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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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GitHub Resource Report Resource Website 1000+ mentions |
GitHub (RRID:SCR_002630) | GitHub | software resource, software repository, software application, mobile app, service resource, commercial organization | A web-based hosting service for software development projects that use the Git revision control system offering powerful collaboration, code review, and code management. It offers both paid plans for private repositories, and free accounts for open source projects. Large or small, every repository comes with the same powerful tools. These tools are open to the community for public projects and secure for private projects. Features include: * Integrated issue tracking * Collaborative code review * Easily manage teams within organizations * Text entry with understated power * A growing list of programming languages and data formats * On the desktop and in your pocket - Android app and mobile web views let you keep track of your projects on the go. | source code, database, java, php, python, objective-c, c++, c, c#, perl, issue, computer science, FASEB list |
is used by: Observational Medical Outcomes Partnership is used by: NIH Heal Project lists: Digital Asset Management System lists: IBMA toolbox lists: NeuroSynth lists: MIAPA lists: FACS lists: RSEM lists: flowPeaks lists: BRAINSCut lists: Mspire-Simulator is listed by: FORCE11 is listed by: re3data.org is related to: Karma is related to: ImpactStory hosts: SciUnit hosts: FlashX hosts: BioBlend Library hosts: Vision Egg hosts: Cufflinks hosts: MetAMOS hosts: ProtVista hosts: Big Data Bag hosts: FUSIM hosts: GDC hosts: ProtTest hosts: State Space Models hosts: OpenWorm hosts: Zero Mode Waveguide Imaging and Analysis package tools hosts: Taxonomer hosts: Eelbrain hosts: N2A hosts: Pilon hosts: MicroDraw hosts: BrainBox hosts: Stanford CoreNLP hosts: AnaMorph hosts: wMICA hosts: SEER hosts: phytools hosts: PhenVar hosts: JuncBASE hosts: HISAT2 hosts: NeuroManager |
Free, Available for download, Freely available | nlx_156051 | http://www.force11.org/node/4710 | SCR_002630 | 2026-08-04 09:40:42 | 3528 | |||||||
|
Karma Resource Report Resource Website 50+ mentions |
Karma (RRID:SCR_003732) | Karma | software application, software resource, data management software | An information integration software tool that enables users to integrate data from a variety of data sources including databases, spreadsheets, delimited text files, XML, JSON, KML and Web APIs. Users integrate information by modeling it according to an ontology of their choice using a graphical user interface that automates much of the process. Karma learns to recognize the mapping of data to ontology classes and then uses the ontology to propose a model that ties together these classes. Users then interact with the system to adjust the automatically generated model. During this process, users can transform the data as needed to normalize data expressed in different formats and to restructure it. Once the model is complete, users can publish the integrated data as RDF or store it in a database. | integration, FASEB list |
is related to: GitHub has parent organization: University of Southern California; Los Angeles; USA |
Air Force Research Laboratory FA8750-14-C-0240; NCRR 1 U24 RR025736-01; NCRR 1 UL1 RR031986-01; NSF IIS-1117913; NSF CMMI-0753124 |
PMID:15215426 | Apache License, v2 | nlx_157923 | https://github.com/InformationIntegrationGroup/Web-Karma | SCR_003732 | Karma A Data Integration Tool, Karma - A Data Integration Tool | 2026-08-04 09:40:58 | 83 | ||||
|
ImpactStory Resource Report Resource Website 1+ mentions |
ImpactStory (RRID:SCR_002632) | software resource, source code, production service resource, service resource | A web application which provides altmetrics to help researchers measure and share the impacts of their research outputs. After making a profile, scientists can track which of their publications are most popular through number of citations, frequency of PDF downloads, etc. Information from research outputs such as journal articles, blog posts, datasets, and software contribute to a user's impact, which is viewable in their profile. | altmetrics, metric, citeulike, crossref, scienceseeker, scopus, slideshare, topsy, twitter, vimeo, wordpress.com, plos, youtube |
is used by: Publons is listed by: FORCE11 is listed by: Connected Researchers is listed by: PLOS Article-Level Metrics is related to: PubMed is related to: GitHub is related to: FigShare is related to: Dryad Digital Repository is related to: Wikipedia is related to: Mendeley |
Alfred P. Sloan Foundation ; NSF ; Open Society Foundation |
Free, Freely available | nlx_156056 | SCR_002632 | ImpactStory | 2026-08-04 09:40:42 | 8 | |||||||
|
IBMA toolbox Resource Report Resource Website |
IBMA toolbox (RRID:SCR_003772) | software resource | Image-Based Meta-Analysis toolbox for SPM. Implementation of z-based statistics: Fisher's, Stouffer's. |
is listed by: GitHub is related to: SPM has parent organization: University of Warwick; Coventry; United Kingdom |
Wellcome Trust | nlx_158042 | SCR_003772 | 2026-08-01 12:02:25 | 0 | ||||||||||
|
SciUnit Resource Report Resource Website 1+ mentions |
SciUnit (RRID:SCR_014528) | software resource | A test-driven framework for formally validating scientific models against data. | python, framework, validation, scientific method |
is used by: NeuronUnit is related to: NetworkUnit is hosted by: GitHub |
SCR_014528 | 2026-08-01 12:05:13 | 6 | |||||||||||
|
Big Data Bag Resource Report Resource Website 1+ mentions |
Big Data Bag (RRID:SCR_014624) | software resource | Software package with tools which assemble, identify, and provide access to subsets of data in a large and complex data collection workflow. The software utilities work primarily with BagIt packages that conform the BDDS Bagit and BDDS Bagit/RO profiles. JSON-LD is used to provide a standard way for linking metadata with existing ontologies and vocabularies. | software, big data, data collection workflow, metadata | is hosted by: GitHub | Source code available, Beta | https://github.com/ini-bdds/bdbag | SCR_014624 | 2026-08-01 12:05:05 | 1 | |||||||||
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Observational Medical Outcomes Partnership Resource Report Resource Website 1+ mentions |
Observational Medical Outcomes Partnership (RRID:SCR_003724) | OMOP | portal, organization portal, data or information resource, consortium | Initiative to improve the safety of drugs on the market that utilized information drawn from patient medical record databases and health insurance claims to develop and test methods to detect and evaluate drug safety issues over time. The OMOP pilot project focused on the following objectives: * Defining and evaluating analytical methods that can be used to identify associations between drugs and health-related conditions. * Developing tools for organizing access to and evaluating the usefulness of multiple observational datasets. * Study how information from analyses of observational data can be used to inform ongoing pharmacovigilence efforts. The software tools - packaged as the OMOP Web RL Platform was developed and made available to the public, https://github.com/OMOP . In addition to these data tools, this collaborative research effort discovered methods for using data to reliably identify correlations between individual medical interventions and specific health outcomes. These insights are being used to help inform the FDA Sentinel Initiative as part of the Innovation in Medical Evidence Development and Surveillance (IMEDS) program. The achievements of the program include: * Establishment of a common data model and creation of data characterization tools, and vocabulary mappings * Implementation of Health Outcome of Interest definitions, including a program to implement these definitions as part of the Regularized Identification of Cohorts (RICO) * Release of 14 analysis methods to evaluate the performance of methods and data in identifying drug safety issues | consortium, drug, drug safety, observational data, claim, electronic medical record, surveillance, prescription medication, health outcome, medical intervention, drug development, safety, common data model, vocabulary |
uses: GitHub is listed by: Consortia-pedia has parent organization: Foundation for the National Institutes of Health |
Biopharmaceutical members | nlx_157903 | SCR_003724 | Observational Medical Outcomes Partnership (OMOP) | 2026-08-04 09:40:58 | 5 | |||||||
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FORCE11 Resource Report Resource Website 10+ mentions |
FORCE11 (RRID:SCR_005334) | FORCE11 | portal, blog, knowledge environment, community building portal, narrative resource, data or information resource | A collaboration which works to transform scholarly communications through advanced use of computers and the Web. FORCE11 advocates the digital publishing of papers in order to enable more effective scholarly communication. The virtual community also advocates the publication of software tools and research communication by means of social media channels. As such, FORCE11 provides access to information and tools for the wider scientific community. | scholarly communication, scholarship, dissemination, data sharing, knowledge, information technology, semantics, digital publishing, information gathering, research communication, e-scholarship, digital object, scientific communication |
lists: Scholarly Ontologies Project lists: Academia.edu lists: StratML lists: Evernote lists: NPG publishing format lists: Fiduswriter lists: Altmetric Bookmarklet lists: Altmetric Explorer lists: Epistemio lists: Hypothes.is lists: Bio-Formats lists: iSpyBio.com lists: BioLexicon lists: Craig Mod lists: KLEIO lists: aTag Generator lists: Knowledge Engineering from Experimental Design lists: Utopia Docs lists: Zebrafish - SCORE Imaging: Specimen in a Corrected Optical Rotational Enclosure lists: Semantic Measures Library lists: Open Education Database lists: Brainspell lists: IPython lists: Adobe FormsCentral lists: Altmetric API lists: myExperiment lists: ISA Infrastructure for Managing Experimental Metadata lists: Minimum Information for Biological and Biomedical Investigations lists: A modular structure for scientific articles in an electronic environment lists: Liquid Publications: Scientific Publications meet the Web lists: AQnowledge Bookmarklet lists: Authorea lists: Bamboo DiRT lists: Altmetric Badges lists: ESIP Data Management Short Course for Scientists lists: Etherpad lists: Commons In A Box lists: CKAN lists: DMPTool lists: eScholarship lists: Git2PROV lists: OMERO lists: GitHub lists: GROTOAP lists: ImpactStory lists: JCB DataViewer lists: Memento lists: OME-TIFF Format lists: OpenDOAR lists: Open Journal Systems lists: Paper Rejection Repository lists: PLoS Impact Explorer lists: RDFaCE lists: Scholarly Open Access lists: ShareLaTeX lists: Mendeley lists: W3C Provenance Incubator Group Wiki lists: A.nnotate lists: Annotation Ontology lists: Support-of-PDF-annotations lists: Neuroscience Information Framework lists: AlzSWAN Knowledge Base lists: ResearchCompendia lists: resExomeDB lists: SobekCM lists: W3C Open Annotation Community Group lists: Webmaker lists: Wikispaces lists: Mobile Assay lists: WorkingWiki lists: Overleaf lists: Xournal lists: Citation Style Language lists: EnablingOpenScholarship lists: JournalGuide lists: Mindtouch DekiWiki lists: Knowledge Blog lists: DataCite lists: FAIRsharing lists: FigShare lists: CiTO - the Citation Typing Ontology lists: DOAJ - Directory of Open Access Journals lists: Code4Lib Journal WordPress Customizations lists: U-Compare lists: SciCrunch Registry lists: Google Docs lists: CSIBS lists: Europe PubMed Central lists: ORNL DAAC Data Product Citation Policy lists: Pensoft lists: OpenCalais lists: Universal Numerical Fingerprint lists: FAIRSharing Catalogue of Standards lists: Nanopub.org lists: JISC Open Citations lists: W3C Provenance Working Group lists: Workflow4Ever lists: Scholarly Electronic Publishing Bibliography lists: ROARMAP: Registry of Open Access Repositories Mandatory Archiving Policies lists: ROAR lists: total impact.org lists: Publish or perish lists: Scalar lists: PDFX lists: lapdftext lists: Cohere lists: Data Citation Awareness lists: DataCite Ontology lists: Semantic MediaWiki lists: Rubriq lists: VisTrails lists: RSC Prospect lists: HyBrow (Hypothesis Browser) lists: Biotea lists: crowdLabs lists: Argumentative Zoning: Information Extraction from Scientific Articles lists: Synapse lists: BioCreative lists: EZID lists: ResearchGate lists: F1000: Faculty of 1000 Post-Publication Peer Review lists: Acumen Consortium lists: DOI lists: GREC Corpus lists: National Centre for Text Mining lists: SPAR - Semantic Publishing and Referencing Ontologies lists: re3data.org lists: DataUp lists: Open Archives Initiative - Object Reuse and Exchange Initiative lists: Sapienta lists: OBO lists: GENIA Project: Mining literature for knowledge in molecular biology lists: ORCID - Open Researcher and Contributor ID lists: Wikibooks lists: CERMINE lists: CiteAb lists: iAnnotate lists: Eagle I lists: AcroMine lists: FACTA+. lists: Open Provenance Model lists: RightField lists: SEEK lists: BioPortal lists: Reflect lists: Ontology Development and Information Extraction lists: PubMed lists: Open PHACTS lists: NIFSTD lists: Open Provenance Model Vocabulary lists: MEDIE lists: Ontology for Biomedical Investigations lists: Antibody Registry lists: Semantic Web Applications in Neuromedicine (SWAN) Ontology is related to: ShareLaTeX is related to: ResearchCompendia is related to: Overleaf has parent organization: University of California at San Diego; California; USA |
Gordon and Betty Moore Foundation | Free, Public, The community can contribute to this resource, Acknowledgement requested | nlx_149434 | SCR_005334 | FORCE11 - the Future of Research Communications and e-Scholarship, Force 11 | 2026-08-04 09:41:20 | 13 | ||||||
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State Space Models Resource Report Resource Website 1+ mentions |
State Space Models (RRID:SCR_014647) | SSM | software resource, source code | An open source library built to reduce technical friction and help modelers share their work. Models within SSM can be used for inference of time-series analysis. | inference, model, model library, open source library, time series analysis | is hosted by: GitHub | Source code available, Free | SCR_014647 | S|S|M, State Space Models (SSM) | 2026-08-03 09:35:47 | 1 | ||||||||
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AnaMorph Resource Report Resource Website 1+ mentions |
AnaMorph (RRID:SCR_015012) | software resource, source code | Framework for creating 3D neuronal morphologies from point/diameter descriptions. | 3d morphology, neuronal morphology, morphology software, surface mesh | is hosted by: GitHub | Available for download | SCR_015012 | 2026-08-03 09:35:58 | 2 | ||||||||||
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Digital Asset Management System Resource Report Resource Website |
Digital Asset Management System (RRID:SCR_000491) | DAMS | image repository, storage service resource, software resource, software repository, data repository, service resource | A digital repository designed to store and manage digital assets of UC San Diego. The flexible architecture can accept a variety of data formats, schemas and web services when ingesting digital assets. It stores digital content files and allows for the creation, indexing and searching of associated metadata to locate and retrieve the content files. Content can be composed of files in any format, including text, sound, video, and images. The DAMS is also designed to facilitate the transfer and submission of the Library's digital assets to Chronopolis and the California Digital Library's Merritt, and can easily be extended to serve other purposes. Additionally, the DAMS is able to export data in many formats, including METS, HTML, OAI, RSS, CSV. Future plans include linking data sets with other universities and organizations. For more information about the DAMS, including the data model and technical diagram, see Github, https://github.com/ucsdlib: * DAMS Manual, https://github.com/ucsdlib/dams/wiki/DAMS-Manual * DAMS Hydra Head, https://github.com/ucsdlib/damspas * DAMS REST API, https://github.com/ucsdlib/dams/wiki/REST-API * DAMS Ontology, https://github.com/ucsdlib/dams/tree/master/ontology Additional information on Hydra is available at Project Hydra and Duraspace. | digital repository, store and manage digital assets of UC San Diego, digital repository designed to store and manage digital assets, |
is listed by: GitHub is related to: UC3 Merritt is related to: chronopolis has parent organization: University of California at San Diego; California; USA |
Restricted | nlx_158282 | https://github.com/ucsdlib/dams | http://libraries.ucsd.edu/about/digital-library/dams.html | SCR_000491 | UC San Diego Library DAMS repository, UC San Diego Library Digital Asset Management System | 2026-08-04 09:40:08 | 0 | |||||
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FUSIM Resource Report Resource Website |
FUSIM (RRID:SCR_001015) | FUSIM | simulation software, software application, software resource | A software tool for simulating fusion transcripts from a reference genome. | fusion, simulator, simulation software, fusion transcript, genomics |
is listed by: OMICtools is hosted by: GitHub |
PMID:23323884 | Free, Available for download, Freely available | OMICS_01366 | SCR_001015 | FUsion SIMulator, Fusion Simulator | 2026-08-04 09:40:16 | 0 | ||||||
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BRAINSCut Resource Report Resource Website |
BRAINSCut (RRID:SCR_000861) | BRAINSCut | segmentation software, data processing software, software resource, software application, image analysis software | A software package for segmentation of structures using automated neual networks. This is the reference implementation using NAMIC software development best practices and the Insight Toolkit of the paper Registration and machine learning-based automated segmentation of subcortical and cerebellar brain structures. (PMID: 17904870). The program uses the Slicer3 execution model framework to define the command line arguments and can be fully integrated with Slicer3 using the module discovery capabilities of Slicer3. | magnetic resonance |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: GitHub is listed by: INCF Software Center has parent organization: BRAINSTools |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_155699 | SCR_000861 | 2026-08-04 09:40:15 | 0 | ||||||||
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OpenWorm Resource Report Resource Website 10+ mentions |
OpenWorm (RRID:SCR_014650) | web application, software application, software resource, simulation software | 3D web browser that allows users to simulate and dissect virtual C. elegans. Users can explore the anatomy of a virtual, 3D worm by zooming in and out, rotating the model, and viewing the worm's different layers. NeuroML format and connector are used to enhance the simulation, and supporting programs and code are available for coders. | simulation, model, web application, web browser, c elegans, nematode, worm, roundworm, open source, 3d, dissect, anatomy, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: WormBase is hosted by: GitHub |
PMID:25404913 DOI:10.3389/fncom.2014.00137 |
Open source, Code is available on GitHub, Available on the App Store | SCR_014984, biotools:OpenWorm | https://bio.tools/OpenWorm | SCR_014650 | OpenWorm Browser, Open Worm | 2026-08-04 09:43:30 | 21 | ||||||
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Taxonomer Resource Report Resource Website 1+ mentions |
Taxonomer (RRID:SCR_014655) | data processing software, source code, data analysis software, software resource, software application, web application | Genome sequence classification tool based on kmer. The code allows users to build nucleotide databases and protein databases, classify reads, construct binner databases, and create taxonomic relationship files. The website provides information on how to perform these actions with code, though users can access a web-based Taxonomer if they need/want to. | metagenomics toolkit, metagenomics analysis, analysis tool, microorganism detection, sequencing, genome sequence classification, kmer, nucleotide database, protein database, read classification, binner database, taxonomic relationship, source code, web application | is hosted by: GitHub | Free, Available for download, Written in c and python | http://taxonomer.iobio.io | SCR_014655 | 2026-08-04 09:43:30 | 6 | |||||||||
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ProtVista Resource Report Resource Website 1+ mentions |
ProtVista (RRID:SCR_014623) | data processing software, source code, data analysis software, software resource, sequence analysis software, software application | A BioJS viewer for protein sequence features. | protein sequence, viewer, sequence analysis software, biojs | is hosted by: GitHub | Available for download | SCR_014623 | 2026-08-04 09:43:29 | 4 | ||||||||||
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ProtTest Resource Report Resource Website 1000+ mentions |
ProtTest (RRID:SCR_014628) | data processing software, data analysis software, software resource, software application, web application | Web-based software used for the selection of best-fit models of protein evolution., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | bioinformatics, model, best fit model, protein evolution, amino acid replacement, server, bio.tools |
uses: PhyML is listed by: Debian is listed by: bio.tools is listed by: OMICtools is listed by: SoftCite is hosted by: GitHub |
PMID:15647292 DOI:10.1093/bioinformatics/btr088 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_11547, biotools:prottest | https://github.com/ddarriba/prottest3, https://bio.tools/prottest, https://sources.debian.org/src/prottest/ | SCR_014628 | 2026-08-04 09:43:29 | 1981 | |||||||
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Stanford CoreNLP Resource Report Resource Website 1+ mentions |
Stanford CoreNLP (RRID:SCR_014778) | data processing software, software application, software resource, data analysis software | A Java suite of core natural language analysis tools. It can take raw human language text input and give multiple outputs, including the base forms of words, their parts of speech, and marked up structure of sentences in terms of phrases or word dependencies. Supported languages include English, Arabic, Chinese, French, German, and Spanish. | java, language analysis, natural language, human language |
is used by: Biocemid is used by: Limitation-Recognizer has parent organization: Stanford University; Stanford; California works with: word2vec is hosted by: GitHub |
Acknowledgement requested, Available for download | https://github.com/stanfordnlp/CoreNLP http://search.maven.org/#search%7Cga%7C1%7Ca%3A%22stanford-corenlp%22 | SCR_014778 | 2026-08-04 09:43:32 | 6 | |||||||||
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MicroDraw Resource Report Resource Website 1+ mentions |
MicroDraw (RRID:SCR_014748) | collaboration tool, software resource, web application, atlas, data or information resource | Web application used to visualise and annotate collaboratively high resolution histology data. In short, it uses public ontologies to create collaborative, community-curated atlases. Annotations are vectorial, and users can use boolean operations to combine, subtract and split regions. | web application, annotate, atlas, ontology, high resolution, histology, histology data |
uses: NeuroLex is hosted by: GitHub |
Available to the research community | https://github.com/neuroanatomy/microdraw | SCR_014748 | 2026-08-04 09:43:31 | 5 | |||||||||
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NeuroManager Resource Report Resource Website 1+ mentions |
NeuroManager (RRID:SCR_015559) | simulation software, software application, software resource, source code | Simulation submission manager for computational neuroscience. It manages simulation processing, file transfers, and job submission for a heterogeneous mixture of standalone server, cluster, and cloud servers. | computational neuroscience, simulation manager, simulation management |
has parent organization: University of Texas at San Antonio; Texas; USA is hosted by: GitHub |
NSF EF 1137897; NSF DBI 1451032; NIMHD G12MD007591; Texas Advanced Computing Center |
PMID:26528175 | Open source | http://journal.frontiersin.org/article/10.3389/fninf.2015.00024/abstract | SCR_015559 | 2026-08-04 09:43:40 | 1 |
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