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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

218 Results - per page

Resource NameResource TypeDescriptionKeywordsResource IDProper CitationParent OrganizationRelated ConditionFunding AgencyRelationReferenceWebsite StatusAlternate IDsAlternate URLsOld URLs
SimThyrResource, software resource, software application, simulation softwareSimulation software for thyroid homeostasis, which is based on a published nonlinear model of pituitary-thyroid feedback control. Specifically, the program simulates pituitary thyroid feedback control, which allows users to study the relationship between structure and behaviour of thyroid homeostasis.thyroid, homeostasis, simulation, software, modelling, pituitary, modelSCR_014351(SimThyr, RRID:SCR_014351)Ludwig-Maximilians-University; Bavaria; Germany , Ruhr University Bochum; North Rhine-Westphalia; Germany hypothyroidism, hyperthyroidism, thyrotoxicosis, resistance to thyroid hormone (RTH Beta), non-thyroidal illness syndrome (NTIS), euthyroid sick syndrome (ESS), thyroid allostasis in critical illness, tumors, uremia and starvation (TACITUS), subclinical thyroid diseases, syndrome TDOI:10.1080/01969720490443354, DOI:10.1155/2012/351864, DOI:10.5281/zenodo.1303822, PMID:23365787Last checked downDOI:10.5281/zenodo.1303822
eXpression2KinasesResource, software resource, software applicationSoftware tool to produce inferred networks of transcription factors, proteins, and kinases predicted to regulate the expression of the inputted gene list by combining transcription factor enrichment analysis, protein-protein interaction network expansion, with kinase enrichment analysis. It provides the results as tables and interactive vector graphic figures.inferred, network, transcription, factor, protein, kinase, regulate, expression, gene, analysis, combineSCR_016307(eXpression2Kinases, RRID:SCR_016307)NCRR, NIDDK, NIGMS, NLMPMID:22080467Last checked up
CellProfiler Image Analysis SoftwareResource, software resource, image analysis software, data processing software, software applicationCellProfiler cell image analysis software is free and open-source software designed to enable biologists without training in computer vision or programming to quantitatively measure phenotypes from thousands of images automatically. It counts cells and also measures the size, shape, intensity and texture of every cell (and every labeled subcellular compartment) in every image. It was designed for high throughput screening but can perform automated image analysis for images from time-lapse movies and low-throughput experiments. CellProfiler has an increasing number of algorithms to identify and measure properties of neuronal cell types.high-throughput, high content imaging, software, image, cell, phenotype, measurement, subcellular, intensity, size, shape, analysis, algorithmSCR_007358(CellProfiler Image Analysis Software, RRID:SCR_007358)Broad Institute NHGRI, NIGMSrelated to: CellProfiler AnalystReferences (4)Last checked upnif-0000-00280, nlx_66812, SCR_010649
Visualization and Analysis of Networks containing Experimental Data (VANTED)Resource, data visualization software, software application, data analysis software, data processing software, software resourceSoftware tool for extendable network visualization and analysis for the life sciences. It is Java-based and allows users to create, edit and map data onto existing or new networks. Experimental datasets can be visualized on network elements as graphical charts to show time series data or data of different treatments, as well as environmental conditions in the context of the underlying biological processes. Users can utilize built-in statistical algorithms to evaluate mapped data.binary executable, simulation software, signal processing software, java, network visualization, statistical analysisSCR_001138(Visualization and Analysis of Networks containing Experimental Data (VANTED), RRID:SCR_001138)PMID:23140568Last checked upnif-0000-00373
PlinyResource, annotation toolSet of plugins for the Eclipse platform which facilities note-taking and annotation of web-based works and non-web-based works.annotation, plug inSCR_003107(Pliny, RRID:SCR_003107)King's College London; London; United Kingdom Andrew W. Mellon FoundationLast checked upnif-0000-00556
MadagascarResource, source code, data analysis software, data processing software, software application, software resource, software toolkitSoftware package for multidimensional data analysis and reproducible computational experiments. It aims to provide a powerful environment and a convenient technology transfer tool for researchers working with digital image and data processing in geophysics and related fields.geophysics, seismology, seismic data, python, c, reproducibilitySCR_003274(Madagascar, RRID:SCR_003274)Last checked upnif-0000-01270,
CommentpressResource, software resource, annotation, web applicationWeb application for blogging on WordPress that allows users to annotate in the margins of an online text.plugin, wordpress, comment, annotate, website annotationSCR_001962(Commentpress, RRID:SCR_001962)plug-in for: WordPressLast checked upnif-0000-02602
Digress.itResource, software resource, source codeTHIS RESOURCE IS NO LONGER IN SERVICE. Documented October 5, 2018. is a tool (plugin) that offers paragraph-level commenting in the margins of a text. is based on the WordPress blogging architecture, but is geared toward in-depth discussions of longer documents: article, essay or even book-length. allows you run blog-style comment threads digressions, if you will off of individual paragraphs. To do this efficiently, we've re-jiggered the conventional post-discussion hierarchy of blogs, moving the comment area from beneath the post to beside it (floating to the right) hearkening back to the age-old practice of scribbling in page margins. We see great possibilities for educators, literary groups, political or civic activists, legal scholars, and pretty much anyone who wants to do a communal close reading. Since its initial launch has been used by universities, publishers and governments across the world and is cited on various academic and scientific journals as an exemplary online collaboration tool. is first an foremost a public service. The source code is completely free software and open to be used and customized by anyone without restriction. The hosting service is also free and has no ads. The project is primarily funded by grants, donations and people interested in seeing the project stay alive.k-12, plug-in, tool, training material, annotateSCR_002278(, RRID:SCR_002278)University of Lincoln; Lincoln; United Kingdom Cornell University; New York; USA, JISC, New Media Consortium, New York Public Library; New York; USA, Trinity College, University of Leicester; Leicester; United Kingdom, University of Lincoln; Lincoln; United KingdomLast checked downnif-0000-02700
EcoGeneResource, data or information resource, databaseDatabase that contains updated information about the Escherichia coli K-12 genome and proteome sequences, including extensive gene bibliographies. Users are able to download customized tables, perform Boolean query comparisons, generate sets of paired DNA sequences, and download any E. coli K-12 genomic DNA sub-sequence. BLAST functions, microarray data, an alphabetical index of genes, and gene overlap queries are also available. The Database Table Downloads Page provides a full list of EG numbers cross-referenced to the new cross-database ECK numbers and other common accession numbers, as well as gene names and synonyms. Monthly release archival downloads are available, but the live, daily updated version of EcoGene is the default mysql database for download sciences, genomics, proteomics, gene, gene expression, genetics, protein, protein binding, protein-protein interaction, membrane, rna, dna, structure, function, functional annotation, annotation, blastSCR_002437(EcoGene, RRID:SCR_002437)University of Miami Miller School of Medicine; Florida; USA Lucille P. Markey Foundation, NIGMS, NIHrelated to: RefSeq, Colibri, listed by: re3data.orgReferences (2)Last checked upnif-0000-02784
GreengenesResource, data or information resource, databaseDatabase that provides access to the current and comprehensive 16S rRNA gene sequence alignment for browsing, blasting, probing, and downloading. The data and tools can assist the researcher in choosing phylogenetically specific probes, interpreting microarray results, and aligning/annotating novel sequences. The 16S rRNA gene database provides chimera screening, standard alignment, and taxonomic classification using multiple published taxonomies. ARB users can use Greengenes to update local databases.microbiome, rrna, 16s rrna, gene, dna, rna, chimera, alignment, taxonomic classification, taxonomySCR_002830(Greengenes, RRID:SCR_002830)Lawrence Berkeley National Laboratory Department of Energylisted by: OMICtools,, Human Microbiome ProjectPMID:16820507Last checked upnif-0000-02927, OMICS_01512
ReactomeResource, data analysis service, production service resource, analysis service resource, database, service resource, data or information resourceCollection of pathways and pathway annotations. The core unit of the Reactome data model is the reaction. Entities (nucleic acids, proteins, complexes and small molecules) participating in reactions form a network of biological interactions and are grouped into pathways (signaling, innate and acquired immune function, transcriptional regulation, translation, apoptosis and classical intermediary metabolism) . Provides website to navigate pathway knowledge and a suite of data analysis tools to support the pathway-based analysis of complex experimental and computational data sets.pathway, interaction, reaction, nucleic acid, protein, complex, small molecule, signaling pathway, immune function, transcriptional regulation, translation, apoptosis, metabolism, ortholog, visualization, protein-protein interaction, web service, book, biomart, gold standardSCR_003485(Reactome, RRID:SCR_003485) European Bioinformatics Institute , Cold Spring Harbor Laboratory , Ontario Institute for Cancer Research , New York University School of Medicine; New York; USA European Molecular Biology Laboratory, European Union FP6 ENFIN, NHGRI, NIGMS, Ontario Research Fundrelated to: WikiPathways, Pathway Commons, ConsensusPathDB, FlyMine, AmiGO, PSICQUIC, Monarch Initiative, Integrated Molecular Interaction Database, NCBI BioSystems Database, MOPED - Model Organism Protein Expression Database , KOBAS, PSICQUIC Registry, Pathway Interaction Database, hiPathDB - human integrated Pathway DB with facile visualization, Algal Functional Annotation Tool, used by: NIF Data Federation, DisGeNET, Pathway Analysis Tool for Integration and Knowledge Acquisition, listed by:, works_with: PathwayMatcherReferences (2)Last checked upnif-0000-03390
Ribosomal Database Project Resource, data or information resource, resource, databaseA database which provides ribosome related data services to the scientific community, including online data analysis, rRNA derived phylogenetic trees, and aligned and annotated rRNA sequences. It specifically contains information on quality-controlled, aligned and annotated bacterial and archaean 16S rRNA sequences, fungal 28S rRNA sequences, and a suite of analysis tools for the scientific community. Most of the RDP tools are now available as open source packages for users to incorporate in their local workflow.microbiome, database, rrna gene sequence, rrna, ribosome, genome browser, high-throughput sequencing, bacteria, archaea, fungiSCR_006633( Ribosomal Database Project , RRID:SCR_006633)Michigan State University; Michigan; USA DOE, NHLBI, NIDDK, NIEHS, NSF, USDAlisted by: OMICtools, Human Microbiome ProjectReferences (2)Last checked upnif-0000-03404, OMICS_01513
BrainstormResource, image analysis software, data processing software, software application, data visualization software, software resource, image processing softwareOpen-source application dedicated to magnetoencephalography (MEG) and electroencephalography(EEG) data analysis (visualization, processing and advanced source modeling). Its rich and intuitive graphic interface does not require any programming knowledge or experience with Matlab. Although Brainstorm is developed with Matlab (and Java), it does not require users to own a Matlab license: an executable, platform-independent (Windows, MacOS, Linux) version is made available in the downloadable package. What you can do with Brainstorm * MEG/EEG recordings: ** Read data from the most popular file formats ** Interactive access to data files in native formats ** Import data in Matlab ** Import and order data in a well-organized database (by studies, subjects, conditions) ** Review, edit, import, export event markers in continuous, ongoing recordings ** Automatic detection of well-defined artifacts (eye blinks, heartbeats...) ** Artifact correction using Signal Space Projections (SSP) * Pre-processing: Epoching; Detection of bad trials / bad channels; Baseline correction; Frequency filtering; Resampling; Multiple options for epoch averaging; Estimation of noise statistics for improved source modeling * Powerful and versatile visualization: ** Various time series displays (epoched, continuous raw, butterfly, columns, etc.) ** Data mapping on 2D or 3D surfaces (disks, true geometry of sensor array, scalp surface, etc.) ** Generate slides and animations (export as contact sheets, movies, jpegs, ...) ** Channel selection and sensor clustering (save and organize your favorites, share with your collaborators, etc.) * MRI visualization and coregistration: ** Use individual or template anatomy (MNI / Colin27 brain) ** Template anatomy can be warped to individual head surface ** Import MRI volumes and tessellated surface envelopes from most of the existing file formats ** Automatic or interactive co-registration with the MEG/EEG coordinate system ** Volume rendering (multiple display modes) * Database: Keep your data organized ** Ordering of data, source models, time-frequency maps, statistical maps, etc. by protocol, subject and condition/event ** Quick access to all the data in a study for efficient, batch processing ** Quick access to comparisons between subjects or conditions ** Graphical batching tools (apply the same process to many files e.g., your entire study, in a few clicks) * Head modeling: ** MEG: Single sphere, overlapping spheres ** EEG: Berg's three-layer sphere, Boundary Element Models (with OpenMEEG) ** Interactive interface to define the best-fitting sphere * Source modeling: L2 Minimum-norm current estimates; dSPM; sLORETA; All models can be cortically-constrained or not, and with/without constrained orientations * Source display and analysis: ** Multiple options for surface and volume rendering of the source maps ** Re-projection of the sources in the MRI volume (from surface points to voxels) ** Definition of regions of interest (scouts) ** Re-projection of estimated sources on a surface with higher or lower resolution, on a group template ** Surface or volume spatial smoothing (group analysis) ** Share your results: screen captures, make movies and contact sheets! ** Import and display of Xfit (MEG Elekta software) dipole models * Time-frequency decompositions: Time-frequency analyses of sensor data and sources time series using Morlet wavelet, Fast Fourier Transfor, and Hilbert transform; Define time and frequency scales of interest; Multiple display modes available * Group analysis: Registration of individual brains to a brain template (MNI/Colin27); Statistical analysis (t-tests) * Documentation and support: Easy and automatic updates of the software; Detailed step-by-step tutorials for most common features; Active user forumfmri, anatomy, animation, cortical, current, density, imaging, import, matlab, modeling, mri, neuroimaging, processing, scalp, segmentation, selection, slide, software, toolbox, volume, brain, magnetoencephalography, electroencephalography, visualization, processing, cortical, algorithm or reusable library, atlas application, connectivity analysis, database application, format conversion, eeg modeling, meg modeling, mesh generation, spatial transformation, statistical operation, temporal transformation, time domain analysis, java, matlab, mriSCR_001761(Brainstorm, RRID:SCR_001761)University of Southern California; Los Angeles; USA NIBIBrelated to: Internet Analysis Tools Registry, OpenMEEG, Open MEG Archive, listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)PMID:21584256Last checked upnif-0000-10267
CytoscapeResource, software resource, software application, data analysis software, data processing software, data visualization softwareSoftware platform for complex network analysis and visualization. Used for visualization of molecular interaction networks and biological pathways and integrating these networks with annotations, gene expression profiles and other state data.biological, network, visualization, analysis, data, gene, pathway, molecular, interactionSCR_003032(Cytoscape, RRID:SCR_003032)Institute for Systems Biology; Washington; USA , University of California at San Diego; California; USA National Resource for Network Biology, NCRR, NIGMSrelated to: PhosphoSitePlus: Protein Modification Site, TRIP Database, CoryneRegNet, AltAnalyze - Alternative Splicing Analysis Tool, MiMI Plugin for Cytoscape, Network Data Exchange (NDEx), GeneMANIA, DroID - Drosophila Interactions Database, Network-based Prediction of Human Tissue-specific Metabolism, BioGRID, DaTo, PiNGO, iBIOFind, cPath, BiNGO: A Biological Networks Gene Ontology tool, ClueGO, RamiGO, EGAN: Exploratory Gene Association Networks, used by: CytoSPADE, HDBase, DisGeNET, categoryCompare, lists: PEPPER, has plug-in: CluePedia Cytoscape plugin, CytoSPADE, EnrichmentMap, works_with: NetCirChro, IMEx - The International Molecular Exchange ConsortiumReferences (2)Last checked upnif-0000-30404
Protein Subcellular Location Image DatabaseResource, database, data set, service resource, storage service resource, data repository, image analysis service, data or information resourceTHIS RESOURCE IS NO LONGER IN SERVICE. Documented August 23, 2017.\\n\\nAnnotated database of fluorescence microscope images depicting subcellular location proteins with two interfaces: a text and image content search interface, and a graphical interface for exploring location patterns grouped into Subcellular Location Trees. The annotations in PSLID provide a description of sample preparation and fluorescence microscope imaging.protein, structure, subcellular, organelle, image, fluorescence microscope, annotation, classify, rank, cluster, subcellular localization, 3d spatial image, 2d spatial image, micrograph, content-based retrieval, green fluorescent proteinSCR_008663(Protein Subcellular Location Image Database, RRID:SCR_008663)Carnegie Mellon University; Pennsylvania; USA Merck Company Foundation, NCI, NIGMS, NSFlisted by: 3DVC, BiositemapsLast checked upnif-0000-33313
Disease OntologyResource, wiki, narrative resource, ontology, data or information resource, controlled vocabularyOpen source ontology for the integration of biomedical data associated with human disease. This community-driven ontology links disparate datasets through disease concepts. A computable structure of inheritable, environmental and infectious origins of human disease will be provided to facilitate the connection of genetic data, clinical data, and symptoms through the lens of human disease. The Ontology enables the cross-walk between disease concepts, genes contributing to disease, and associated symptoms, findings and signs.disease, biomedical, genetic, clinical, symptom, clinical research, medicine, genetic disease, environmental disease, infectious disease, phenotype, environmentSCR_003491(Disease Ontology, RRID:SCR_003491) University of Maryland School of Medicine; Maryland; USA , Northwestern University; Illinois; USA NCRRrelated to: Neurocarta, FunDO, NUgene Project, GWASdb, PharmGKB Ontology, used by: DOAFPMID:22080554Last checked upnif-0000-35926
Semantic Automated Discovery and IntegrationResource, software resource, source code, service resourceFramework for discovery of, and interoperability between, distributed data and analytical resources. It combines GET/POST-based Web Services with standards from the W3C Semantic Web initiative. The objective is to make it easy for data and analytical tool providers to make their resources available on the Semantic Web with minimal disruption to their usual practices. It simply defines an open set of best-practices and conventions, within the spectrum of existing standards, that allow for a high degree of semantic discoverability and interoperability between participating services.interoperability framework, discovery framework, interoperability softwareSCR_004130(Semantic Automated Discovery and Integration, RRID:SCR_004130)University of British Columbia; British Columbia; Canada Canadian Institutes of Health Research, CANARIE, Heart and Stroke Foundation of B.C. and Yukon, Microsoft ResearchPMID:21210986Last checked upnlx_143562
AIDA ToolkitResource, software resource, software toolkit, data access protocol, web serviceA generic set of components that can perform a variety of tasks, such as learn new pattern recognition models, perform specialized search on resource collections, and store knowledge in a repository. W3C standards are used to make data accessible and manageable with semantic web technologies such as OWL, RDF(S), and SKOS. The AIDA Toolkit is directed at groups of knowledge workers that cooperatively search, annotate, interpret, and enrich large collections of heterogeneous documents from diverse locations. The server offers services for: text indexing and statistics, metadata storage and querying, thesaurus reasoning, annotation, text retrieval, spelling correction, synonym detection, and model toolkit, web service, search, learning, storage, workflow, text indexing, text statistics, metadata storage, metadata querying, thesaurus reasoning, annotation, text retrieval, spelling correction, synonym detection, model learningSCR_005914(AIDA Toolkit, RRID:SCR_005914)related to: TavernaLast checked upnlx_149497
Viking Viewer for ConnectomicsResource, software resource, software application, data processing software, data management software, collaboration toolA web-compliant application that allows connectomics visualization by converting datasets to web-optimized tiles, delivering volume transforms to client devices, and providing groups of users with connectome annotation tools and data simultaneously via conventional internet connections. Viking is an extensible tool for connectomics analysis and is generalizable to histomics applications.annotation, 2d image, microscopy image, volume, serial section, 3d reconstruction, segmentation, microscopy, visualization, optical imaging, connectomics, synapse, retina, brainSCR_005986(Viking Viewer for Connectomics, RRID:SCR_005986)University of Utah; Utah; USA Graduate Research Fellowship, NEI, NIBIB, NIDCD, NSF, Research to Prevent Blindness, University of Utah; Utah; USA, Utah Science Technology and Research Initiativelisted by: NeuroImaging Tools and Resources Collaboratory (NITRC), 3DVCPMID:21118201Last checked upnlx_151360
eQuilibratorResource, software resource, database, data or information resource, web applicationWeb interface designed for thermodynamic analysis of biochemical systems. eQuilibrator enables free-text search for biochemical compounds and reactions and provides thermodynamic estimates for both in a variety of conditions. It can provide estimates for compounds in the KEGG database, and individual compounds and enzymes can be searched for by their common names (water, glucosamine, hexokinase). Reactions can be entered in a free-text format that eQuilibrator parses automatically. eQuilibrator also allows manipulation of the conditions of a reaction - pH, ionic strength, and reactant and product concentrations.web interface, thermodynamics, biochemical systemSCR_006011(eQuilibrator, RRID:SCR_006011)Azrieli Foundation, European Research Council, Israel Academy of Sciences and Humanitiesrelated to: KEGGPMID:22064852Last checked upnlx_151400
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