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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
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tbrowse Resource Report Resource Website |
tbrowse (RRID:SCR_001918) | tbrowse | software resource | Software providing a HTML5/javascript based browser for visualizing RNA-seq results in the familiar track layout of common genome browser. But given the quantitative nature of RNA-seq data, in addition to visualizing sequence coverage, the browser quantitates transcript abundance across regions of interest. The HTML5 functionality is made of use to render all the tracks using the canvas drawing element. This greatly reduces the load on servers and allows for rich interactive graphics without the need for third-party plugins. Furthermore, this framework completely segregates data from visualization, making development much easier. The browser is designed to run on all modern browsers: Firefox, Safari, Chrome, Opera and Internet Explorer (though not recommended). | genome, browser, transcriptome, html5, canvas, extjs, visualization, rna-seq |
is listed by: OMICtools has parent organization: Google Code |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01935 | SCR_001918 | SciCrunch Registry | tbrowse - HTML5 Transcriptome Browser | 2026-10-31 12:12:59 | 0 | |||||||
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Stanford Genomic Resourses Resource Report Resource Website |
Stanford Genomic Resourses (RRID:SCR_001874) | data or information resource, portal, topical portal | This resource hyperlinks to systematic analysis projects, resources, laboratories, and departments at Stanford University. | gene, genes, aspergillus, candida, genome, genomics, human, mouse | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-10436 | SCR_001874 | SciCrunch Registry | Genomic Databases | 2026-10-31 12:12:58 | 0 | |||||||||
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BioChemWeb.org - The Virtual Library of Biochemistry Molecular Biology and Cell Biology Resource Report Resource Website |
BioChemWeb.org - The Virtual Library of Biochemistry Molecular Biology and Cell Biology (RRID:SCR_001912) | BioChemWeb.org | data or information resource, portal, topical portal | This site is provided as a service to scientists, educators, students and others simply interested in the Biological subjects. While many of the resources listed on these pages are designed for scientific professionals, those that require little or no background are labeled as Beginner's Level. Topics include: Angiogenesis, Apoptosis, Carbohydrates, Cell Adhesion & ECM, Cell Cycle, Cell Senescence, Chemical Biology, Cytoskeleton & Motility, Development, Enzymes, Genes, Lipids & Membranes, Metabolism, Microscopy, Organelles, Proteins, Signaling, Structural Biology, Systems Biology Other available categories include: General Resources & Tutorials, Scientific Research Groups, Databases & Tools, Methods, Software, Vendors, Books, Journals, Literature Search, Career & Funding, Organizations & Meetings | educator, biochemistry, biology, cell biology, molecular biology, scientist, student, database, funding, job, software, data storage repository | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-10483 | SCR_001912 | SciCrunch Registry | BioChemWeb, BioChemWeb.org - The Virtual Library of Biochemistry Molecular Biology Cell Biology | 2026-10-31 12:12:59 | 0 | ||||||||
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National Center for e-Social Science: Obesity e-Lab Resource Report Resource Website |
National Center for e-Social Science: Obesity e-Lab (RRID:SCR_001796) | data or information resource, portal, topical portal | THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. Obesity e-Lab is a unique, secure environment for producing, sharing, communicating and finding obesity research between epidemiologists, public health researchers and social scientists. Features of e-Lab: - Tools to share: it enables social and biomedical researchers to share data, information and analytical tools for obesity research. First, it will create a portal to provide access to the platform and facilitate social networking. - Navigation tools: Second, it will generate search and navigation tools for researchers in academic, NHS or local government organizations to find data from administrative and secure data services, via social science views of health datasets, and health science views of social datasets. Within the NHS, e-Lab links records from a variety of administrative and health (and social) care sources for broadly-specified obesity research, and make pseudonymised extracts of NHS-linked datasets available via the portal. - Analytical tools: Third, it will develop analytical tools, focused on: i) easy, reliable and privacy-protecting transformation of geo-codes in health records to other geographies and area-based social and economic measures; ii) epidemiological extensions to geographical information systems; iii) growth-standardization of child obesity measures. The tool-building will employ as much existing software as possible, focusing on the provision of simple, intuitive interfaces to proven software to make it easy for social or biomedical researchers to use collaboratively. | epidemiologist, biomedical, geo-code, health science, networking, obesity, portal, public health, researcher, science, social researcher, social science, social scientist | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-10310 | http://www.ncess.ac.uk/research/obesity/ | SCR_001796 | SciCrunch Registry | NCeSS: Obesity e-Lab | 2026-10-31 12:12:57 | 0 | ||||||||
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Online Encyclopedia for Genetic Epidemiology studies Resource Report Resource Website 10+ mentions |
Online Encyclopedia for Genetic Epidemiology studies (RRID:SCR_001825) | OEGE | data or information resource, portal, topical portal | Portal for researchers to locate information relevant to interpretation and follow-up of human genetic epidemiological discoveries, including: a range of population and case and family genetic epidemiological studies, relevant gene and sequence databases, genetic variation databases, trait measurement, resource labs, journals, software, general information, disease genes and genetic diversity. | encyclopedia, epidemiology, gene, genealogist, genetic, genetic variation, diversity, health, journal, molecular genealogy, population genetics, sequence, software, trait, genome wide association study, genotyping, phenotyping, next generation sequencing, gene association study | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-10388 | SCR_001825 | SciCrunch Registry | OEGE - Online Encyclopedia for Genetic Epidemiology studies | 2026-10-31 12:12:57 | 12 | ||||||||
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SPADE Resource Report Resource Website 100+ mentions |
SPADE (RRID:SCR_001810) | data analysis software, data processing software, data visualization software, software application, software resource | An analysis and visualization software tool for high dimensional flow cytometry data that organizes cells into hierarchies of related phenotypes. | software package, mac os x, unix/linux, windows, r, clustering, flow cytometry, gui, graph, network, visualization |
is listed by: OMICtools has parent organization: Bioconductor is a plug in for: FlowJo |
PMID:21964415 | Free, Available for download, Freely available | OMICS_05639 | http://cytospade.org/ | http://www.bioconductor.org/packages/release/bioc/html/spade.html | SCR_001810 | SciCrunch Registry | Spanning tree Progression of Density normalized Events, SPADE - An analysis and visualization tool for Flow Cytometry | 2026-10-31 12:12:57 | 285 | |||||
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Neural Systems and Graphics Computing Laboratory: Micro3D Software Resource Report Resource Website |
Neural Systems and Graphics Computing Laboratory: Micro3D Software (RRID:SCR_001811) | data analysis software, data processing software, data visualization software, software application, software resource | The Micro3D 2004 is a software for 3-D reconstruction, visualization, and analysis of neuronal populations and brain regions. Micro3D generates geometric models from line and point coded data sets, representing labeled objects such as cell bodies or axonal plexuses, and boundaries of brain regions in serial sections. Data are typically imported from image-combining computerized microscopy systems, such as Neurolucida (MicroBrightField, Colchester, VT). The models may be rotated and zoomed in real-time. Surfaces are re-synthesized on the basis of stacks of contour lines. Clipping is used for defining section-independent subdivisions of the model. Flattening of sheets of points in curved layers (e.g., neurons in a cortical lamina) facilitates inspection of complicated distribution patterns. Micro3D computes color-coded density maps, and allows production of mpeg videos. Micro3D 2004 runs on LINUX PCs equipped with Open Inventor. It performs operations similar to the Silicon Graphics based version that has been used in more than 25 investigations and in various species, ranging from insects to monkeys, at the LM- and EM-level. Sponsors:Micro 3D was developed with support from The Research Council of Norway and The Oslo Research Park / FORNY. | 3-d reconstruction, analysis, axonal plexus, brain, cell body, computerized, contour line, density map, geometric, insect, microscopy, model, monkey, neuronal, object, population, region, serial section, software, specie, visualization, image | PMID:16596747 | Free, Available for download, Freely available | nif-0000-10375 | SCR_001811 | SciCrunch Registry | NeSys Micro3D | 2026-10-31 12:12:57 | 0 | ||||||||
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Kindai University; Osaka; Japan Resource Report Resource Website 1+ mentions |
Kindai University; Osaka; Japan (RRID:SCR_001814) | university | Private non-sectarian and coeducational university based in Higashiosaka, Osaka, Japan. | private, university, osaka, japan | is parent organization of: Kindai University School of Medicine; Osaka; Japan | Free | ISNI:0000 0004 1936 9967, nlx_149308, grid.258622.9, Wikidata:Q912329 | https://ror.org/05kt9ap64 | SCR_001814 | SciCrunch Registry | Kinki University | 2026-10-31 12:12:57 | 1 | |||||||
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AStalavista Resource Report Resource Website 50+ mentions |
AStalavista (RRID:SCR_001815) | AStalavista | analysis service resource, data analysis service, production service resource, service resource, software resource | Tool that extracts and displays alternative splicing (AS) events from a given genomic annotation of exon-intron gene coordinates. By comparing all given transcripts, it detects the variations in their splicing structure and identifies all AS events (like exon skipping, alternate donor, etc) by assigning to each of them an AS code. It provides a visual summary of the AS landscape in the analyzed dataset, the possibility to browse the results on the UCSC website or to download them in GTF or ASTA format. You can use AStalavista for any genome by providing your own annotation set, the identifier of your gene(s) of interest, or analyze the AS landscape of reference annotation datasets like Gencode, RefSeq, Ensembl, FlyBase, etc. | alternative splicing event, alternative splicing, visualization, genome, transcript |
is listed by: OMICtools is listed by: SoftCite has parent organization: Center for Genomic Regulation; Barcelona; Spain |
PMID:17485470 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01943 | http://genome.imim.es/astalavista, http://genome.crg.es/astalavista/ | SCR_001815 | SciCrunch Registry | Alternative Splicing transcriptional landscape visualization tool | 2026-10-31 12:12:57 | 86 | |||||
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PDtrials- Parkinsons Disease Clinical Trials Resource Report Resource Website 1+ mentions |
PDtrials- Parkinsons Disease Clinical Trials (RRID:SCR_002027) | data or information resource, database, disease-related portal, portal, topical portal | THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. A collaborative initiative of Parkinson's organizations dedicated to increasing education and awareness about clinical research. PDtrials provides up-to-date information on Parkinson's disease trials currently enrolling participants in the U.S. and Canada, as well as information about Parkinson's studies for people living with PD, their families and caregivers. Researchers can list their own trials on the PDtrials website. Patients can browse trial listings by type, location, symptom, or keyword. | parkinson's disease, parkinson's disease clinical trial, pd, pd clinical trial, disease related portal, database, topical portal, patient care | Parkinson's disease | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-11762 | SCR_002027 | SciCrunch Registry | PDtrials | 2026-10-31 12:13:00 | 8 | ||||||||
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VideoLectures.NET Resource Report Resource Website |
VideoLectures.NET (RRID:SCR_001972) | VideoLectures.NET | data or information resource, narrative resource, training material, video resource | Award-winning free and open access educational video lectures repository. The lectures are given by distinguished scholars and scientists at the most important and prominent events like conferences, summer schools, workshops and science promotional events from many fields of Science. The portal is aimed at promoting science, exchanging ideas and fostering knowledge sharing by providing high quality didactic contents not only to the scientific community but also to the general public. All lectures, accompanying documents, information and links are systematically selected and classified through the editorial process taking into account also users' comments. | artificial science, machine learning, network, science, semantic, lecture, biology, chemistry, computers, computer science. environment, health sciences, life science, mathematics, medicine, physics, thechnology | has parent organization: Jozef Stefan Institute; Ljubljana; Slovenia | European Union | Unless otherwise noted, Creative Commons Attribution-NonCommercial-NoDerivs License, v3 | nif-0000-10544 | SCR_001972 | SciCrunch Registry | VideoLectures, Video Lectures: Exchange Ideas and Share Thoughts, VideoLectures.Net: Exchange Ideas & Share Thoughts | 2026-10-31 12:12:59 | 0 | ||||||
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SHARCGS Resource Report Resource Website 1+ mentions |
SHARCGS (RRID:SCR_002026) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software package for a DNA assembly program designed for de novo assembly of 25-40mer input fragments and deep sequence coverage. | dna, assembly, de novo, rna, sequencing, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Max Planck Institute for Molecular Genetics; Berlin; Germany |
PMID:17908823 | Free, Available for download, Freely available | OMICS_00029, biotools:sharcgs | https://bio.tools/sharcgs | SCR_002026 | SciCrunch Registry | SHort read Assembler based on Robust Contig extension for Genome Sequencing (SHARCGS), SHARCGS - SHort read Assembler based on Robust Contig extension for Genome Sequencing, SHort read Assembler based on Robust Contig extension for Genome Sequencing | 2026-10-31 12:13:00 | 4 | ||||||
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Pennsylvania State Hershey College of Medicine; Pennsylvania; USA Resource Report Resource Website |
Pennsylvania State Hershey College of Medicine; Pennsylvania; USA (RRID:SCR_002019) | university | Public, land-grant research university in Pennsylvania, USA. The College of Medicine offers professional degree programs in medicine. | medicine, public, research, university |
has parent organization: Pennsylvania State University is parent organization of: Pennsylvania State University College of Medicine Neuroscience is parent organization of: Penn State College of Medicine Genome Sciences Core Facility is parent organization of: Penn State Hershey College of Medicine Clinical Research Biospecimen Core Facility is parent organization of: Penn State Hershey College of Medicine MRI Core Facility is parent organization of: Penn State Hershey College of Medicine Zebrafish Functional Genomics Core Facility is parent organization of: Penn State Hershey College of Medicine Transmission Electron Microscopy Core Facility is parent organization of: Penn State Hershey College of Medicine Light Microscopy Imaging Core Facility is parent organization of: Pennsylvania State University Hershey College of Medicine Custom Antibody Core Facility is parent organization of: Penn State College of Medicine High Performance Computing Core Facility is parent organization of: Penn State Hershey College of Medicine Comparative Medicine Imaging Core Facility is parent organization of: Penn State College of Medicine Biomolecular NMR Core Facility is parent organization of: Penn State Hershey College of Medicine Atomic Force Microscopy Core Facility is parent organization of: Penn State College of Medicine Pulmonary Immunology and Physiology Core Facility is parent organization of: Penn State Hershey College of Medicine Institutional Biorepository Core Facility is parent organization of: Penn State Hershey College of Medicine Flow Cytometry and Cell Sorting Core Facility is parent organization of: Penn State Hershey College of Medicine cryo-EM Core Facility |
nlx_82737 | http://med.psu.edu/web/college/home | SCR_002019 | SciCrunch Registry | Penn State Hershey College of Medicine; Pennsylvania; USA, Pennsylvania State Hershey College of Medicine, Penn State Hershey College of Medicine | 2026-10-31 12:13:00 | 0 | ||||||||
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SNPper Resource Report Resource Website 50+ mentions |
SNPper (RRID:SCR_001963) | SNPper | software resource | Retrieve known single-nucleotide polymorphisms (SNPs) by position or by association with a gene; save, filter, analyze, display or export SNP sets; explore known genes using names or chromosome positions. | single-nucleotide polymorphism, gene, chromosome |
is listed by: OMICtools has parent organization: University of Florida; Florida; USA |
PMID:12490454 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01926 | SCR_001963 | SciCrunch Registry | 2026-10-31 12:12:59 | 50 | |||||||
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National Center for PTSD Resource Report Resource Website 10+ mentions |
National Center for PTSD (RRID:SCR_001967) | NCPTSD | institution | We are the center of excellence for research and education on the prevention, understanding, and treatment of PTSD. Our Center has seven divisions across the country. Although we provide no direct clinical care, our purpose is to improve the well-being and understanding of American Veterans. We conduct cutting edge research and apply resultant findings to: Advance the Science and Promote Understanding of Traumatic Stress. The National Center has emerged as the world's leading research and educational center of excellence on PTSD. Its vision is to be the foremost leader in information on PTSD and trauma; information generated internally through its extensive research program, and information synthesized from published scientific research and collective clinical experience that is efficiently disseminated to the field. The Center is organized to facilitate rapid translation of science into practice, assuring that the latest research findings inform clinical care; and translation of practice into science, assuring that questions raised by clinical challenges are addressed using rigorous experimental protocols. By drawing on the specific expertise vested at each separate division (e.g., behavioral, neuroscientific, etc.), the National Center provides a unique infrastructure within which to implement multidisciplinary initiatives regarding the etiology, pathophysiology, diagnosis and treatment of PTSD. | post-traumatic stress disorder, stress, trauma, treatment, stress-related disorder, clinical care, human, traumatic stress disorder, one mind ptsd | has parent organization: U.S. Department of Veterans Affairs | US Department of Veterans Affairs | nif-0000-10538, grid.497281.1, ISNI: 0000 0004 0374 606X | https://ror.org/01dbbht76 | http://www.ncptsd.va.gov/ | SCR_001967 | SciCrunch Registry | National Center for Posttraumatic Stress Disorder, VA National Center for PTSD | 2026-10-31 12:12:59 | 17 | |||||
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Neurofed Resource Report Resource Website |
Neurofed (RRID:SCR_002011) | Neurofed | people resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented on August 26, 2016. The NeuroFed resource is a listing of neuroscience research funding contacts in the Federal government. It is an informal compendium (PDF) of names and contact information for nearly 300 research grant and scientific review administrators in 21 organizational units of the federal government. An electronic (PDF) version of the most recent update of this list is available on the Society for Neuroscience website at: http://www.sfn.org/index.aspx?pagename=professionalDevelopment_training. The list is updated annually by NIH personnel. |
is used by: NIF Data Federation has parent organization: National Institutes of Health |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-10988 | SCR_002011 | SciCrunch Registry | 2026-10-31 12:13:00 | 0 | |||||||||
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Parkinson Society Canada Resource Report Resource Website 1+ mentions |
Parkinson Society Canada (RRID:SCR_002014) | nonprofit organization | A not-for-profit, volunteer based charity whose purpose is to find a cure for Parkinson's disease through research, advocacy, education and support services. Parkinson Society Canadas leads initiatives that include: raising funds for research through national events; funding research, movement disorder clinics, and outreach programs across Canada; staffing a national Information and Referral Centre; developing educational and information materials; providing up to date detailed information about Parkinson's disease; and providing support for regional partners to better meet the needs of people living with Parkinson's services. Researchers can apply for various funding awards and fellowships by following the funding process outlined by Parkinson Society Canada. | parkinson's disease, parkinson's disease online community, parkinson's disease organizations, parkinson's disease patient care, parkinson's disease therapy, parkinson's disease treatment center | Parkinson's Disease | Public, Funding is available to researchers in the form of awards and fellowships | grid.453461.1, Crossref funder ID: 501100000263, nif-0000-11672 | https://ror.org/04amfk357 | SCR_002014 | SciCrunch Registry | 2026-10-31 12:13:00 | 5 | ||||||||
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SA Instruments: Model 1025 MR-compatible Small Animal Monitoring and Gating System Resource Report Resource Website 1+ mentions |
SA Instruments: Model 1025 MR-compatible Small Animal Monitoring and Gating System (RRID:SCR_002090) | Model 1025 Monitoring & Gating System | instrument resource | Magnetic resonance compatible monitoring and gating system, including software, that enables monitoring rectal temperature, electrocardiogram and respiration rate during magnetic resonance imaging scan time. The PC displays multiple waveforms, measured values, trends and gating pulses. The data Acquisition modules are controlled by menu driven software from the PC. Data acquisition modules are available to measure the following parameters: ECG, respiration (three ways), temperature (two ways), pressure including invasive blood pressure (two ways), oxygen saturation and end-tidal CO2. | hardware, instrument, equipment, physiology, monitoring, gating, mr environment, respiration, temperature, blood pressure, oxygen saturation, end-tidal co2, magnetic resonance, electrocardiogram, magnetic resonance imaging, software resource | Free, Freely available | SciRes_000157 | https://wikihost.uib.no/mriwiki/images/4/4c/SAInstruments_1025.pdf | http://www.i4sa.com/web_app/main/defaultProduct.aspx?ID=82&PT=3 | SCR_002090 | SciCrunch Registry | Model 1025 Monitoring and Gating System, MR-Compatible Model 1025 Monitoring and Gating System, Small Animal Monitoring and Gating System | 2026-10-31 12:13:01 | 3 | ||||||
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Cvapp Resource Report Resource Website 1+ mentions |
Cvapp (RRID:SCR_002095) | data or information resource, data processing software, database, software application, software resource, source code | Online platform for visualizing and editing the morphology of neurons. Written in Java. | neuron morphology, java applet, visualization platform, editing platform |
has parent organization: George Mason University; Virginia; USA has parent organization: Duke University; North Carolina; USA has parent organization: University of Southampton; Southampton; United Kingdom |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-00109 | https://github.com/pgleeson/Cvapp-NeuroMorpho.org | http://www.compneuro.org/CDROM/docs/cvapp.html | SCR_002095 | SciCrunch Registry | 2026-10-31 12:13:01 | 2 | |||||||
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Korea National Institute of Health Resource Report Resource Website 10+ mentions |
Korea National Institute of Health (RRID:SCR_001959) | KNIH | institution | Institute dedicated to medical research to improve biomedical innovation and public health in South Korea. | health research institute, south korea | is parent organization of: Genovar | THIS RESOURCE IS NO LONGER IN SERVICE | grid.415482.e, ISNI: 0000 0004 0647 4899, nlx_156100, Crossref funder ID: 501100003653 | https://ror.org/00qdsfq65 | SCR_001959 | SciCrunch Registry | Korea NIH | 2026-10-31 12:12:59 | 13 |
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