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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

85 Results - per page

Resource NameResource TypeDescriptionKeywordsResource IDProper CitationParent OrganizationRelated ConditionFunding AgencyRelationReferenceWebsite StatusAlternate IDsAlternate URLsOld URLs
nih-ipad-app-end-pointResource, software resource, data acquisition software, data storage software, data processing software, software applicationData collection software for centrally and securely storing data from the NIH iPad application. It allows users to capture results from multiple iPads at a central location.abcd, collect, tool, central, storing, data, NIH, iPad, application, secure, capture, result, multiple, locationSCR_016029(nih-ipad-app-end-point, RRID:SCR_016029)NIDArelated to: University of California at San Diego, California, USALast checked up
delay-discountingResource, software resource, software applicationSoftware that performs a delay-discounting task measuring impulsivity. Used in ABCD study.abcd, delay, discounting, task, measure, impulsivity, software, application, toolSCR_016031(delay-discounting, RRID:SCR_016031)NIDArelated to: University of California at San Diego, California, USALast checked up
Collaboratory of AIDS Researchers for Eradciation (CARE)Resource, organization portal, portal, consortium, data or information resourceThe Collaboratory of AIDS Researchers for Eradication (CARE) is a consortium of scientific experts in the field of HIV latency from several U.S. and European academic research institutions as well as Merck Research Laboratories working together to find a cure for HIV.AIDS, HIV, drug development, data-sharing enablerSCR_013681(Collaboratory of AIDS Researchers for Eradciation (CARE), RRID:SCR_013681)NIAID, NIMHrelated to: University of North Carolina at Chapel Hill School of Medicine, North Carolina, USA, Gladstone Institute of Neurological Disease, UCSF School of Medicine, California, USA, Case Western Reserve University, Ohio, USA, Merck, UC Davis School of Medicine, California, USA, University of California at San Diego, California, USA, University of Utah School of Medicine, Utah, USA, University of Minnesota Twin Cities, Minnesota, USALast checked down
TopHatResource, image analysis software, data analysis software, data processing software, alignment software, software application, sequence analysis software, software resource, software toolkitSoftware tool for fast and high throughput alignment of shotgun cDNA sequencing reads generated by transcriptomics technologies. Fast splice junction mapper for RNA-Seq reads. Aligns RNA-Seq reads to mammalian-sized genomes using the ultra high-throughput short read aligner Bowtie, and then analyzes the mapping results to identify splice junctions between exons.align, RNA-Seq, read, cDNA, sequencing, transcriptomics, fast, splice, junction, mapper, exon, analysisSCR_013035(TopHat, RRID:SCR_013035) University of California; Berkeley; USA , University of Maryland; Maryland; USA related to: HISAT2, Johns Hopkins University, Maryland, USA, University of Washington, Seattle, USA, used by: CIRCexplorer, uses: Bowtie, listed by: OMICtools, works_with: GeneScissorsLast checked upOMICS_01257
Symbolic SPICEResource, software resource, software application, data analysis software, data processing softwareAnalog circuit analyzer and approximator used as a pre-processor to find design formulas or as a post-processor to approximate design formulas. The program performs the .AC analysis in SPICE symbolically with optional numeric evaluation and user selected threshold approximation.analog circuit, circuit analysis, circuit approximation, data analysis software, ac analysis, symbolicSCR_014743(Symbolic SPICE, RRID:SCR_014743)related to: Michigan State University, Michigan, USALast checked up
Cancer Imaging Phenomics ToolkitResource, software resource, image analysis software, data processing software, software applicationSoftware platform for analysis of radiographic cancer images. Used as quantitative imaging analytics for precision diagnostics and predictive modeling of clinical outcome.analysis, radiographic, cancer, image, quantitative, analyticsSCR_017323(Cancer Imaging Phenomics Toolkit, RRID:SCR_017323)CancerNCIrelated to: University of Pennsylvania Perelman School of Medicine, Pennsylvania, USA, submitted by: Resource Identification PortalPMID:29340286Last checked up
DSHBResource, reagent supplier, material resource, antibody supplierAn antibody supplier which banks and distributes hybridomas and monoclonal antibodies for use in research. The bank includes antibodies against targets such as GFP, transcription factors, stem cells, and human.antibody supplier, hybridoma, monoclonal, bank, developmental studiesSCR_013527(DSHB, RRID:SCR_013527)NICHDhosted by: University of Iowa, Iowa, USALast checked upnlx_152343
FIONA-protocol-complianceResource, software resource, software application, data analysis software, data processing softwareSoftware that contains multiple sequential lines of MATLAB commands and function calls for numerical computing for ABCD study protocol compliance.application, multiple, sequential, lines, commands, function, numerical, computing, protocol, complianceSCR_016027(FIONA-protocol-compliance, RRID:SCR_016027)NIDArelated to: University of California at San Diego, California, USALast checked up
tick-tockResource, data visualization software, software application, web application, data processing software, software resourceSoftware for research study observation that visualizes study related events per day. Any event generating function sends a 'tick' event to this application which will be visible on this applications web-interface.application, research, study, visualization, event, web, interface, observation, abcdSCR_016023(tick-tock, RRID:SCR_016023)NIDArelated to: University of California at San Diego, California, USA, works_with: ABCD StudyLast checked up
Ascidian Stock Center (ASC)Resource, biomaterial supply resource, material resource, organism supplierSupplier of Ciona (C. robusta and C. savignyi) adults and stable transgenic animals expressing tissue-specific fluorescent proteins for research laboratories. This ascidian culturing facility is located at the marine laboratory of the University of California at Santa Barbara (UCSB).ascidian, model organism, ciona, embryology, marine organism, culturing facilitySCR_014949(Ascidian Stock Center (ASC), RRID:SCR_014949)NIGMShosted by: University of California at Santa Barbara, California, USALast checked down
FIONASITEResource, data processing software, software application, data transfer software, data management software, software resource, data acquisition softwareSoftware for uploading data to FIONA and capturing MR images and k-space data from medical image systems. It provides a web-interface to automate the data review (image viewer), integrate with the centralized electronic data record for assigning anonymized id's, and forward the data to the central archive.automate, data, upload, collection, network, appliance, abcd, studySCR_016012(FIONASITE, RRID:SCR_016012)NIDArelated to: University of California at San Diego, California, USALast checked upSCR_016013, SCR_016014
redcap-importerResource, software resource, data acquisition software, data processing software, software applicationSoftware that automates the process of retrieving and converting data to the format of a RedCap table and allows selection of directories and files for import.automate, process, retrvinig, converting, data, format, research, electronic, data, capture, table, selection, directory, importSCR_016032(redcap-importer, RRID:SCR_016032)NIDArelated to: University of California at San Diego, California, USALast checked up
BioJupiesResource, software resource, web applicationSoftware as an open source web server that automatically generates RNA-seq data analysis of jupyter notebooks. It allows creation and containment of documents that have live code, visualizations and narrative text.automatically, generate, RNAseq, data, analysis, notebook, create, visualize, report, custom, raw, processed, user, interfaceSCR_016346(BioJupies, RRID:SCR_016346)affiliated with: Icahn School of Medicine at Mount Sinai, New York, USALast checked up
Bacillus Genetic Stock Center (BGSC)Resource, biomaterial supply resource, material resourceSupplier of genetically characterized strains, cloning vectors, and bacteriophages for the genus Bacillus and related organisms. The BGSC can distribute these materials to qualified scientists and educators throughout the world.bacillus, integration vector, cloning vector, strain, bacteriophageSCR_014950(Bacillus Genetic Stock Center (BGSC), RRID:SCR_014950)Ohio State University; Ohio; USA , National Science Foundation NSFhosted by: Ohio State University, Ohio, USALast checked up
LINCS Information FrameworkResource, data or information resource, databaseDatabase for Library of Integrated Network-Based Cellular Signatures (LINCS) data that leverages semantic-web technologies and domain level ontologies. The NIH LINCS program aims to generate an extensive reference set of cellular response signatures to a variety of small molecule and genetic perturbations. The goal is to create a sustainable and widely accessible knowledge resource to advance understanding of the highly orchestrated interplay of molecular biological components in maintaining healthy development and how their perturbation causes disease. The data sets produced at LINCS span a variety of assay formats and technologies, including biochemical and single cell phenotypic responses, and genome-wide transcriptional profiling. This knowledge-based, extensible information system of interconnected components is designed to help scientists to use data and results produced in the LINCS and other NIH screening programs in their own research and to support their translation towards the development of novel therapeutics.bioassay, cell, small molecule, kinase protein, compound, cell, gene, metadata standard, cell line, primary cell, rnai reagent, rnai, reagent, protein reagent, protein, antibody reagent, antibody, perturbagen, growth factor, ligand, linked data, organ, disease, data setSCR_003937(LINCS Information Framework, RRID:SCR_003937)University of Miami; Florida; USA NHGRI, NHLBIrelated to: Broad Institute, Harvard Medical School, Massachusetts, USA, Columbia University, New York, USA, Yale University, Connecticut, USA, Arizona State University, Arizona, USA, uses: HMS LINCS Database, Bioassay Ontology, Molecular Libraries ProgramLast checked upnlx_158348
Cooperative Human Tissue NetworkResource, biomaterial supply resource, material resource, tissue bankThe Cancer Diagnosis Program of the National Cancer Institute (NCI) initiated the Cooperative Human Tissue Network (CHTN) in 1987 to provide increased access to human tissue for basic and applied scientists from academia and industry to accelerate the advancement of discoveries in cancer diagnosis and treatment. This unique resource provides remnant human tissues and fluids from routine procedures to investigators who utilize human biospecimens in their research. Unlike tissue banks, the CHTN works prospectively with each investigator to tailor specimen acquisition and processing to meet their specific project requirements. Because the CHTN is funded by the NCI, the CHTN is able to maintain nominal processing fees for its services. The CHTN is comprised of five adult divisions and one pediatric division. Each of the adult divisions coordinates investigator applications/requests based upon the investigator's geographic location within North America. The Pediatric Division manages all investigators who request pediatric specimens only. The CHTN divisions share coordination for requests from outside North America. The CHTN divisions work both independently with individual investigators and together as a seamless unit to fulfill requests that are difficult to serve by any single division. The CHTN's unique informatics system allows each division to effectively communicate and network the needs of its investigators to all CHTN divisions. The Network as a whole can then help fulfill an investigator's request. Biospecimens from surgeries, autopsies and other routine procedures: Malignant, Benign, Diseased, Normal, Biofluids (urine, serum, plasma, buffy coat) High quality specimens at LOW processing fees: Fresh, Frozen, Floating in fixative, RNAlater, Paraffin embedded or and/or unstained slidesbiomaterial supply resource, human tissue, network, cancer, NCISCR_004446(Cooperative Human Tissue Network, RRID:SCR_004446)NCIrelated to: UAB SPORE Biorepository Banks, University of Alabama, Alabama, USA, University of Pennsylvania, Philadelphia, Pennsylvania, University of Virginia, Virginia, USA, Ohio State University College of Medicine, Ohio, USA, Vanderbilt University, Tennessee, USA, listed by: One Mind Biospecimen Bank ListingLast checked downnlx_44126
Clinical and Translational Science Awards ConsortiumResource, knowledge environmentNational consortium of medical research institutions working together to transform the local, regional, and national environment to increase the efficiency and speed of clinical and translational research across the country. Consortium members share a common vision to reduce the time it takes for laboratory discoveries to become treatments for patients, to engage communities in clinical research efforts and to train clinical and translational researchers. This consortium includes 60 medical research institutions located throughout the nation, linking them together to energize the discipline of clinical and translational science. The CTSA consortium has five Strategic Goals: * National Clinical and Translational Research Capability * The Training and Career Development of Clinical and Translational Scientists * Consortium-Wide Collaborations * The Health of our Communities and the Nation * T1 Translational Researchbiomedical, clinical, community, consortium, institution, laboratory, medical, patient, research, researcher, science, translational, translational research, treatmentSCR_008339(Clinical and Translational Science Awards Consortium, RRID:SCR_008339) U.S. Department of Health and Human Services , Vanderbilt University; Tennessee; USA National Center for Advancing Translational Sciencesrelated to: REDCap, eBIRT, VIVO, CTSA ShareCenter, CUSP, CDART, cTAKES, CTSA-IP, FURTHeR, HUBzero, ePRISM, ResearchMatch, SPARC, Albert Einstein College of Medicine, New York, USA, Clinical Research Resource HUB, Eagle I, CTSAconnect, Boston University, Massachusetts, USA, Case Western Reserve University, Ohio, USA, Columbia University, New York, USA, Duke University, North Carolina, USA, Emory University, Georgia, USA, Morehouse School of Medicine, Georgia, USA, Georgia Institute of Technology, Georgia, USA, Georgetown University, Washington D.C., USA, Howard University, Washington D.C., Indiana University School of Medicine, Indiana, USA, Johns Hopkins University, Maryland, USA, Mayo Clinic, Medical College of Wisconsin, Wisconsin, USA, Medical University of South Carolina, South Carolina, USA, Icahn School of Medicine at Mount Sinai, New York, USA, New York University School of Medicine, New York, USA, Northwestern University, Illinois, USA, Oregon Health and Science University, Oregon, USA, Penn State Milton S. Hershey Medical Center, Pennsylvania, USA, Stanford University, Stanford, California, Ohio State University, Ohio, USA, Rockefeller University, New York, USA, The Scripps Research Institute, University of Alabama at Birmingham, Alabama, USA, University of North Carolina at Chapel Hill, North Carolina, USA, University of Texas Health Science Center at San Antonio, Texas, USA, University of Utah, Utah, USA, Tufts University, Massachusetts, USA, University of Arkansas for Medical Sciences, Arkansas, USA, University of California at Los Angeles, California, USA, University of California at Davis, California, USA, University of California at Irvine, California, USA, University of California at San Diego, California, USA, University of California at San Francisco, California, USA, University of Chicago, Illinois, USA, University of Cincinnati, Ohio, USA, University of Colorado Denver, Colorado, USA, University of Florida, Florida, USA, University of Illinois at Chicago, Illinois, USA, University of Iowa, Iowa, USA, University of Kansas Medical Center, Kansas, USA, University of Massachusetts Medical School, Massachusetts, USA, University of Miami, Florida, USA, University of Michigan, Michigan, USA, University of Minnesota Twin Cities, Minnesota, USA, University of New Mexico, New Mexico, USA, University of Pennsylvania, Philadelphia, Pennsylvania, University of Pittsburgh, Pennsylvania, USA, University of Rochester School of Medicine and Dentistry, New York, USA, University of Southern California, Los Angeles, USA, University of Texas Health Science Center at Houston, Texas, USA, University of Texas Medical Branch at Galveston, University of Texas Southwestern Medical Center, Texas, USA, University of Washington, Seattle, USA, University of Wisconsin-Madison, Wisconsin, USA, Vanderbilt University, Tennessee, USA, Meharry Medical College, Virginia Commonwealth University, Virginia, USA, Washington University in St. Louis, Missouri, USA, Weill Cornell Medical College, New York, USA, Hunter College, New York, USA, Yale University, Connecticut, USALast checked downnif-0000-24968
MIT Center for Biomedical InnovationResource, organization portal, portal, consortium, data or information resourceConsortium formed to improve global health by overcoming obstacles to the development and implementation of biomedical innovation. CBI provides a safe and transparent environment for collaborative research among industry, academia, and government, and draws on the expertise of the Massachusetts Institute of Technology''''s (MIT) Schools of Engineering, Science, and Management, as well as the Harvard-MIT Division of Health Sciences and Technology (HST). The center manages several consortia addressing a variety of challenges in the global biomedical industry by developing, testing, and disseminating new knowledge and tools designed for real world application through the following programs: the Biomanufacturing Program (BioMAN), the Consortium on Adventitious Agents in Biomanufacturing (CAACB), and New Drug Development Paradigms (NEWDIGS). The consortia managed by CBI include: * Biomanufacturing (BioMAN): a collaborative research and educational program in biotherapeutic manufacturing. The objective is to develop new knowledge, science, technologies and strategies that advance the manufacture and global delivery of high quality biopharmaceuticals. BioMAN activities bring together thought leaders from industry, the government/FDA and academia and involve faculty from across the Schools of Science, Engineering and Management at MIT * Consortium on Adventitious Agent Contamination in Biomanufacturing (CAACB): Their mission is to develop a comprehensive understanding of adventitious agents encountered in biomanufacturing, the sources of such agents, and a systematic, risk-based analysis of the most effective strategies and technologies to prevent contamination. * NEW Drug Development ParaDIGmS (NEWDIGS): focuses on transforming the current global pharmaceutical innovation ecosystem to more reliably and sustainably deliver new, better, affordable drugs to the right patients faster. System re-engineering projects are designed and executed with input from industry; regulators from US, Europe, Singapore, and Canada; payers and health technology assessment officials; providers, patients, and academic researchers from MIT, Harvard and other leading academic institutions.biomedical innovation, biomedical, innovation, biomanufacturing, biopharmaceutical, pharmaceutical, drug development, product development, tool development, clinical trial, drug, biotechnology, diagnostics, medical deviceSCR_004027(MIT Center for Biomedical Innovation, RRID:SCR_004027)Massachusetts Institute of Technology; Massachusetts; USA government, industry, Massachusetts Institute of Technology; Massachusetts; USA, Membership fees, Merck Company Foundation, MTC/JAII, Office of the Provost, Office of the Vice President for Research and Associate Provost, philanthropic organizations, School of Science, the MIT Sloan School of Management, the School of Engineeringrelated to: Alfred P. Sloan Foundation, Georgetown University, Washington D.C., USA, Northeastern University, Massachusetts, USA, Rensselaer Polytechnic Institute, New York, USA, listed by: Consortia-pediaLast checked upnlx_158454
little-man-taskResource, software resource, software application, data transfer software, data management software, data processing softwareSoftware tool to manage data and derived results. It is used for import of derived measures into REDCap (Research Electronic Data Capture).capture, data, manage, derive, measure, abcd, studySCR_016018(little-man-task, RRID:SCR_016018)NIDArelated to: University of California at San Diego, California, USALast checked up
timeline-followbackResource, software resource, software application, standalone software, data processing software, data acquisition softwareSoftware to capture subject information about substance use using local copies of external files provided by the abcd-report framework of ABCD. No connection to REDCap is attempted to get events and participant names but local files are read in to supply this information.capture, subject, information, drug, abuse, local, copy, event, abcd, participantSCR_016017(timeline-followback, RRID:SCR_016017)NIDArelated to: University of California at San Diego, California, USALast checked up
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