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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: Aug 10, 2019)

Physical Resource or Software Tool Software

16,721 Results - per page

Resource NameResource TypeDescriptionKeywordsResource IDProper CitationParent OrganizationRelated ConditionFunding AgencyRelationReferenceWebsite StatusAlternate IDsAlternate URLsOld URLs
TransGenicResource, reagent supplier, material resource, antibody supplierA commercial antibody supplier and knockout mice producer.commercial organization, antibody supplier, knockout mouseSCR_000001(TransGenic, RRID:SCR_000001)Last checked upnlx_152482
monarch-ontologiesResource, ontology, data or information resource, controlled vocabularyThe set of ontologies used within the Monarch Initiative. MONARCH members are free to add new imports.phenotypeSCR_000002(monarch-ontologies, RRID:SCR_000002)Monarch Initiative related to: Vertebrate Trait OntologyLast checked upnlx_152901
Sarah Cannon Research Institute; Tennessee; USAResource, institutionA global cancer institute of the Hospital Corporation of America which offers integrated cancer services with access to current therapies.cancer institute, cancer service, cancer therapySCR_000003(Sarah Cannon Research Institute; Tennessee; USA, RRID:SCR_000003)Last checked upnlx_158000
GE HealthcareResource, reagent supplier, material resource, antibody supplierA commercial antibody supplier and provider of various services.antibody supplier, service provider, commercialSCR_000004(GE Healthcare, RRID:SCR_000004)lists: Amersham BiosciencesLast checked upnlx_152368
Neuroshare - Open data specifications and software for neurophysiologyResource, software resource, software toolkit, software libraryNeuroshare aims to develop a standard for accessing neurophysiological data from any vendor's acquisition device or software. An API is defined, and vendors and communities are encouraged to provide implementations of a library of functions that can read data files collected with that vendor's instrument or software. The website is a collaborative, vendor-neutral area dedicated to public domain standards and software for neurophysiology.This website is part of an SBIR program funded by the National Institute for Neural Disorders and Stroke and it is currently being administered by Bionic Technologies, LLC. The goals of the SBIR program are to (Phase I) create open library and format standards for neurophysiological experiment data and (Phase II) create a set of free, open-source software tools for low-level handling and processing of neurophysiological data. Upon completion of Phase I and II, will be maintained by a yet to be determined consortium of government, academic and industry partners. The SBIR was awarded in the fall of 2001 and Phase I officially began in Dec, 2001. The detailed goals of the program are summarized below:Phase I goals :(1) Establish a working group to develop and define the API library of functions.(2) A vendor-neutral web site to facilitate the development of the standards and software and publish the completed products. This site has been dubbed Neuroshare. The home page can be found at An open, standardized API library definition for accessing neurophysiology data files. This will allow developers to produce analysis programs that can access a variety of proprietary data formats through libraries supplied by the data format owners. The manner of support will be completely determined by the research groups and vendors that supply the libraries. The Phase I standard was created by a working group consisting of international members from industry and academia. Draft standards were published for public review and comment on the neuroshare web site and revised by the working group.The grant has been awarded as a fast-track program so that Phase II begins immediately upon completion of the Phase I milestones in June 2002. Phase II will produce :(1) A set of neuroshare-compliant API libraries for existing data formats developed in collaboration with individual equipment vendors and research groups.(2) A utility for analyzing compliant API libraries for integrity and specification conformance, as well as for error checking imported data files.(3) A set of template programs in C that are meant to be used as an example on how to create a Neuroshare API compliant library and how to call it from an application,(4) An open, standardized file format for neurophysiological experiment data. This format will provide research groups and vendors with a file format for exchanging and/or publishing neural data. The format will also be powerful enough for use as a native format for researchers or vendors that wish to support it in data acquisition hardware/software.(5) Import filters that interface neuroshare-compliant API libraries to Visual Basic, MATLAB, and LabVIEW, NeuroExplorer, and Stranger analysis environments.(6) A utility program for quick header information viewing and searching to aid the organization and management of data files in the standard and proprietary formats.(7) A data file editing program for reviewing, editing, annotating, and splicing neural data files through the neuroshare API libraries and/or standard file formats. The suite will be developed in C, optimized for speed, and will run within 32-bit Windows operating systems. The availability of source code will enable eventual ports to Unix/Linux if desired(8) An add-on for the editing program that will allow review and real-time playback of multi-modal data accessible through the API and/or standard file format. These modes will include neurophysiological signals such as spikes, local field potentials and EEG, as well as experimental signals such as kinematics, stimulation, audio, video, and imaging data.(9) C and MATLAB framework programs for detection and classification of extracellular spikes in the standard data files based on classical and user-supplied algorithms.(10) A complete MATLAB application for reading data from the standard format and performing reverse correlation analysis. This program will serve as a tutorial and modifiable template for users performing analysis in MATLAB.(11) A set of export filters for creating neurophysiological data files with the neural simulation environments NEURON, NEOSIM, GENESIS, and NSL.(12) A comprehensive documentation, and help file set for all of the developed applications.Phase II will require two years of development work and software products will be made available as they are completed. As stated above, the Phase II software products will be made available as free, open-source tools. We have not decided on a license model yet, but are currently leaning towards the GNU General Public License. Revisions and bug-fixes will be maintained through the website. The mission of is very focused, but the specific goal list of Phase II may evolve somewhat as software is released and user feedback is received. We very interested in public suggestions about how to improve this development effort and web site. Please direct your feedback to or refer to our contacts page for other addresses.BackgroundThis endeavor grew out of a meeting held at the Society for Neuroscience 2000 Annual Conference in New Orleans (agenda posted here) to discuss the development of standard data formats for neuroscience. From this meeting, it was clear that although everyone supported the idea of better data portability, many vendors present wanted a standardized API (Application Program Interface) library rather than a universal data format. Based on this meeting, we submitted an SBIR application (with letters of support from key attendants of the SFN meeting) to fund the development of a standardized API definition, data format, and a suite of open source data handling and review management, development, interoperability software, softwareSCR_000005(Neuroshare - Open data specifications and software for neurophysiology, RRID:SCR_000005)related to: BrainLinerLast checked upnif-0000-00023
University of Algarve; Faro; PortugalResource, topical portal, portal, data or information resourceA young state university located in the southern part of, portugal, topical portalSCR_000006(University of Algarve; Faro; Portugal, RRID:SCR_000006)Last checked upnlx_157657
G BiosciencesResource, reagent supplier, material resource, antibody supplierA commercial antibody supplier that provides research materials for projects such as: protein purification, protein analysis, protein estimation assays, DNA purification, plasmid DNA isolation and transformation, protein quantification assays, and coupled assays for methylation. This supplier also provides buffers, reagents, education programs, and training programs.antibody vendor, buffer vendor, education programs, training programs, reagentSCR_000007(G Biosciences, RRID:SCR_000007)Last checked upnlx_152367
University at Albany SUNY Labs and FacilitiesResource, service resource, portal, core facility, access service resource, data or information resourceA facility that conducts a wide variety of research programs ranging from cell biology to community-based participatory research. Research is conducted through four academic departments including: the Cancer Research Center, the Prevention Research Center, the Public Health Preparedness Center, the Cardiac Quality improvement initiative and the Center for Health Workforce Studies. This facility also hosts research projects and faculty scholarships to aid Master's and Doctoral students in course work, laboratory rotations and internships.cell biology, cancer research, disease prevention, public health, cardiac, laboratory rotations, internships, course workSCR_000008(University at Albany SUNY Labs and Facilities, RRID:SCR_000008)University at Albany; New York; USA related to: University at Albany Center for Functional Genomics Labs and Facilities, listed by: Science ExchangeLast checked upSciEx_4303
ncdfFlowResource, software resourceSoftware package that provides netCDF storage based methods and functions for manipulation of flow cytometry package, mac os x, unix/linux, windows, r, flow cytometrySCR_000009(ncdfFlow, RRID:SCR_000009)Bioconductor listed by: OMICtoolsLast checked upOMICS_05617
Computational Neuroscience on the WebResource, topical portal, portal, data or information resourceAnnotated index for computational neurobiology, focusing on compartmental modeling and realistic simulations of biological neural systems. Has resources to find modeling software and software for computational morphology, phase plane and spike train analysis, and web based neuroinformatics. Provides links to major laboratories, researchers, conferences, education and funding for theoretical neurobiology.computational, neuroscience, compartmental, modeling, simulation, biological, neural, system, neuroinformatics, indexSCR_000010(Computational Neuroscience on the Web, RRID:SCR_000010)Last checked upnif-0000-00107
Leica DMRE Fluorescence MicroscopeResource, resourceMicroscope that enables bright field and fluorescence imaging options.microscope, fluorescence, imaging, hardware, instrument, equipmentSCR_000011(Leica DMRE Fluorescence Microscope, RRID:SCR_000011)Leica Microsystems Last checked upSciRes_000155
Offline SorterResource, software resource, commercial organizationOffline spike sorting software. This software tool for viewing and classifying action potential waveforms (spikes) previously collected from single electrodes, stereotrodes and tetrodes accepts file types from many data acquisition companies and software xp, windows 7, action potential, waveform, spike, classifySCR_000012(Offline Sorter, RRID:SCR_000012)Last checked upnlx_158484
BSmooth-alignResource, software resource, data processing software, data analysis software, sequence analysis software, software applicationA statistics and alignment pipeline software that performs the alignment of bisulfite sequence reads and tabulates read-level methylation measurements.bisulfite sequence, read-level methylation, software analysisSCR_000013(BSmooth-align, RRID:SCR_000013)listed by: OMICtoolsLast checked upOMICS_01846
University of Pittsburgh Conte Center for the Neuroscience of Mental DisordersResource, disease-related portal, topical portal, training resource, degree granting program, undergraduate program resource, portal, postdoctoral program resource, data or information resourceThe Conte Center for the Neuroscience of Mental Disorders (CCNMD) at the University of Pittsburgh offers a highly interactive scientific environment for the study of the neurobiology of schizophrenia. The Center, directed by David A. Lewis, MD, integrates the laboratory and clinical research activities of investigators from the University of Pittsburgh Schools of Medicine and Arts and Sciences and the adjacent Carnegie Mellon University. Collectively, the CCNMD represents a broad array of expertise spanning molecular, systems, cognitive, computational and clinical neuroscience that provides complementary approaches to testing one central hypothesis about the disease process of schizophrenia: A distinctive pattern of molecular alterations in subpopulations of GABA neurons (pathology) creates disturbances in cortical network oscillations (pathophysiology) that underlie the information processing deficits (clinical syndrome) of schizophrenia. The Center's hypothesis is based on widely-replicated data showing reduced expression of the gene that synthesizes the neurotransmitter GABA in the cerebral cortex of individuals with schizophrenia. CCNMD investigators are working to understand how the resulting reduced levels of GABA could lead to impaired synchronization of other networks of neurons in the cerebral cortex specifically, the neuronal networks which subserve cognitive functions that are disturbed in schizophrenia. The CCNMD is composed of 5 research projects that are designed to provide convergent tests of this hypothesis. The synergism of these projects facilitates a translational approach to schizophrenia research, making laboratory findings readily relevant to clinical treatment. The CCNMD's work is directed at identifying pathophysiology-based molecular targets for new therapeutic interventions and at developing biomarkers of this pathophysiology that can be used to monitor the efficacy of such interventions. Thus, the CCNMD is a multi-disciplinary effort directed at testing a mechanistic hypothesis in order to improve our understanding of a core component of the disease process of schizophrenia. In addition, the Conte Center represents a rich environment for training and career development in which individuals can become involved in studies that bring the methods and knowledge of basic neuroscience to address critical questions in clinical schizophrenia research, The CCNMD hopes to help propel the development of new and more effective treatments for individuals with schizophrenia and to provide a vehicle for disseminating the knowledge gained from translational studies of schizophrenia to the broader scientific and lay communities. The Post-Doctoral Training Program in Schizophrenia Research provides extensive training in cutting-edge basic and clinical research strategies for schizophrenia. The National Institute of Mental Health Conte Center for the Neuroscience of Mental Disorders (CCNMD) Undergraduate Research Fellowship provides highly talented undergraduate students with early-career, hands-on engagement in cutting edge neuroscience research. Research opportunities focus on schizophrenia and related disorders and are primarily translational in approach; that is, the CCNMD research approach begins with clinical observations about the disease process that are converted into hypotheses that can be tested in the more tractable conditions of the laboratory in order to guide the development of novel therapeutic interventions.schizophrenia, gabaSCR_000014(University of Pittsburgh Conte Center for the Neuroscience of Mental Disorders, RRID:SCR_000014)University of Pittsburgh; Pennsylvania; USA NIMHLast checked upnlx_144496
4PeaksResource, software resource, software applicationSoftware application for viewing and editing sequence trace files.mac os x, sequence, trace fileSCR_000015(4Peaks, RRID:SCR_000015)listed by: OMICtoolsLast checked upOMICS_01015
CSDeconvResource, software resource, data processing software, data analysis software, sequence analysis software, software applicationA software application that maps transcription factor binding sites from ChIP-seq data to high resolution using a blind deconvolution approach.sequence analysis software, transcription factor binding site, chip-seq, blind deconvolution, transcription bindingSCR_000016(CSDeconv, RRID:SCR_000016)Rutgers University; New Jersey; USA , University of South Australia; Adelaide; Australia listed by: OMICtoolsPMID:20028542Last checked upOMICS_00436
TabletResource, software resourceA lightweight, high-performance graphical viewer for next generation sequence assemblies and generation sequence, assembly, alignmentSCR_000017(Tablet, RRID:SCR_000017)James Hutton Institute; Scotland; United Kingdom listed by: OMICtoolsPMID:22445902Last checked upOMICS_00896
Midwest Transplant NetworkResource, biomaterial supply resource, material resource, tissue bankAn organization that specifically operates in Kansas and the the western half of Missouri, and provides help with connecting the community to organ and tissue procurement, as well as generates general public awareness. This organization is a federally certified non-profit Organ Procurement Organization (OPO) that is meant to help in several facets of transplant and procurement services.organ procurement, transplant, tissue procurement, public awareness, kansa, western missouriSCR_000018(Midwest Transplant Network, RRID:SCR_000018)listed by: One Mind Biospecimen Bank ListingLast checked upnlx_87553
NeuroTribesResource, blog, narrative resource, data or information resourceSteve Silberman's personal blog highlighting science, culture, politics and neurodiversity. Steve is an investigative reporter for Wired and other national magazines.mind, science, culture, steve silbermanSCR_000019(NeuroTribes, RRID:SCR_000019)PLoS Blogs Last checked upnlx_91543
Ludwig Boltzmann Cluster Translationale OnkologieResource, topical portal, portal, data or information resourceThe projected cluster includes the LBIs for Applied Cancer Research, Clinical Oncology and Photodynamic Therapy, Gynecology and Gynecologic Oncology, Stem Cell Transplantation and Surgical Oncology. The aim of the projected cluster Translational Oncology is the cooperative investigation of genetic and molecular biological characteristics of the tumor cells involved in minimal residual disease (MRD) in vitro and translation of the experimental and diagnostic results into the clinical practice involving therapeutic modalities with the newest generation of antitumoral drugs. Minimal residual disease is the designation for the occurrence of a low number of tumor cells remaining clinically undetected following curative therapy that give rise to tumor relapses. MRD is a central question in cancer therapy, since a major subpopulation of patients which underwent curative resection and therapy ultimately relapse and would have received more aggressive adjuvant therapy, provided that residual disease had been clearly proven. Otherwise low-risk patients would have not been treated aggressively in an adjuvant setting. MRD can be detected by methods in bone marrow or by extremely sensitive PCR (polymerase-chain-reaction)-based methods in peripheral blood. PCR-based methods allow for the characterization of tumor-specific gene expression in circulating tumor cells and thereby provide additional information in regard to malignity of cells and prognosis. The different participating institutions have extensive experience in patient care, organization of clinical studies and laboratory investigation. In particular, expert knowledge in stem cell transplantation and histological detection of MRD, multicentric clinical testing of new anticancer drugs, specialized treatment of various selected tumor entities such as neuroendocrine tumors, gene expression analysis of circulating tumor cells and tumor signatures, and in vitro characterization of chemosensitivity as well as tumor cell biology have been acquired at the individual LBIs in the past and are complementary to each other to be combined in a larger cluster structure. The detection of circulating tumor cells will be supported by ongoing EU (OVCAD OVarian CAncer Diagnosis) and GenAU projects aiming at identification of ovarian cancer cells in the blood. The assessment of methylated DNA sequences (suppressor genes) in peripheral blood as an indicator of MRD can be performed with the help of OncoLab Diagnostics GmbH. Cooperative action in this cluster, using a common tumor bank/clinical data collection and the combined clinical and experimental efforts are the base for the execution of the presented MRD project.cancer, tumor, clinical, oncology, photodynamic therapy, gynecology, gynecologic oncology, stem cell transplantation, surgical oncology, tumor cellSCR_000020(Ludwig Boltzmann Cluster Translationale Onkologie, RRID:SCR_000020)Last checked upnlx_143958
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