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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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NVM Resource Report Resource Website |
NVM (RRID:SCR_000600) | data visualization software, software resource, software application, data processing software | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 6, 2023. Software tool for quantitative neuroanatomical measurements in volumetric image data. Used to draw regions of interest for subsequent fMRI analysis. | quantitative, neuroanatomical, measurement, volumetric, image, data, draw, region, fMRI, analysis, morphology, |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Neuromorphometrics |
NIMH R43 MH60507; NIMH R44 MH60507; NIMH R43 MH084358 |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_149080 | http://www.nitrc.org/projects/nvm | SCR_000600 | 2026-07-28 09:40:01 | 0 | |||||||
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University of Colorado at Boulder Labs and Facilities Resource Report Resource Website |
University of Colorado at Boulder Labs and Facilities (RRID:SCR_001054) | service resource, material service resource, data or information resource, production service resource, analysis service resource, portal | A portal for the core labs and facilities at the University of Colorado at Boulder. | electron microprobe, electron microscope, imaging, analysis, portal, labs, facilities, production service resource |
is listed by: ScienceExchange is related to: CU Boulder Electron Microprobe Laboratory is related to: CU Boulder Institute for Behavioral Genetics is related to: Colorado University Boulder BioFrontiers Advanced Light Microscopy Core Facility has parent organization: University of Colorado Boulder; Colorado; USA |
THIS RESOURCE IS NO LONGER IN SERVICE | SciEx_850 | SCR_001054 | CU Boulder Labs and Facilities, CU Boulder Labs & Facilities, University of Colorado at Boulder Labs & Facilities | 2026-07-28 09:40:11 | 0 | ||||||||
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EZ BioResearch Resource Report Resource Website 1+ mentions |
EZ BioResearch (RRID:SCR_001050) | material service resource, service resource, production service resource, reagent manufacture | A biotechnology company that develops, manufactures and distributes molecular biology tool kits and laboratory consumable products. Services include DNA and RNA microarrays, PCR and transgenic genotyping, and DNA/RNA analysis and quality control. | molecular biology, tool kit, dna, rna, microarray, pcr, transgenic, genotyping, analysis, biotechnology | is listed by: ScienceExchange | Commercial | SciEx_571 | http://www.scienceexchange.com/facilities/ez-bioresearch | SCR_001050 | EZ BioResearch LLC | 2026-07-28 09:40:10 | 3 | |||||||
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Diffusion MRI of Traumatic Brain Injury Resource Report Resource Website |
Diffusion MRI of Traumatic Brain Injury (RRID:SCR_001637) | Diffusion MRI of TBI | data or information resource, topical portal, portal | Project to define a roadmap for diffusion MR imaging of traumatic brain imaging and design an infrastructure to implement the recommendations and tested to ensure feasibility, disseminate results, and facilitate deployment and adoption. The research roadmap and infrastructure development will concentrate on three areas: 1) standardization of diffusion imaging methodology, 2) trial design and patient selection for acute or chronic therapy, and 3) development of multi-center collaborations and repositories for evaluating whether advanced diffusion imaging does improve decision making and TBI patients' outcomes. # DTI MRI reproducability: One of the major areas of investigation in this project is to study the reproducibility of data acquisition and image analysis algorithms. Understanding reproducibility defines a base level of deviation from which scans can be analyzed with statistical significance. As part of this work they are also developing site qualification criteria with the intention of setting limits on the MR system minimal performance for acceptable use in TBI evaluation. # Infrastructure for image storage, analysis and visualization: There is a continuing need to refine and extend software methods for diffusion MRI data analysis and visualization. Not only to translate tools into clinical practice, but also to encourage continuation of the innovation and development of new tools and techniques. To deliver upon these goals they are designing and implementing a storage and computational infrastructure to provide access to shared datasets and intuitive interfaces for analysis and visualization through a variety of tools. A strong emphasis has been placed on providing secure data sharing and the ability to add community defined common data elements. The infrastructure is built upon a Software-as-a-Service model, in which tools are hosted and managed remotely allowing users access through well-defined interfaces. The final service will also facilitate composition or orchestration of workflows composed of different analysis and processing tasks (for example using LONI or XNAT pipelines) with the ultimate goal of providing automated no-click evaluations of diffusion MRI data. # Tool development: The final aspect of this project aims to facilitate and encourage tool development and contribution. By providing access to open datasets, they will create a platform on which tool developers can compare and improve and their tools. When tools are sufficiently mature they can be exposed in the infrastructure mentioned above and used by researchers and other developers. | diffusion tensor imaging, diffusion mri, standard specification, image repository, analysis, visualization, data sharing, common data element, service resource, data set |
is related to: vIST/e is related to: Camino is related to: DTI and Fibertools Software Package is related to: Diffusion Tensor Imaging ToolKit is related to: ExploreDTI is related to: Connectome Mapping Toolkit is related to: TORTOISE is related to: MITK Diffusion is related to: MRtrix is related to: MIPAV: Medical Image Processing and Visualization is related to: DTI Blog is related to: FSL has parent organization: University of Chicago; Illinois; USA |
Traumatic brain injury | NINDS | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_153906 | SCR_001637 | 2026-07-28 09:40:14 | 0 | ||||||
|
Mesquite Resource Report Resource Website 100+ mentions |
Mesquite (RRID:SCR_017994) | software application, software resource, data analysis software, data processing software | Software tool as modular system for evolutionary analysis. Software for evolutionary biology, designed to organize and analyze comparative data about organisms. Its emphasis is on phylogenetic analysis, but some of its modules concern population genetics, while others do non-phylogenetic multivariate analysis. Analyses available depend on modules installed. Comes with many packages already installed. | Modular, evolutionary, analysis, organize, comparative data, organism, phylogenetic, population genetic, non-pylogenetic | is listed by: Debian | NSF DEB 1258220; David and Lucile Packard Foundation ; NSERC Discovery grant ; NSF |
Free, Available for download, Freely available | https://sources.debian.org/src/mesquite/ | SCR_017994 | Mesquite 3.04, Mesquite 3.61 | 2026-07-28 09:44:40 | 151 | |||||||
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VG Studio MAX Resource Report Resource Website 10+ mentions |
VG Studio MAX (RRID:SCR_017997) | software application, data analysis software, software resource, data processing software, data visualization software | Software tool for analysis and processing of µCT data, e.g. compiling virtual 3D models of morphological structures in site by Volume Graphics GmbH. Used for visualization of CT data. | Computed tomography, CT, data, analysis, processing, 3D, visualization, CT data | Restricted | SCR_017997 | VGStudio MAX, VG Studio MAX 3.1, VGStudio | 2026-07-28 09:44:36 | 11 | ||||||||||
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LibreOfficeCalc Resource Report Resource Website 10+ mentions |
LibreOfficeCalc (RRID:SCR_018013) | software application, data analysis software, software resource, data management software, data processing software, data visualization software | Open source software application with data analysis tools and spreadsheet templates used to manage, process and visualize data. LibreOffice Calc is spreadsheet component of LibreOffice software package developed by Document Foundation. | Data, analysis, spreadsheet, template, process, visualize | Free, Available for download, Freely available | SCR_018013 | 2026-07-28 09:44:37 | 24 | |||||||||||
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NeuroChaT Resource Report Resource Website 1+ mentions |
NeuroChaT (RRID:SCR_018020) | software application, data analysis software, software resource, data processing software, software toolkit | Software open source python toolbox to analyse neuronal signals recorded in vivo in freely behaving animal, with particular emphasis on spatial coding. Can be used as application programming interface, or as general user interface, and is designed to help simplify adoption of standardised analyses for behavioural neurophysiology and facilitate open data sharing and collaboration between laboratories. | Neuronal signal, analysis, freely behaving animal, spatial coding, behavioural neurophysiology, data, bio.tools |
is listed by: Debian is listed by: bio.tools |
Wellcome Trust | DOI:12688/wellcomeopenres.15533.1 | Free, Available for download, Freely available | biotools:NeuroChat | https://bio.tools/NeuroChaT | SCR_018020 | Neuron Characterisation Toolbox | 2026-07-28 09:44:41 | 2 | |||||
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DichroWeb Resource Report Resource Website 50+ mentions |
DichroWeb (RRID:SCR_018125) | service resource, data analysis service, data access protocol, software resource, production service resource, web service, analysis service resource | Web server for analysis of protein circular dichroism spectra. Provides access to circular dichroism secondary structure calculation algorithms and reference databases. Used in analysis of protein secondary structures. | Analysis, protein, circular dichroism spectra, secondary structure, reference database, algorithm, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: University of London; London; United Kingdom |
BBSRC | PMID:17896349 PMID:15215473 |
Restricted | biotools:dichroweb | https://bio.tools/dichroweb | SCR_018125 | 2026-07-28 09:44:37 | 62 | ||||||
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CNV webstore Resource Report Resource Website 1+ mentions |
CNV webstore (RRID:SCR_018007) | software application, data analysis software, software resource, data processing software, data visualization software, data storage software, software toolkit | Integrated platform to analyse, store, visualise and interpret CopyNumber Variation data. Analysis is supported for Illumina data, all CNV-reports and raw data can be imported after third-party analysis. Platform to streamline processing and downstream interpretation of microarray data in clinical context. Analysis tools include CNV analysis, parent of origin and uniparental disomy detection. Interpretation tools include data visualisation, gene prioritisation, automated PubMed searching, linking data to several genome browsers and annotation of CNVs based on several public databases. | Copy number variation, data, Illumina, CNV report, raw data, microarray data, clinical, analysis, visualization, gene prioritisation, PubMed searching, annotation, | Belgian National Fund for Scientific Research - Flanders ; Marguerite-Marie Delacroix foundation |
PMID:21208430 | http://cnv-webstore.ua.ac.be/cnv-webstore/ | SCR_018007 | CNV-webstore, CNV-WebStore | 2026-07-28 09:44:36 | 1 | ||||||||
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EMBL-EBI COVID-19 Portal Resource Report Resource Website 10+ mentions |
EMBL-EBI COVID-19 Portal (RRID:SCR_018337) | service resource, disease-related portal, data or information resource, data repository, database, storage service resource, topical portal, portal | EMBL-EBI portal to enable researchers to upload, access and analyse COVID-19 related reference data and specialist datasets submitted to EMBL-EBI and other major centers for biomedical data. Used to facilitate data sharing and analysis to accelerate coronavirus research. The aim of the COVID-19 Data Portal is to facilitate data sharing and analysis, and to accelerate coronavirus research. EMBL-EBI and partners have set up the COVID-19 Data Portal, which will bring together relevant datasets submitted to EMBL-EBI and other major centres for biomedical data. The aim is to facilitate data sharing and analysis, and to accelerate coronavirus research. The COVID-19 Data Portal will enable researchers to upload, access and analyse COVID-19 related reference data and specialist datasets. The COVID-19 Data Portal will be the primary entry point into the functions of a wider project, the European COVID-19 Data Platform. | COVID-19, COVID-19 data, sequence, expression, protein sequence, protein structure, proteome, translatome, analysis, EMBL-EBI | is related to: EMBL-EBI Pathogens - COVID-19 | COVID-19 | Free, Freely available | SCR_018816 | https://www.covid19dataportal.org/, https://www.ebi.ac.uk/about/news/press-releases/embl-ebi-launches-covid-19-data-portal | SCR_018337 | EMBL-EBI COVID-19 Data Portal, COVID-19 Data Portal | 2026-07-28 09:44:40 | 10 | ||||||
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Cytosplore Viewer Resource Report Resource Website 10+ mentions |
Cytosplore Viewer (RRID:SCR_018330) | service resource, data access protocol, software resource, production service resource, web service, analysis service resource | Web based interactive visual analysis system for exploration of single cell data published in Allen Cell Types Database and for number of single cell data resources of Brain Initiative Single Cell Network. Allows interactive exploration of hierarchies of cell types, visualization of transcriptome wide gene expression in combination with metadata of individual cells, performing differential analyses and statistics between manual selections of cells, or between pre-defined clusters throughout cellular hierarchy and more. | BICCN, visualization, transcriptomics, single cell data, gene expression, metadata, analysis, statistic, cellular hierarchy, Cytosplore |
uses: Allen Cell Types Database is used by: BICCN is used by: BRAIN Initiative Cell Atlas Network is related to: Allen Institute for Brain Science is related to: Leiden University; Leiden; Netherlands |
Free, Available for download, Freely available | SCR_018330 | 2026-07-28 09:44:40 | 17 | ||||||||||
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MOLEonline Resource Report Resource Website 10+ mentions |
MOLEonline (RRID:SCR_018314) | service resource, data access protocol, software resource, production service resource, web service, analysis service resource | Interactive web based tool for analyzing biomacromolecular channels, tunnels and pores. Enables two modes of calculation with one dedicated to analysis of channels and another for transmembrane pores. Can use PDB and mmCIF formats. Can analyze biomacromolecular structures stemming from NMR, X-ray and cryo-EM techniques. Interconnected with PDBe, CSA, ChannelsDB, OPM, UniProt to help setup and analysis of acquired results. Provides analytics for detection and structural characterization of channels and information about their physicochemical features. | biomacromolecular channel, analysis, biomacromolecular pore, biomacromolecular tunnel, transmembrane pore analysis, analysis, biomacromolecular sturcture, physicochemical feature |
works with: PDBe - Protein Data Bank in Europe works with: CSA - Catalytic Site Atlas works with: UniProt |
PMID:29718451 | Free, Freely available | https://mole.upol.cz/online/ | http://old.mole.upol.cz/ | SCR_018314 | MOLEonline 2.0 | 2026-07-28 09:44:40 | 30 | ||||||
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Proteomic Data Commons Resource Report Resource Website 50+ mentions |
Proteomic Data Commons (RRID:SCR_018273) | PDC | analysis service resource, service resource, data or information resource, data repository, database, production service resource, storage service resource | Portal to make cancer related proteomic datasets easily accessible to public. Facilitates multiomic integration in support of precision medicine through interoperability with other resources. Developed to advance our understanding of how proteins help to shape risk, diagnosis, development, progression, and treatment of cancer. One of several repositories within NCI Cancer Research Data Commons which enables researchers to link proteomic data with other data sets (e.g., genomic and imaging data) and to submit, collect, analyze, store, and share data throughout cancer data ecosystem. PDC provides access to highly curated and standardized biospecimen, clinical, and proteomic data, intuitive interface to filter, query, search, visualize and download data and metadata. Provides common data harmonization pipeline to uniformly analyze all PDC data and provides advanced visualization of quantitative information. Cloud based (Amazon Web Services) infrastructure facilitates interoperability with AWS based data analysis tools and platforms natively. Application programming interface (API) provides cloud-agnostic data access and allows third parties to extend functionality beyond PDC. Structured workspace that serves as private user data store and also data submission portal. Distributes controlled access data, such as patient-specific protein fasta sequence databases, with dbGaP authorization and eRA Commons authentication. | Cancer, proteomic, data, precision medicine, diagnosis, treatment, analysis, biospeciment, clinical data, metadata |
is related to: Cancer Research Data Commons has parent organization: National Cancer Institute |
cancer | Restricted | SCR_018273 | 2026-07-28 09:44:53 | 66 | ||||||||
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Interactive Repeated Experiments Dotplot Resource Report Resource Website |
Interactive Repeated Experiments Dotplot (RRID:SCR_018328) | service resource, data access protocol, software resource, production service resource, web service, analysis service resource | Web tool for creating interactive graphics. Enables authors to create interactive graphics from data obtained with repeated independent experiments. Designed for laboratory studies with repeated experiments. | Interactive graphic, repeated independent experiment, repeated experiment data, graph, analysis, dot plot | NCATS UL1 TR000135 | PMID:28974579 | Free, Freely available | SCR_018328 | 2026-07-28 09:44:44 | 0 | |||||||||
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Watchdog Resource Report Resource Website 1+ mentions |
Watchdog (RRID:SCR_018355) | software application, data analysis software, software resource, data management software, data processing software | Software workflow management system for automated and distributed analysis of large scale experimental data. Implemented in Java and is thus platform independent. | Workflow management system, automated data analysis, next generation sequencing, large scale experimental data, analysis | Free, Available for download, Freely available | https://github.com/klugem/watchdog, https://anaconda.org/bioconda/watchdog-wms | SCR_018355 | 2026-07-28 09:44:55 | 2 | ||||||||||
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Big Data Processor Resource Report Resource Website 1+ mentions |
Big Data Processor (RRID:SCR_018484) | BDP | software application, software resource, data processing software, image processing software, image analysis software | Software tool for visual inspection and processing of big image data. Enables loading of Tiff and Hdf5 based image data. BDC supports cropping and saving of big image data including binning and bit depth conversion. Used for analysis of TB sized image data like light sheet microscopy or electron microscopy. | Image, image processor, data processor, data, processing, analysis, image data, microscopy | is a plug in for: Fiji | Free, Available for download, Freely available | https://github.com/embl-cba/fiji-plugin-bigDataProcessor | SCR_018484 | 2026-07-28 09:44:45 | 2 | ||||||||
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Harmony Resource Report Resource Website 10+ mentions |
Harmony (RRID:SCR_018809) | software application, software resource, data processing software, image acquisition software, image analysis software, data acquisition software | Harmony high content imaging and analysis software. Used to quantify complex cellular phenotypes. Designed for PerkinElmer high content screening systems. | Imaging, analysis, cellular phenotype quantification, PerkinElmer, high content, screening system, cell phenotypic screening, live cell imaging, | is related to: Perkin Elmer: Operetta CLS | Restricted | SCR_018809 | Harmony 4.8 | 2026-07-28 09:44:50 | 29 | |||||||||
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IMGT/StatClonotype Resource Report Resource Website 1+ mentions |
IMGT/StatClonotype (RRID:SCR_018963) | software application, software resource, data analysis software, data processing software | Software tool to evaluate and visualize statistical significance of pairwise comparisons of IMGT clonotype (AA) diversity or expression, per variable,diversity, and joining gene of given IG or TR group, from NGS IMGT/HighV-QUEST statistical output. Antibody clonotype analysis based on NGS sequences. | T cell receptor, antibody, immunoglobulin, immunoinformatics, next generation sequencing, statistical significance, clonotype diversity, clonotype expression, pairwise comparison, gene, NGS, analysis, antybody clonotype, bio.tools |
is listed by: bio.tools is listed by: Debian |
PMID:27667992 | Free, Available for download, Freely available | biotools:IMGt_StatClonotype | https://bio.tools/IMGT_StatClonotype | SCR_018963 | IMGTStatClonotype, ImMunoGeneTics/StatClonotype | 2026-07-28 09:44:52 | 3 | ||||||
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ClinTrajAn Resource Report Resource Website 1+ mentions |
ClinTrajAn (RRID:SCR_019018) | software application, data analysis software, software resource, data processing software, data visualization software | Software Python package for analysis of trajectories in clinical datasets. | Trajectories analysis, clinical datasets, analysis, data, , bio.tools |
is listed by: bio.tools is listed by: Debian |
Free, Available for download, Freely available | biotools:clintrajan | https://bio.tools/clintrajan | SCR_019018 | 2026-07-28 09:44:49 | 1 |
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