vision pipeline that pulls volumes from the 3ddb and outputs neural circuits. - a work in progress. As soon as we have a stable version, it will be released. * Mr. Cap - The Magnetic Resonance Connectome Automated Pipeline (Mr. Cap) is built on JIST/MIPAV for high-throughput estimation of connectomes from diffusion and structural imaging data. * Graph Invariant Computation - Upload your graphs or streamlines, and download some invariants. * iPad App - WholeSlide is an iPad app that accesses utilizes our open data and API to serve images on the go. | human, primary visual cortex, data sharing, male, electron microscopy, mri, connectome, annotation, image collection, array tomography |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: CATMAID is related to: neurodata is parent organization of: Rambo3D |
Johns Hopkins University; Maryland; USA ; JHU Applied Research Laboratory IRAD ; JHU Whiting School of Engineering ; Dean's Award ; NIBIB 1RO1EB016411-01 (CRCNS); DARPA N66001-14-1-4028 (GRAPHS); NSF ACI-1261715; NSF OCI-1040114; NIDA 1R01DA036400-01 |
PMID:23707591 | THIS RESOURCE IS NO LONGER IN SERVICE | SciRes_000189, nlx_143645 | http://openconnecto.me, http://www.nitrc.org/projects/ocp/ | SCR_004232 | openconnectomeproject, Open Connectome Project: Collectively reverse-engineering the brain one synapse at a time., Open Connectome Project: Collectively reverse-engineering the brain one synapse at a time | 2026-09-05 06:25:16 | 7 | ||||
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DRUT Resource Report Resource Website |
DRUT (RRID:SCR_004351) | DRUT | software resource | Software for Discovery and Reconstruction of Unannotated Transcripts in Partially Annotated Genomes from High-Throughput RNA-Seq Data. | c++, reconstruction, frequency estimation, transcript, rna-seq, annotation |
is listed by: OMICtools has parent organization: Georgia State University; Georgia; USA |
NSF IIS-0546457; NSF IIS-0916401; NSF IIS-0916948 |
PMID:23202426 | OMICS_01273 | SCR_004351 | Discovery and Reconstruction of Unannotated Transcripts | 2026-09-05 06:25:18 | 0 | ||||||
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DigiMorph Resource Report Resource Website 50+ mentions |
DigiMorph (RRID:SCR_004416) | DigiMorph | data or information resource, database, image, narrative resource, training material, video resource | A dynamic archive of information on digital morphology and high-resolution X-ray computed tomography of biological specimens serving imagery for more than 750 specimens contributed by almost 150 collaborating researchers from the world''s premiere natural history museums and universities. Browse through the site and see spectacular imagery and animations and details on the morphology of many representatives of the Earth''s biota. Digital Morphology, part of the National Science Foundation Digital Libraries Initiative, develops and serves unique 2D and 3D visualizations of the internal and external structure of living and extinct vertebrates, and a growing number of ''invertebrates.'' The Digital Morphology library contains nearly a terabyte of imagery of natural history specimens that are important to education and central to ongoing cutting-edge research efforts. Digital Morphology visualizations are now in use in classrooms and research labs around the world and can be seen in a growing number of museum exhibition halls. The Digital Morphology site currently presents: * QuickTime animations of complete stacks of serial CT sections * Animated 3D volumetric movies of complete specimens * Stereolithography (STL) files of 3D objects that can be viewed interactively and rapidly prototyped into scalable physical 3D objects that can be handled and studied as if they were the original specimens * Informative introductions to the scanned organisms, often written by world authorities * Pertinent bibliographic information on each specimen * Useful links * A course resource for our ''Digital Methods for Paleontology'' course, in which students learn how to generate all of the types of imagery displayed on the Digital Morphology site | image archive, x-ray computed tomographic scanner, x-ray computed tomography, scientific name, common name, cladogram, dinosaur, tapir, horned lizard, endocast, bat, primate, FASEB list | has parent organization: University of Texas at Austin; Texas; USA | NSF | The images may be used for the personal education of website visitors. Any commercial reproduction, Redistribution, Publication, Or other use of the website content, By electronic means or otherwise, Is prohibited unless pursuant to a written agreement signed by the copyright holder. | nlx_143746, r3d100011511 | https://doi.org/10.17616/R3TD0C | SCR_004416 | Digital Morphology library, Digital Morphology | 2026-09-05 06:25:19 | 78 | |||||
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Catalog of Fishes Resource Report Resource Website |
Catalog of Fishes (RRID:SCR_004408) | CASGEN, CASSPC, CASREF, | bibliography, book, data or information resource, database, narrative resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 11, 2023. The Catalog of Fishes is the authoritative reference for taxonomic fish names, featuring a searchable on-line database. The Catalog of Fishes covers more than 53,000 species and subspecies, over 10,000 genera and subgenera, and includes in excess of 16,000 bibliographic references. The Catalog of Fishes consists of three hardbound volumes of 900-1000 pages each, along with a CD-ROM. The online database is updated about every 8 weeks and is now about twice the size of the published version. It is one of the oldest and most complete databases for any large animal group. References are over 30,000. Valid species are over 30,000. This work is an essential reference for taxonomists, scientific historians, and for any specialist dealing with fishes. Entries for species, for example, consist of species/subspecies name, genus, author, date, publication, pages, figures, type locality, location of type specimen(s), current status (with references), family/subfamily, and important publication, taxonomic, or nomenclatural notes. Nearly all original descriptions have been examined, and much effort has gone into determining the location of type specimens. The Genera are updated from Eschmeyer''s 1990 Genera of Recent Fishes. Both genera and species are listed in a classification using recent taxonomic schemes. Also included are a lengthy list of museum acronyms, an interpretation of the International Code of Zoological Nomenclature, and Opinions of the International Commission involving fishes. | genus, species, reference, publication |
is related to: Teleost Taxonomy Ontology is related to: Phenoscape Knowledgebase has parent organization: California Academy of Sciences |
NSF ; Alfred P. Sloan Foundation |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_41737 | SCR_004408 | Catalog of Fishes database | 2026-09-05 06:25:19 | 0 | ||||||
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PGN Resource Report Resource Website |
PGN (RRID:SCR_004559) | PGN | analysis service resource, data analysis service, data or information resource, data repository, data set, database, production service resource, service resource, storage service resource | Resource for the storage, retrieval and annotation of plant ESTs, with a focus on comparative genomics. PGN comprises an analysis pipeline and a website, and presently contains mainly data from the Floral Genome Project. However, it accepts submission from other sources. All data in PGN is directly derived from chromatograms and all original and intermediate data are stored in the database. The current datasets on PGN come from the floral genome project and includes the following species: Acorus americanus, Amborella trichopoda, Asparagus officinalis, Cucumis sativus, Eschscholzia californica, Eschscholzia californica, Illicium parviflorum, Ipomopsis aggregata, Liriodendron tulipifera, Mesembryanthemum crystallinum, Mimulus guttatus, Nuphar advena, Papaver somniferum, Persea americana, Prymnesium parvum, Ribes americanum, Saruma henryi, Stenogyne rugosa, Vaccinium corymbosa, Welwitschia mirabilis, Yucca filamentosa, Zamia fischeri. For functional annotation, blast is used to compare find the best match of each unigene sequence to in the Genbank NR database, and the in complete coding sequences from Arabidopsis. These annotations are stored in the database and serve as the primary source of annotation. The annotation framework will be extended to Gene Ontology annotations in the future. | expressed sequence tag, genomics, functional annotation, blast, sequencing, chromatogram | has parent organization: Cornell University; New York; USA | NSF DBI-9872617; NSF DBI-0115684 |
nlx_55223 | SCR_004559 | PGN - Plant Genome Network, Plant Genome Network | 2026-09-05 06:25:21 | 0 | |||||||
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Picky Resource Report Resource Website 10+ mentions |
Picky (RRID:SCR_010963) | Picky | software resource | A software tool for selecting optimal oligonucleotides (oligos) that allows the rapid and efficient determination of gene-specific oligos based on given gene sets, and can be used for large, complex genomes such as human, mouse, or maize. |
is listed by: OMICtools has parent organization: Iowa State University; Iowa; USA |
NSF DBI0850195 | PMID:15180932 PMID:19849862 PMID:20406469 |
Free, Public, Acknowledgement requested | OMICS_00833 | SCR_010963 | Picky: Optimal Oligonucleotide Design and Analysis | 2026-09-05 06:26:51 | 39 | ||||||
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Integrated Earth Data Applications Resource Report Resource Website 1+ mentions |
Integrated Earth Data Applications (RRID:SCR_006739) | IEDA | analysis service resource, data analysis service, data or information resource, data repository, database, production service resource, service resource, storage service resource | A community-based data facility to support, sustain, and advance the geosciences by providing data services for observational solid earth data from the Ocean, Earth, and Polar Sciences. IEDA systems enable these data to be discovered and reused by a diverse community now and in the future. Data services include data access, data analysis, data compliance, data publication, DOI search, and web services. Desktop apps GeoMapApp and Virtual Ocean are available to explore, visualize and analyze your own data within the context of hundreds of other earth science data from around the world. IEDA is a partnership between EarthChem and the Marine Geoscience Data System (MGDS). EarthChem and MGDS systems include the geochemical databases PetDB and SedDB, the geochemistry data network EarthChem, the Ridge2000 and MARGINS Data Portals, the Academic Seismic Portal field data collection, the Antarctic and Southern Ocean Data System, the Global Multi Resolution Topography synthesis, and the System for Earth Sample Registration SESAR. | map, ocean, earth, polar, sciences, ocean sciences, earth sciences, polar sciences, doi, global geochemistry, marine geoscience |
has parent organization: Columbia University; New York; USA is parent organization of: Marine Geoscience Data System is parent organization of: Global-Multi Resolution Topography Image Service is parent organization of: Global-Multi Resolution Topography Grid Service |
NSF | The community can contribute to this resource, Free, Open unspecified license | nlx_156096 | SCR_006739 | 2026-09-05 06:26:00 | 1 | |||||||
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REDfly Regulatory Element Database for Drosophilia Resource Report Resource Website 10+ mentions |
REDfly Regulatory Element Database for Drosophilia (RRID:SCR_006790) | REDfly | data or information resource, data repository, database, service resource, storage service resource | Curated collection of known Drosophila transcriptional cis-regulatory modules (CRMs) and transcription factor binding sites (TFBSs). Includes experimentally verified fly regulatory elements along with their DNA sequence, associated genes, and expression patterns they direct. Submission of experimentally verified cis-regulatory elements that are not included in REDfly database are welcome. | transcriptional cis-regulatory module, transcription factor binding site, dna sequence, gene, expression pattern, genome, gene expression, transcription factor, cis-regulatory module, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: Drosophila anatomy and development ontologies is related to: FlyMine has parent organization: University at Buffalo; New York; USA |
NIGMS U24 GM144232; NSF EF0843229 |
PMID:20965965 PMID:18039705 PMID:16303794 |
Acknowledgement requested | OMICS_01870, biotools:redfly, nif-0000-03393 | https://bio.tools/redfly | SCR_006790 | Regulatory Element Database for Drosophilia, Regulatory Element Database | 2026-09-05 06:26:01 | 15 | ||||
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Open Archives Initiative - Object Reuse and Exchange Initiative Resource Report Resource Website 1+ mentions |
Open Archives Initiative - Object Reuse and Exchange Initiative (RRID:SCR_006982) | OAI-ORE, OAI ORE | data or information resource, narrative resource, standard specification | Initiative which defines standards for the description and exchange of aggregations of Web resources. The intent of the effort is to develop standards that generalize across all web-based information including the increasing popular social networks of web 2.0. The goal of these standards is to expose the rich content in these aggregations (sometimes called compound digital objects, they may combine distributed resources with multiple media types including text, images, data, and video) to applications that support authoring, deposit, exchange, visualization, reuse, and preservation. The specific aim of the ORE effort is to promote (through creation or endorsement) effective and consistent mechanisms which: facilitate discovery of compound digital objects; reference (or link to) these objects (as well as parts thereof); obtain a variety of disseminations of these objects; aggregate and disaggregate objects; and enable processing of objects by automated agents. | compound digital object, aggregation, metadata standard, ontology, interoperability, atom, rdf, xml, rdfa | is listed by: FORCE11 | Open Archives Initiative ; Andrew W. Mellon Foundation ; NSF |
Creative Commons Attribution-NonCommercial-ShareAlike License, v3 Unported | nif-0000-10391 | http://dltj.org/article/ore-introduction/InSeries-oai-object-reuse-and-exchange | SCR_006982 | 2026-09-05 06:26:05 | 2 | ||||||
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Comparative Sequencing of Plant Small RNAs Resource Report Resource Website 1+ mentions |
Comparative Sequencing of Plant Small RNAs (RRID:SCR_007003) | analysis service resource, data analysis service, data or information resource, data set, production service resource, service resource | This project has developed a sequence dataset of plant small RNAs based on the hypothesis that most if not all plants utilize important small RNA signaling networks. Different plant families are likely to have both common and lineage-specific miRNAs or other small RNAs with important biological roles. Comparative genomics approaches can be applied to distinguish potential miRNAs from siRNAs and to match the miRNAs to the target sequences. This project develops an unparalleled resource of millions of plant small RNAs for comparative analyses. The project includes sequencing of small RNAs from a diverse and agronomically-relevant set of plant species, focused analyses of important members of the Solanaceae and Poaceae, and development of a small RNA database and web interface for public access and analysis of data. These data will allow the experimental characterization of the majority of biologically important small RNAs for a range of plant species, and will be tremendously useful to a broad set of plant biologists interested in development, stress responses, epigenetics, evolution, RNA biology and other traits impacted by small RNAs. We offer a variety of tools to query the small RNA data set, with options to identify sequences based on homology, expression levels, conservation, or potential function: 1. Small RNA mapping tool: searches for small RNAs perfectly matching a genomic sequence provided by the user. 2. Small RNA mismatch tool: searches the database for small RNAs or other short sequences provided by the user, allowing mismatches. 3. Library-comparison tool to identify conserved small RNAs. 4. Library-comparison tool to identify differentially regulated small RNAs. 5. Reverse Target Prediction. | has parent organization: University of Delaware; Delaware; USA | NSF 0638525 | nlx_37749 | SCR_007003 | 2026-09-05 06:26:05 | 1 | ||||||||||
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Lyngby Resource Report Resource Website 1+ mentions |
Lyngby (RRID:SCR_007143) | Lyngby | data analysis software, data processing software, software application, software resource | Matlab toolbox for the analysis of functional neuroimages (PET, fMRI). The toolbox contains a number of models: FIR-filter, Lange-Zeger, K-means clustering among others, visualizations and reading of neuroimaging files. | functional, statistical, fmri, pet, matlab, neuroimaging |
is listed by: Biositemaps has parent organization: THOR Center for Neuroinformatics |
Human Brain Project ; Danish Research Council ; European Union ; BIOMED2 ; MAPAWAMO ; NASA ; NSF ; DOE ; NIDA R01 DA09246; NIMH P20 MH57180 |
Free, Non-commercial | nif-0000-00324 | SCR_007143 | Lyngby Toolbox, Lyngby - A Toolbox for Functional Neuroimaging | 2026-09-05 06:26:07 | 2 | ||||||
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Magnetics Information Consortium Resource Report Resource Website 10+ mentions |
Magnetics Information Consortium (RRID:SCR_007098) | MagIC | data or information resource, data repository, database, service resource, software resource, storage service resource | Databases that accept and provide access to paleomagnetic and rock magnetic data. The paleomagnetic data range from individual measurements to specimen, sample or site level results, including a wide variety of derived parameters or associated rock magnetic measurements. The rock magnetic database includes data collected during rock magnetic experiments on remanence, anisotropy, hysteresis and susceptibility. The MagIC Console Software provides an effective environment in Microsoft Excel where users can collate and prepare their paleomagentic and rock magnetic data for uploading in the Online MagIC Database. | paleomagnetism, rock, magnetic, paleomagnetic, geomagnetic, rock magnetic |
is listed by: CINERGI has parent organization: San Diego Supercomputer Center |
NSF EAR 0202996; NSF EAR-IF 0318672-0744107-0744108 |
Non-commercial, For scientific or educational purposes, Acknowledgement required, Copyrighted, The community can contribute to this resource | nlx_154712, SciRes_000151, r3d100011910 | https://doi.org/10.17616/R3NM0W | SCR_007098 | Magnetics Information Consortium (MagIC), MagIC Portal, MagIC database | 2026-09-05 06:26:06 | 34 | |||||
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Genes to Cognition: Neuroscience Research Programme Resource Report Resource Website 10+ mentions |
Genes to Cognition: Neuroscience Research Programme (RRID:SCR_007121) | data or information resource, portal, topical portal | A neuroscience research program that studies genes, the brain and behavior in an integrated manner, established to elucidate the molecular mechanisms of learning and memory, and shed light on the pathogenesis of disorders of cognition. Central to G2C investigations is the NMDA receptor complex (NRC/MASC), that is found at the synapses in the central nervous system which constitute the functional connections between neurons. Changes in the receptor and associated components are thought to be in a large part responsible for the phenomenon of synaptic plasticity, that may underlie learning and memory. G2C is addressing the function of synapse proteins using large scale approaches combining genomics, proteomics and genetic methods with electrophysiological and behavioral studies. This is incorporated with computational models of the organization of molecular networks at the synapse. These combined approaches provide a powerful and unique opportunity to understand the mechanisms of disease genes in behavior and brain pathology as well as provide fundamental insights into the complexity of the human brain. Additionally, Genes to Cognition makes available its biological resources, including gene-targeting vectors, ES cell lines, antibodies, and transgenic mice, generated for its phenotyping pipeline. The resources are freely-available to interested researchers. | cognition, gene, neuroscience |
is listed by: 3DVC has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
Wellcome Trust ; MRC ; BBSRC ; Gatsby Charitable Foundation ; Human Frontiers Science Programme ; European Union ; Framework Programme ; EPSRC ; NSF |
nif-0000-10235 | SCR_007121 | G2C Neuroscience Research Program, G2C Research Programme, Genes to Cognition: Neuroscience Research Program, Genes to Cognition, G2C, Genes to Cognition - Neuroscience Research Programme, Genes to Cognition-Neuroscience Research Programme, G2C Research Program | 2026-09-05 06:26:07 | 20 | ||||||||
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fMRI Data Center Resource Report Resource Website 10+ mentions |
fMRI Data Center (RRID:SCR_007278) | fMRIDC | data or information resource, data repository, database, service resource, storage service resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented August 25, 2013 Public curated repository of peer reviewed fMRI studies and their underlying data. This Web-accessible database has data mining capabilities and the means to deliver requested data to the user (via Web, CD, or digital tape). Datasets available: 107 NOTE: The fMRIDC is down temporarily while it moves to a new home at UCLA. Check back again in late Jan 2013! The goal of the Center is to help speed the progress and the understanding of cognitive processes and the neural substrates that underlie them by: * Providing a publicly accessible repository of peer-reviewed fMRI studies. * Providing all data necessary to interpret, analyze, and replicate these fMRI studies. * Provide training for both the academic and professional communities. The Center will accept data from those researchers who are publishing fMRI imaging articles in peer-reviewed journals. The goal is to serve the entire fMRI community. | fmri, cognitive, cortex, mri, talairach, neuroimaging, cognitive neuroscience, brain, structure, function, magnetic resonance, intellect, image collection, data set |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Biositemaps is listed by: re3data.org has parent organization: University of California at Santa Barbara; California; USA |
NSF ; W. M. Keck Foundation ; NIMH ; Sun Microsystems Center of Excellence |
PMID:11545705 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-00025 | http://www.fmridc.org/ | SCR_007278 | The fMRI Data Center | 2026-09-05 06:26:09 | 16 | ||||
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NSR Physiome Project Resource Report Resource Website 1+ mentions |
NSR Physiome Project (RRID:SCR_007379) | NSR Physiome Project | data or information resource, portal, professional program, simulation software, software application, software resource, topical portal, training resource | Database of physiological, pharmacological, and pathological information on humans and other organisms and integration through computational modeling. Models include everything from diagrammatic schema, suggesting relationships among elements composing a system, to fully quantitative, computational models describing the behavior of physiological systems and an organism''s response to environmental change. Each mathematical model is an internally self-consistent summary of available information, and thereby defines a working hypothesis about how a system operates. Predictions from such models are subject to test, with new results leading to new models.BR /> A Tool developed for the NSR Physiome project is JSim, an open source, free software. JSim is a Java-based simulation system for building quantitative numeric models and analyzing them with respect to experimental reference data. JSim''s primary focus is in physiology and biomedicine, however its computational engine is quite general and applicable to a wide range of scientific domains. JSim models may intermix ODEs, PDEs, implicit equations, integrals, summations, discrete events and procedural code as appropriate. JSim''s model compiler can automatically insert conversion factors for compatible physical units as well as detect and reject unit unbalanced equations. JSim also imports the SBML and CellML model archival formats. All JSim models are open source. Goals of the Physiome Project: - To develop and database observations of physiological phenomenon and interpret these in terms of mechanism (a fundamentally reductionist goal). - To integrate experimental information into quantitative descriptions of the functioning of humans and other organisms (modern integrative biology glued together via modeling). - To disseminate experimental data and integrative models for teaching and research. - To foster collaboration amongst investigators worldwide, to speed up the discovery of how biological systems work. - To determine the most effective targets (molecules or systems) for therapy, either pharmaceutic or genomic. - To provide information for the design of tissue-engineered, biocompatible implants. | physiome, computational modeling, cell, organ, organism, human, model, physiological, pharmacological, pathological, model repository, sbml, cellml, biophysics, biochemistry, database, proteome, jsim simulation analysis system, data analysis tool, parameter optimization tool, integrating biological system | has parent organization: University of Washington; Seattle; USA | NSF BE08407; NHLBI T15 HL88516-01; NSF BES-0506477; NHLBI R01HL073598; NIBIB R01EB001973 |
nif-0000-00532 | SCR_007379 | National Simulation Resource Physiome Project | 2026-09-05 06:26:11 | 3 | |||||||
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Neural Decoding Toolbox Resource Report Resource Website 10+ mentions |
Neural Decoding Toolbox (RRID:SCR_009012) | NDT | data analysis software, data processing software, software application, software resource, software toolkit | Matlab toolbox that makes it easy to apply decoding analyses to neural data. The design of the toolbox revolves around four abstract object classes which enables users to interchange particular modules in order to try different analyses while keeping the rest of the processing stream intact. The toolbox is capable of analyzing data from many different types of recording modalities, and examples are given on how it can be used to decode basic visual information from neural spiking activity and how it can be used to examine how invariant the activity of a neural population is to stimulus transformations. | population decoding, neuron, analysis, matlab, data analysis, machine learning, multivariate pattern analysis, neural decoding | has parent organization: Massachusetts Institute of Technology; Massachusetts; USA; | DARPA ; IPTO ; DSO ; AFSOR-THRL ; Adobe Systems ; Honda Research Institute USA ; King Abdullah University of Science and Technology ; NEU ; Sony ; Eugene McDermott Foundation ; NSF 0640097; NSF 0827427; NSF FA8650-05-C-7262 |
PMID:23734125 | Acknowledgement requested, Account required | nlx_152729 | SCR_009012 | 2026-09-05 06:26:31 | 19 | ||||||
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UBERON Resource Report Resource Website 50+ mentions |
UBERON (RRID:SCR_010668) | UBERON | controlled vocabulary, data or information resource, ontology | An integrated cross-species anatomy ontology representing a variety of entities classified according to traditional anatomical criteria such as structure, function and developmental lineage. The ontology includes comprehensive relationships to taxon-specific anatomical ontologies, allowing integration of functional, phenotype and expression data. Uberon consists of over 10000 classes (March 2014) representing structures that are shared across a variety of metazoans. The majority of these classes are chordate specific, and there is large bias towards model organisms and human. | anatomy, comparative, evolution, organ system, anatomical structure, body part, organ, tissue, body, vertebrate, function, phenotype, expression, model organism, obo |
is used by: Neuroscience Information Framework is listed by: BioPortal is related to: Gene Ontology has parent organization: OBO |
ARRA ; NSF ; NHGRI 5R01HG004838; NHGRI P41HG002273; DOE DE-AC02-05CH11231; NCRR 1U24RR029825-01; NHGRI P41HG002273-09S1 |
PMID:22293552 | nlx_74404 | SCR_010668 | Uber anatomy ontology, Uber-anatomy ontology | 2026-09-05 06:26:44 | 62 | ||||||
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Brain Observatory Resource Report Resource Website |
Brain Observatory (RRID:SCR_010641) | Brain Observatory | biospecimen repository, data or information resource, material storage repository, portal, service resource, storage service resource, topical portal, video resource | Formerly a topical portal studying the brain which collected and imaged 1000 human brains, the Brain Observatory has partnered with the Institute for Brain and Society to build virtual laboratories that will feed directly into the database of images and knowledge created in the context of the Human Brain Library. The Brain Observatory will also host exhibits, conferences, and events aimed at promoting a heightened awareness of brain research and how its results can benefit personal brain fitness and mental health. | human, brain, visual cortex, neuroimaging | has parent organization: University of California San Diego School of Medicine; California; USA | Human immunodeficiency virus, NeuroAIDS, AIDS, Amnesia | NIMH ; NSF ; The Dana Foundation ; NEI |
Public | nlx_69083 | http://thebrainobservatory.ucsd.edu/ | SCR_010641 | The Brain Observatory | 2026-09-05 06:26:44 | 0 | ||||
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Databrary Resource Report Resource Website 10+ mentions |
Databrary (RRID:SCR_010471) | Databrary | data or information resource, data repository, database, portal, project portal, service resource, software repository, software resource, storage service resource | Project aims to promote data sharing, archiving, and reuse among researchers who study human development. Focuses on creating tools for scientists to store, manage, preserve, analyze and share video and related data. | behavior, development, data, sharing, audio track, video |
is listed by: re3data.org is related to: Datavyu is related to: Datavyu has parent organization: New York University; New York; USA has parent organization: Pennsylvania State University |
NICHD U01 HD076595; NSF BCS-1238599 |
Restricted | nlx_157733, r3d100011023 | https://github.com/databrary | SCR_010471 | 2026-09-05 06:26:42 | 17 |
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The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant U24DK097771.
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