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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Global Catalogue of Microorganisms Resource Report Resource Website 1+ mentions |
Global Catalogue of Microorganisms (RRID:SCR_016460) | GCM | data or information resource, database, organism-related portal, topical portal, portal | Database and information retrieval, analysis, and visualization system for microbial resources to help culture collections to manage, disseminate and share the information related to their holdings. Provides an interface for the scientific and industrial communities to access the microbial resource information. | research, deep, mining, genomic, data, retrival, analysis, visualisation, , microbial, resource, | the Strategic Priority Research Program of the Chinese Academy of Sciences ; the Bureau of International Cooperation of the Chinese Academy of Sciences ; the National Key Research Program of China ; the 13th Five-year Informatization Plan of the Chinese Academy of Sciences ; the National Science Foundation for Young Scientists of China |
PMID:29718202 | Free, Available to the scientific and industrial communities | r3d100010696 | https://doi.org/10.17616/R3J315 | SCR_016460 | GCM:Global Catalogue of Microorganisms | 2026-07-28 09:44:14 | 5 | |||||
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Distributed Annotation System Resource Report Resource Website 10+ mentions |
Distributed Annotation System (RRID:SCR_008427) | data or information resource, narrative resource, standard specification, software resource | The Distributed Annotation System (DAS) defines a communication protocol used to exchange annotations on genomic or protein sequences. It is motivated by the idea that such annotations should not be provided by single centralized databases, but should instead be spread over multiple sites. Data distribution, performed by DAS servers, is separated from visualization, which is done by DAS clients. The advantages of this system are that control over the data is retained by data providers, data is freed from the constraints of specific organisations and the normal issues of release cycles, API updates and data duplication are avoided. DAS is a client-server system in which a single client integrates information from multiple servers. It allows a single machine to gather up sequence annotation information from multiple distant web sites, collate the information, and display it to the user in a single view. Little coordination is needed among the various information providers. DAS is heavily used in the genome bioinformatics community. Over the last years we have also seen growing acceptance in the protein sequence and structure communities. A DAS-enabled website or application can aggregate complex and high-volume data from external providers in an efficient manner. For the biologist, this means the ability to plug in the latest data, possibly including a user''s own data. For the application developer, this means protection from data format changes and the ability to add new data with minimal development cost. Here are some examples of DAS-enabled applications or websites for end users: :- Dalliance Experimental Web/Javascript based Genome Viewer :- IGV Integrative Genome Viewer java based browser for many genomes :- Ensembl uses DAS to pull in genomic, gene and protein annotations. It also provides data via DAS. :- Gbrowse is a generic genome browser, and is both a consumer and provider of DAS. :- IGB is a desktop application for viewing genomic data. :- SPICE is an application for projecting protein annotations onto 3D structures. :- Dasty2 is a web-based viewer for protein annotations :- Jalview is a multiple alignment editor. :- PeppeR is a graphical viewer for 3D electron microscopy data. :- DASMI is an integration portal for protein interaction data. :- DASher is a Java-based viewer for protein annotations. :- EpiC presents structure-function summaries for antibody design. :- STRAP is a STRucture-based sequence Alignment Program. Hundreds of DAS servers are currently running worldwide, including those provided by the European Bioinformatics Institute, Ensembl, the Sanger Institute, UCSC, WormBase, FlyBase, TIGR, and UniProt. For a listing of all available DAS sources please visit the DasRegistry. Sponsors: The initial ideas for DAS were developed in conversations with LaDeana Hillier of the Washington University Genome Sequencing Center. | annotation, database, software, genomic, protein, sequence, visualization, data, client-server, integration, bioinformatics, genome, structure, data integration |
is listed by: 3DVC has parent organization: Uppsala University; Uppsala; Sweden |
Howard Hughes Medical Institute ; NHGRI 2-P01-HG00956 |
nif-0000-30177 | SCR_008427 | BioDAS | 2026-07-28 09:42:20 | 11 | ||||||||
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Agile Protein Interactomes DataServer Resource Report Resource Website 10+ mentions |
Agile Protein Interactomes DataServer (RRID:SCR_008871) | APID | service resource, data or information resource, data analysis service, database, data access protocol, software resource, production service resource, web service, analysis service resource | APID Interactomes (Agile Protein Interactomes DataServer) provides information on the protein interactomes of numerous organisms, based on the integration of known experimentally validated protein-protein physical interactions (PPIs). The interactome data includes a report on quality levels and coverage over the proteomes for each organism included. APID integrates PPIs from primary databases of molecular interactions (BIND, BioGRID, DIP, HPRD, IntAct, MINT) and also from experimentally resolved 3D structures (PDB) where more than two distinct proteins have been identified. This collection references protein interactors, through a UniProt identifier. | protein, protein interaction, interactions, ppi, interactomes, analysis, gene, ontology, functional, environment, data, network, graphic, visualize |
is listed by: Gene Ontology Tools is related to: PSICQUIC Registry is related to: Gene Ontology is related to: BIND is related to: Biological General Repository for Interaction Datasets (BioGRID) is related to: Database of Interacting Proteins (DIP) is related to: HPRD - Human Protein Reference Database is related to: IntAct is related to: MINT has parent organization: University of Salamanca; Salamanca; Spain |
Spanish Ministerio de Sanidad y Consumo ; Junta de Castilla y Leon |
PMID:27131791 PMID:30715274 |
Free for academic use | r3d100012339, nlx_149321 | https://doi.org/10.17616/R3407P, https://doi.org/10.17616/R3407P | SCR_008871 | Agile Protein Interactomes DataServer, APID, APID Interactomes, Agile Protein Interactomes DataServer (APID), APID (Agile Protein Interactomes DataServer) | 2026-07-28 09:42:14 | 14 | ||||
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GeneTraffic Resource Report Resource Website 10+ mentions |
GeneTraffic (RRID:SCR_008651) | software application, data analysis software, software resource, data management software, data processing software | GeneTraffic is a web-based microarray data analysis and management software developed by Iobion Informatics that allows users to log onto a server, upload their microarray data and perform analysis and project management remotely. GeneTraffic was made by Iobion Informatics (now under Stratagene) and can be accessed thorough Internet Explorer 6.0 or greater on Windows XP. | gene, data, management, microarray, software | nif-0000-33028 | SCR_008651 | 2026-07-28 09:42:22 | 24 | |||||||||||
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G-node portal electrophysiology data sharing Resource Report Resource Website 1+ mentions |
G-node portal electrophysiology data sharing (RRID:SCR_008893) | service resource, data or information resource, storage service resource, data repository | Platform for sharing data, with very large storage capability for electrophysiological data, EEG data is included. This service is provided for neuroscientists to facilitate data access, data storage, data analysis and data sharing. This service is developed and maintained by the German Node of the International Neuroinformatics Coordinating Facility. The global scale of neuroinformatics offers unprecedented opportunities for scientific collaborations between and among experimental and theoretical neuroscientists. To fully harvest these possibilities, coordinated activities are required to improve key ingredients of neuroscience: data access, data storage, and data analysis, together with supporting activities for teaching and training. Focusing on the development and free distribution of tools for handling and analyzing neurophysiological data, G-Node aims at addressing these aspects as part of the International Neuroinformatics Coordination Facility (INCF) and the German Bernstein Network for Computational Neuroscience (NNCN). G-Node also serves as an international forum for Computational Neuroscientists that are interested in sharing experimental data and tools for data analysis and modeling. G-Node is funded through the German Federal Ministry of Education and Research and hosted by Ludwig-Maximilians-Universit-Munchen. | neuroinformatics, electrophysiology, data, eeg, odml metadata language, api, neuroshare, data sharing, neurophysiology |
is listed by: 3DVC has parent organization: German Neuroinformatics Node (G-Node) |
BMBF | PMID:18653312 | nlx_151375 | https://portal.g-node.org/data | SCR_008893 | 2026-07-28 09:42:24 | 2 | |||||||
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iTools Resource Report Resource Website 10+ mentions |
iTools (RRID:SCR_009626) | iTools | service resource, data or information resource, data repository, database, data access protocol, software resource, web service, software repository, storage service resource | An infrastructure for managing of diverse computational biology resources - data, software tools and web-services. The iTools design, implementation and meta-data content reflect the broad NCBC needs and expertise (www.NCBCs.org). | computational neuroscience, data, experiment control, hardware, imaging genomics, information specification, java, loni pipeline, model, ontology, os independent, metadata |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: National Centers for Biomedical Computing has parent organization: Laboratory of Neuro Imaging |
NIH Roadmap for Medical Research ; NCRR U54-RR021813; NIDA U54-DA021519; NCI U54-CA121852; NHGRI U54-HG004028; NIGMS U54-GM072970; NIBIB U54-EB005149; NLM U54-LM008748 |
PMID:18509477 | GNU Lesser General Public License | nlx_155852 | http://www.nitrc.org/projects/itools, http://www.loni.usc.edu/research/software | http://itools.loni.ucla.edu/ | SCR_009626 | ITools Resourceome, NCBC iTools | 2026-07-28 09:42:28 | 45 | |||
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Databrary Resource Report Resource Website 10+ mentions |
Databrary (RRID:SCR_010471) | Databrary | service resource, data or information resource, data repository, project portal, database, software resource, software repository, storage service resource, portal | 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 |
NSF BCS-1238599; NICHD U01 HD076595 |
Restricted | nlx_157733, r3d100011023 | https://github.com/databrary | SCR_010471 | 2026-07-28 09:42:48 | 13 | ||||||
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Cytobank Resource Report Resource Website 1000+ mentions |
Cytobank (RRID:SCR_014043) | service resource, web application, software resource, training service resource | A cloud-based platform which allows users to analyze, visualize, and archive multiparamter cytometry data for single-cell biology. Multiple single-cell data sets can be analyzed and visualized simultaneously with a variety of graphics, inlcuding Sunburst, SPADE, and viSNE. Users can store and back up related data such as protocols, microscopy images, and presentations and collaborate and share analysis and data sets with other Cytobank users. Cytobank also provides a variety of services and training sessions to assist with experiment workflow. | single-cell biology, data, platform, cytometry, analyze, visualize, graphic, training service |
is related to: FLOWRepository is related to: FLOWRepository |
Free, Price varies for different options, Available to the research community, Available to industry | SCR_014043 | Cytobank Inc. | 2026-07-28 09:43:23 | 1218 | |||||||||
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ChEMBL Resource Report Resource Website 1000+ mentions |
ChEMBL (RRID:SCR_014042) | data or information resource, database | Collection of bioactive drug-like small molecules that contains 2D structures, calculated properties and abstracted bioactivities. Used for drug discovery and chemical biology research. Clinical progress of new compounds is continuously integrated into the database. | database, compound, data, bioassay, bioactive, molecule, drug, discovery |
is used by: GEROprotectors is used by: PubChem is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases |
Wellcome Trust ; EMBL Member States ; Medicines for Malaria Ventures ; EU Innovative Medicines Initiative ; GSK ; Syngenta ; Pfizer |
PMID:21948594 | Public, Free, Freely available, Acknowledgement requested | r3d100010539 | https://doi.org/10.17616/R3C320, https://doi.org/10.17616/R3C320, https://doi.org/10.17616/R3C320, https://doi.org/10.17616/R3C320, https://doi.org/10.17616/R3C320, https://doi.org/10.17616/R3C320, https://doi.org/10.17616/R3C320, https://doi.org/10.17616/R3C320, https://doi.org/10.17616/R3C320, https://doi.org/10.17616/R3C320, https://doi.org/10.17616/R3C320, https://doi.org/10.17616/R3C320, https://doi.org/10.17616/R3C320, https://doi.org/10.17616/R3C320, https://doi.org/10.17616/R3C320, https://doi.org/10.17616/R3C320, https://doi.org/10.17616/R3C320, https://doi.org/10.17616/R3C320, https://doi.org/10.17616/R3C320, https://doi.org/10.17616/R3C320, https://doi.org/10.17616/R3C320, https://doi.org/10.17616/R3C320 | SCR_014042 | ChEMBLdb, Chembl, ChEMBL Database | 2026-07-28 09:43:41 | 2433 | |||||
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ScanImage Resource Report Resource Website 500+ mentions |
ScanImage (RRID:SCR_014307) | software application, signal processing software, data processing software, software resource, data acquisition software | Open source software application for laser scanning microscopy, electrophysiology, laser scanning photostimulation, and other physiological methods focused on neurobiology. Used to control laser scanning microscopes without need for custom data acquisition hardware. Standard data acquisition boards are used to acquire data and control laser scanning. The tasks of signal integration and image processing are placed on the computer CPU. Multiple versions of ScanImage are available, each with their own features. | Laser, scanning, microscopy, electrophysiology, photostimulation, neurobiology, control, data, acquisition, BRAIN Initiative |
is recommended by: BRAIN Initiative has parent organization: Cold Spring Harbor Laboratory has parent organization: Northwestern University; Illinois; USA |
PMID:12801419 | Restricted | http://scanimage.vidriotechnologies.com/display/SIH/ScanImage+Home | SCR_014307 | Scan Image, ScanImage | 2026-07-28 09:43:27 | 810 | |||||||
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Image Reader LAS-1000 Resource Report Resource Website 10+ mentions |
Image Reader LAS-1000 (RRID:SCR_014585) | software application, software resource, data processing software, data acquisition software | A software which is used to control the LAS-1000plus luminescent image analyzer. This software adjusts the focus, exposure time, sensitivity, and cooling temperature, and will record the data after the sample is scanned. | image analyzer, exposure, focus, sensitivity, cooling temperature, data, software | Commercial, Paired with a scanning system | SCR_014585 | 2026-07-28 09:43:32 | 45 | |||||||||||
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Fred Hutchinson Cancer Research Center Co-operative Center for Excellence in Hematology Bioinformatics Resource Resource Report Resource Website |
Fred Hutchinson Cancer Research Center Co-operative Center for Excellence in Hematology Bioinformatics Resource (RRID:SCR_015324) | service resource, data or information resource, production service resource, access service resource, analysis service resource, core facility | THIS RESOURCE IS NO LONGER IN SERVICE.Documented on July 27,2022. Core provides bioinformatics specialists available to assist researchers with processing, exploring, and understanding genomics data. | hematology, bioinformatics, explore, understand, genomic, data, cancer |
is listed by: NIDDK Information Network (dkNET) has parent organization: Fred Hutchinson Cancer Center |
Cancer | NIDDK P30 DK056465 | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_015907 | SCR_015324 | Hutch, Bioinformatic Resource, Fred, Co-operative Center for Excellence in Hematology, Cancer Center | 2026-07-28 09:43:48 | 0 | ||||||
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Calliope calcium imaging processing package Resource Report Resource Website 1+ mentions |
Calliope calcium imaging processing package (RRID:SCR_021213) | software application, software resource, data processing software, image processing software, software toolkit | Software package for image processing for MATLAB. Used for processing of calcium imaging data. | Image processing, data, calcium imaging data, calcium imaging |
is used by: IRIS two photon acquisition package is related to: MATLAB |
Swiss National Science Foundation ; Novartis Research Foundation |
DOI:10.1016/j.cell.2017.05.023 | Free, Available for download, Freely available | SCR_021213 | 2026-07-28 09:45:04 | 1 | ||||||||
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Cumulus Resource Report Resource Website 1+ mentions |
Cumulus (RRID:SCR_021644) | software application, software resource, data analysis software, data processing software | Software tool as cloud based single cell genomics and spatial transcriptomics data analysis framework that is scalable to massive amounts of data and able to process variety of data types. Consists of cloud analysis workflow, Python analysis package and visualization application. Supports analysis of single-cell RNA-seq, CITE-seq, Perturb-seq, single-cell ATAC-seq, single-cell immune repertoire and spatial transcriptomics data. | Single cell genomics, spatial transcriptomics, single-cell RNA-seq, CITE-seq, Perturb-seq, single-cell ATAC-seq, single-cell immune repertoire, data |
uses: Pegasus uses: Cirrocumulus uses: Pegasus-fus is listed by: Terra is related to: BICCN has parent organization: Broad Institute |
Klarman Cell Observatory ; Manton Foundation ; HHMI ; Ludwig Center at MIT ; Leidos Biomedical Research ; Frederick National Laboratory for Cancer Research ; NCI |
DOI:10.1038/s41592-020-0905-x | Free, Available for download, Freely available | https://app.terra.bio/#workspaces/kco-tech/Cumulus, https://github.com/klarman-cell-observatory/cumulus/blob/91336094646217564a4f8e7b31c03c3c6bf2e84b/docs/index.rst | SCR_021644 | 2026-07-28 09:45:28 | 2 | |||||||
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iMaps Resource Report Resource Website 1+ mentions |
iMaps (RRID:SCR_016705) | service resource, data or information resource, data analysis service, production service resource, analysis service resource, portal | Web server for analysis of high-resolution sequencing data. It can be used with all variants of CLIP,as well as with methods that interrogate RNA or DNA methylation, RNA processing, RNA structure or protein-DNA interactions. | Genialis, analysis, high-resolution, sequencing, data, RNA, DNA, protein, interaction |
is related to: iCount is related to: iCount |
Free, Registration required | SCR_016705 | 2026-07-28 09:44:25 | 9 | ||||||||||
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Pavian Resource Report Resource Website 10+ mentions |
Pavian (RRID:SCR_016679) | service resource, web application, data analysis service, software resource, production service resource, analysis service resource | Software R package for interactive analysis of metagenomics classification results with a special focus on infectious disease diagnosis. Used for analyzing and visualization of metagenomics classification results from classifiers such as Kraken, Centrifuge and MetaPhlAn. Provides an alignment viewer for validation of matches to a particular genome. | interactive, analysis, metagenomics, classification, result, infectious, disease, diagnosis, data, visualization, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: Centrifuge Classifier |
NHGRI R01 HG006677; NIGMS R01 GM083873; U. S. Army Research Office W911NF1410490 |
DOI:10.1101/084715 | Free, Freely available | biotools:pavian | https://fbreitwieser.shinyapps.io/pavian/, https://bio.tools/pavian | SCR_016679 | 2026-07-28 09:44:23 | 22 | ||||||
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iCount Resource Report Resource Website 10+ mentions |
iCount (RRID:SCR_016712) | software application, software resource, data analysis software, data processing software | Software Python package for protein-RNA interaction analysis. Used for analysis of protein-RNA interactions with iCLIP sequencing data and RNA maps. | protein, RNA, interaction, analysis, iCLIP, sequencing, data, map |
is related to: iMaps is related to: iMaps |
Free, Available for download, Freely available, Tutorial available | https://icount.readthedocs.io/en/latest/ref_python.html, https://hub.docker.com/r/tomazc/icount/ | SCR_016712 | 2026-07-28 09:44:25 | 35 | |||||||||
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NeuroAnatomy Toolbox Resource Report Resource Website 1+ mentions |
NeuroAnatomy Toolbox (RRID:SCR_016716) | nat, NAT | software application, data analysis software, software resource, data processing software, data visualization software, image analysis software | Software R package for the (3D) visualisation and analysis of biological image data, especially tracings of single neurons in the context of 3D brain structures. | biological, image, data, visualization, analysis, tracing, single, neuron, 3D, structure, brain |
is listed by: OMICtools is listed by: CRAN is related to: R Project for Statistical Computing is related to: elmr has parent organization: University of Cambridge; Cambridge; United Kingdom |
DOI:10.5281/zenodo.10171 | Free, Available for download, Freely available | https://cran.r-project.org/web/packages/nat/index.html, | SCR_016716 | NeuroAnatomy Toolbox, neuroanatomy toolbox, Neuro Anatomy Toolbox, neuro anatomy toolbox | 2026-07-28 09:44:25 | 5 | ||||||
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BD FACS Sortware sorter software Resource Report Resource Website 1+ mentions |
BD FACS Sortware sorter software (RRID:SCR_016722) | BD FACS Sortware software | software application, data analysis software, software resource, data processing software, data visualization software | Software to provide control of the cell sorter from configuration and compensation setup to acquisition, sorting, and analysis, making it easy to customize the instrument for specific applications. BD implements software solutions that integrate data, devices and systems. | control, cell, sorter, acquisition, analysis, integrate, data, instrument, system, Becton Dickinson and Company | Commercially available | SCR_016722 | , BD FACS Sortware, Becton Dickinson FACS Sortware, BD FACS Sortware software | 2026-07-28 09:44:23 | 5 | |||||||||
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VectorMap Resource Report Resource Website 10+ mentions |
VectorMap (RRID:SCR_016721) | service resource, data or information resource, data repository, database, data access protocol, software resource, web service, storage service resource, portal | Collection of disease maps, and mapped collection data and distribution models for arthropod disease vector species, including mosquitoes, ticks, sand flies, mites, and fleas, as well as the hosts/reservoirs of vector-borne disease pathogens. VectorMap is modeled after MosquitoMap. | disease, map, collection, data, distribution, model, arthropod, disease, vector, species | has parent organization: Walter Reed Biosystematics Unit | arthropod disease | US Department of Defense Global Emerging Infections Surveillance and Response System ; Division of the Armed Forces Health Surveillance Center ; Global Biodiversity Information System |
Public, Free, Available for download, Freely available, Acknowledgement requested, Tutorial available | SCR_016721 | 2026-07-28 09:44:25 | 22 |
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