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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: Sep 14, 2019)

Physical Resource or Software Tool Software

221 Results - per page

Resource NameResource TypeDescriptionKeywordsResource IDProper CitationParent OrganizationRelated ConditionFunding AgencyRelationReferenceWebsite StatusAlternate IDsAlternate URLsOld URLs
I Do ImagingResource, database, portal, data or information resourceWeb-based portal and database aggregate of free and open source software for medical imaging. The programs are categorized and placed in a searchable database.medical imaging, image, medical software, database, freeSCR_001190(I Do Imaging, RRID:SCR_001190)Last checked downnlx_15230
NTAPResource, software resource, software application, data analysis software, data processing softwareSoftware for tiling array data analysis to survey the genome-wide binding sites of transcription factor HY5 in Arabidopsis and the genome-wide histone modifications/DNA methylation level in rice. It was developed in the process of generating NimbleGen analysis. Written in R and, tiling array, data analysis, rice, arabidopsis, hy5, transcription factor, genomeSCR_001488(NTAP, RRID:SCR_001488)Peking University; Beijing; China listed by: OMICtoolsLast checked downOMICS_00808
Chemistry Add-in for WordResource, software resource, software applicationSoftware for the insertion and modification of chemical information within Microsoft Word. Capabilities include inserting labels, formulas, and 2D depictions of chemical structures, as well as creating in-line chemical zones, rendering visual depictions of chemical structures, and the ability to store chemical information in a semantically rich word, chemistry, add in, structure, annotation, labels, formulaSCR_001521(Chemistry Add-in for Word, RRID:SCR_001521)University of Cambridge; Cambridge; United Kingdom Last checked downnlx_152820
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
NRDRResource, software resource, topical portal, web application, portal, data or information resourceSearchable portal for public non-coding RNA databases. The databases are classified by RNA family, information source, information content, and available search mechanisms.public database portal, non coding rna, non coding rna portalSCR_002458(NRDR, RRID:SCR_002458)University of Sao Paulo; Sao Paulo; Brazil listed by: OMICtoolsPMID:22336709Last checked downOMICS_01702
METAREPResource, software resource, software application, data analysis software, data processing softwareA tool for high-performance comparative metagenomics that allows users to view, query, browse, and compare metagenomics annotation profiles from short reads or assemblies. Users can use statistical tests, hierarchical clustering, multidimensional scaling, and heat maps to compare multiple datasets at various functional and taxonomic levels.microbiome, comparison, comparative metagenomics, annotation, short read, short assemblySCR_011926(METAREP, RRID:SCR_011926)J. Craig Venter Institute listed by: OMICtools, Human Microbiome ProjectDOI:10.1093/bioinformatics/btq455Last checked downOMICS_01480
machine learning open source softwareResource, software resource, software repositoryA software repository which provides open source software for machine learning. Software entries include information such as author, license, data format, and programming language. The ultimate goal of is to create a comprehensive open source machine learning environment where open source machine learning software can compete with comercial closed source repository, machine learning, machine learning softwareSCR_013990(machine learning open source software, RRID:SCR_013990)related to: Connected Researchers, listed by: Connected ResearchersLast checked down
AsciidoctorResource, software resource, software applicationA software application which translates plain text written in AsciiDoc syntax to HTML5, DocBook 5, and other backends. Asciidoctor reads and parses text written in the AsciiDoc syntax, then feeds the parse tree into a set of built-in templates to produce HTML5. Users can write their own converter or provide Tilt-supported templates to customize the generated output or produce alternative formats. Asciidoctor also recognizes additional markup and formatting options, such as font-based icons and UI application, AsciiDoc, plain text, backend, HTML5, text processor, publishing toolchain, convertSCR_014003(Asciidoctor, RRID:SCR_014003)related to: Connected Researchers, listed by: Connected ResearchersLast checked down
ERNSTResource, software resource, software application, simulation softwareAn event-based neuronal network simulator designed to handle large, complicated neuronal networks. The software is capable of creating realistic and accurate neuronal models in terms of neuronal dynamics and spike timing. ERNST is written in Java.event related, neuronal network, simulation software, neuronal model, spike timing, neuronal dynamicsSCR_014262(ERNST, RRID:SCR_014262)Last checked down
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
MC DataToolResource, software resource, software application, systems interoperability softwareAn add-on tool used to export data retrieved with the MC_Rack program. This software is used to convert MC_Rack data files into other file interoperability software, add-on tool, mc rack, mc_rack, file format, data file, data conversion, export data, exportSCR_014580(MC DataTool, RRID:SCR_014580)Last checked down
Teaching CommonsResource, data or information resource, databaseA library of open source teaching and educational resources for professors and students. It includes resources such as textbooks, lesson plans, multimedia, and lectures from participating universities and institutions. Subject areas include the life sciences, the arts and humanities, law, social and behavioral sciences, medicine and health, engineering, education, the physical sciences, and mathematics. Users can share their own work and adopt others' on the platform.library, educational, teaching, student, textbook, course material, lesson plan, multimedia, lecture, open sourceSCR_014638(Teaching Commons, RRID:SCR_014638)affiliated with: Digital Commons NetworkLast checked down
NaviComResource, software resource, data visualization software, software application, data processing software, web applicationWeb application which allows users to create interactive molecular network portraits using high-throughput datasets.python package, high throughput data visualization, molecular networkSCR_015039(NaviCom, RRID:SCR_015039)Curie Institute; Paris; France uses: cBioPortalLast checked down
SLiCAPResource, software resource, software toolkit, data analysis software, data processing software, software applicationA software toolbox containing a symbolic linear circuit analysis program. It is a MATLAB application that helps set up and solve design equations of electronic circuits.symbolic network simulation tool, symbolic linear circuit, analysis, electronic circuit, matlab, data analysis software, circuitSCR_014742(SLiCAP, RRID:SCR_014742)Last checked down
PyDSToolResource, software resource, software application, standalone software, simulation softwareIntegrated simulation and analysis environment for dynamic systems models of physical systems. It supports symbolic math, optimization, phase plane analysis, continuation and bifurcation analysis, data analysis, and other tools for modeling. It is written in Python with some underlying C and Fortran legacy code.integrated software, integrated analysis, model, simulation software, physical system, pythonSCR_014771(PyDSTool, RRID:SCR_014771)uses: NumPy, SciPyDOI:10.1371/journal.pcbi.1002628Last checked down
VTKResource, data processing software, software application, data visualization software, software resource, software toolkit, image processing softwareCross-platform visualization software system for 3D computer graphics, image processing, and data visualization. Various visualization algorithms and advanced modeling techniques are supported within VTK, as well as parallel processing and interoperability with select source visualization toolkit, visualization system, 3d computer graphics, image processingSCR_015013(VTK, RRID:SCR_015013)Kitware used by: ParaView, VolView, Insight Segmentation and Registration ToolkitLast checked down
BeCalmResource, software resource, software repositoryServer that contains a registry of text mining tools primarily within the biomedical field. It includes resources for biomedical text annotation visualization, biomedical text annotation prediction, and benchmarking biomedical entity recognition between independent automatic prediction systems.web server, text mining, text mining tool registry, web based infrastructure, web infrastructureSCR_015021(BeCalm, RRID:SCR_015021)Spanish National Cancer Research Center affiliated with: BioCreative, OpenMinTeDLast checked down
OpenStaxResource, narrative resource, training material, data or information resource, group, curriculum materialGroup that provides open source, college-level textbooks to instructors and their students. Educators can use the textbooks in class and access faculty-specific resources and content textbook, education, curriculum, teaching materialSCR_015030(OpenStax, RRID:SCR_015030)Bill and Melinda Gates Foundation, Bill and Stephanie Sick Fund, Calvin K. Kazanjian Economics Foundation, Hewlett Foundation, Laura and John Arnold Foundation, Maxfield Foundation, Michelson 20MM Foundation, Rice UniversityLast checked down
KZNF CatalogResource, catalog, data or information resource, databaseSearchable, manually curated collection of Kruppel-type zinc finger genes (KZNFs) in primates with finished or high quality draft genomes.kruppel type zinc finger gene, kznf, kruppel type zinc finger model, primate finger, primate finger geneSCR_015495(KZNF Catalog, RRID:SCR_015495)University of Illinois at Urbana-Champaign; Illinois; USA Last checked down
Empirical Gramian FrameworkResource, software resource, software applicationSoftware for empirical gramians for model reduction of (nonlinear) input-output systems.model reduction, model order reduction, empirical gramian, empirical cross gramian matrix, combined reductionSCR_015043(Empirical Gramian Framework, RRID:SCR_015043)works_with: MATLAB, GNU OctaveDOI:10.5281/zenodo.2530021Last checked down
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