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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.

(last updated: Oct 12, 2019)

Physical Resource or Software Tool Software

574 Results - per page

Resource NameResource TypeDescriptionKeywordsResource IDProper CitationParent OrganizationRelated ConditionFunding AgencyRelationReferenceWebsite StatusAlternate IDsAlternate URLsOld URLs
Brain Imaging Data StructureResource, narrative resource, standard specification, data or information resourceStandard specification for organizing and describing outputs of neuroimaging experiments.neuroimaging, research, organization, output, data sharing, consensusSCR_016124(Brain Imaging Data Structure, RRID:SCR_016124)used by: OpenNeuro, SPARC Project, listed by: BioSharing, submitted by: Resource Identification PortalPMID:27326542Last checked down
Automatic Tractography-based Parcellation PipelineResource, software resource, software application, workflow software, data processing softwareIntegrated pipeline for tractography-based brain parcellation with automatic processing and massive parallel computing. ATPP offers a CLI version for parcellating multiple brain regions and a GUI version for parcellating a specific brain region.\\n\\n" ATPP completely follows the scientific cultural shift to open science, which aims at making scientific research including journal papers, lab notes, data, and, of course, workflow tools, accessible and transparent to all levels of society. ATPP is publicly accessible in Neuroimaging Informatics Tools and Resources Clearinghouse8 (NITRC) ( Its source codes are hosted in GitHub9 (;, under the GNU generic purpose license version 310 (GPLv3), and are welcome to download and fork. The Digital Object Identifiers (DOIs) providing a persistent way to make digital data easily and uniquely citable was created from Zenodo11 platform with those GitHub repositories (ATPP CLI v2.0.0, doi:; ATPP GUI v2.0.0, doi: "pipeline, integrated pipeline, tractography, brain, parcel, gui, workflowSCR_014815(Automatic Tractography-based Parcellation Pipeline, RRID:SCR_014815)Chinese Academy of Sciences; Beijing; China National Natural Science Foundation of China10.13039/501100001809 911323013162010390581501179listed by: NeuroImaging Tools and Resources Collaboratory (NITRC), submitted by: Resource Identification PortalLast checked up,,
MITE-TrackerResource, software resource, data processing software, data analysis software, sequence analysis software, software applicationOpen source software tool for identifying miniature inverted repeat transposable elements in large genomes. Used to process large scale genomes, to find and classify MITEs using an efficient alignment strategy to retrieve nearby inverted repeat sequences.genomic, sequence, discover, miniature, inverted, repeat, transposable, element, clustering, cdhitSCR_017030(MITE-Tracker, RRID:SCR_017030)Argentina, National Council for Science and Technology, National Institute of Agricultural Technologyrelated to: Python Programming Language, uses: NCBI BLAST, listed by: OMICtools, submitted by: Resource Identification PortalDOI:10.1186/s12859-018-2376-yLast checked upOMICS_32242
Allen Cell Types DatabaseResource, data or information resource, databaseDatabase of neuronal cell types based on multimodal characterization of single cells to enable data-driven approaches to classification. It includes data such as electrophysiology recordings, imaging data, morphological reconstructions, and RNA and DNA sequencing data.database, neuron, classification, imaging, electrophysiology, eeg, imaging, rna, dna, sequencingSCR_014806(Allen Cell Types Database, RRID:SCR_014806)related to: CellTax vignette, submitted by: Resource Identification PortalLast checked upSCR_015719
BrainVision RecorderResource, software resource, software application, data processing softwareSoftware for multifunctional recording designed to provide Brain Products GmbH- Solutions for Neurophysiological Research amplifier with a platform for recording setup and execution.multifunctional, recording, Brain Products GmbH Solutions for Neurophysiological Research, amplifier, platform, recording, execution, setupSCR_016331(BrainVision Recorder, RRID:SCR_016331)submitted by: Resource Identification PortalLast checked downSCR_016332
PICRUStResource, software resource, software application, simulation softwareSoftware package to predict metagenome functional content from marker gene (e.g., 16S rRNA) surveys and full genomes. Used to predict which gene families are present and then combines gene families to estimate the composite metagenome.predict, metagenome, functional, content, DNA, sample, marker, gene, sequence, data, microbiome, 16S, RNASCR_016855(PICRUSt, RRID:SCR_016855)ARO, Canada Research Chairs program, Canadian Institutes of Health Research, Crohn’s and Colitis Foundation of America, Howard Hughes Medical Institute, NHGRI, NIDDK, NSF, Sloan Foundationsubmitted by: Resource Identification PortalPMID:23975157Last checked upSCR_016856
TIGSResource, workflow, narrative resource, service resource, training material, storage service resource, data repository, data or information resourceRepository to share analysis procedure, data and help readers or reviewers to know more detail of this work, reproduce or make use of results they are interested in.Share, analysis, procedure, data, tumor, immunogenicitySCR_017565(TIGS, RRID:SCR_017565)submitted by: Resource Identification PortalLast checked up
Willoughby–Hoye Python Scripts A-DResource, software resource, software application, data analysis software, data processing softwareSoftware tool as scripts for calculating NMR chemical shifts. Warning - this group of Python scripts used to process NMR data, described in Willoughby et al, 2014, has been found to contain bug. Please see PMID:31591889.Python, NMR, script, caluclating, chemical, shift, dataSCR_017562(Willoughby–Hoye Python Scripts A-D, RRID:SCR_017562)NIAsubmitted by: Resource Identification PortalReferences (2)Last checked up
MagVentureOrganization, instrument supplier, production service resource, material service resource, instrument manufacture, service resource, material resourceDanish, privately owned company specializing in non-invasive stimulation systems for treatment of major depressive disorder and neuroscience research based on use of transcranial magnetic stimulation.Danish, company, non invasive, stimulation, system, depressive, disorder, neuroscience, transcranial, magnetic, stimulationSCR_017563(MagVenture, RRID:SCR_017563)submitted by: Resource Identification Portal, provides: MagPro Magnetic StimulatorLast checked up
AnaMorphResource, software resource, source codeFramework for creating 3D neuronal morphologies from point/diameter descriptions.3d morphology, neuronal morphology, morphology software, surface meshSCR_015012( AnaMorph, RRID:SCR_015012)submitted by: Resource Identification Portal, hosted by: GitHubLast checked up
ClickjointResource, software resource, software application, data analysis software, data processing softwareA software for analyzing animal movement on videos and images. The user can define the animal's joints so the software can analyze using a tracking algorithm.image analysis, tracking algorithm, animal movement, animal jointSCR_014482(Clickjoint, RRID:SCR_014482)submitted by: Resource Identification PortalLast checked down
Hybrid Coordinate Ocean ModelResource, model, data or information resourceOcean general circulation model; more specifically, a data-assimilative hybrid isopycnal-sigma-pressure (generalized) coordinate ocean model.ocean circulation model, hybrid coordinates modelSCR_015534(Hybrid Coordinate Ocean Model, RRID:SCR_015534)submitted by: Resource Identification PortalLast checked down
SetRank Resource, software toolImplements an algorithm to conduct advanced gene set enrichment analysis on the results of genomics experiments.\\n\\nSimillion C, Liechti R, Lischer HE, Ioannidis V, Bruggmann R. Avoiding the pitfalls of gene set enrichment analysis with SetRank. BMC bioinformatics. 2017;18(1):151. doi: 10.1186/s12859-017-1571-6.SCR_015689(SetRank , RRID:SCR_015689)submitted by: Resource Identification PortalLast checked up
Oncotopix DiscoveryResource, software resourceOncotopix Discovery is a comprehensive solution powered for whole slide image analysis of tissue sections, TMA slides across any image analysis application. Simple to program also for scientists without an IT background.SCR_015690(Oncotopix Discovery, RRID:SCR_015690)submitted by: Resource Identification PortalLast checked down
GRatio for ImageJResource, software resource, source code, data analysis software, data processing software, software applicationImageJ plugin that performs semiautomated analysis of randomly selected sets of nervous system fibers.myelin sheath, axon diameter, fiber diameter, g ratio, pluginSCR_015580(GRatio for ImageJ, RRID:SCR_015580)neurodegenerationsubmitted by: Resource Identification Portal, plug-in for: ImageJLast checked up
Compilation of Genetics Resource DatabasesResource, portal, data or information resourcePortal provides list of genetic resources such as Brain Atlases and genomes for various species provided by National Institute of Drug Abuse.Genetic, data, brain, atlas, information, National, Institute, Drug, AbuseSCR_017501(Compilation of Genetics Resource Databases, RRID:SCR_017501)submitted by: Resource Identification PortalLast checked up
Italian Twin RegistryResource, topical portal, portal, data or information resourcePortal with information about twins in Italy.Twins, Italy, data, registrySCR_017476(Italian Twin Registry, RRID:SCR_017476)submitted by: Resource Identification PortalLast checked up
InkscapeResource, software resource, software application, image processing software, data processing softwareA vector graphics software which runs on Windows, Mac OS X and GNU/Linux. It can import and export various file formats, including SVG, AI, EPS, PDF, PS and PNG. Features include object creation, object manipulation, color editing, and text editing.image processing softwareSCR_014479(Inkscape, RRID:SCR_014479)submitted by: Resource Identification PortalLast checked up
AutoprotocolResource, software resourceLanguage standard for automating English language protocols. Autoprotocol specifies experimental protocols for biological research as a way to define experiments that could be run over the internet on remote robotic automation.language, protocol, research publication, automation, translationSCR_015764(Autoprotocol, RRID:SCR_015764)submitted by: Resource Identification PortalLast checked up
ZeitzResource, service resource, material service resource, production service resourceManufacturer and supplier of the DMZ Universal electrode pullers which produce pipettes and electrodes with a tip diameter down to 0.2 micrometers.electrode, electrode puller, material service resource, manufacturer, supplier, pipetteSCR_014774(Zeitz, RRID:SCR_014774)submitted by: Resource Identification PortalLast checked up
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