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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
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PLEXdb - Plant Expression Database Resource Report Resource Website 10+ mentions |
PLEXdb - Plant Expression Database (RRID:SCR_006963) | PLEXdb | analysis service resource, data analysis service, data or information resource, data repository, database, portal, production service resource, service resource, storage service resource, topical portal | PLEXdb (Plant Expression Database) is a unified gene expression resource for plants and plant pathogens. PLEXdb is a genotype to phenotype, hypothesis building information warehouse, leveraging highly parallel expression data with seamless portals to related genetic, physical, and pathway data. The integrated tools of PLEXdb allow investigators to use commonalities in plant biology for a comparative approach to functional genomics through use of large-scale expression profiling data sets. | gene expression, plant, plant pathogen, genotype, phenotype, genetic, physical, pathway, plant biology, compare, functional genomics, expression profiling, expression atlas, pathogen, genome, anova, cluster, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: FuncExpression has parent organization: Iowa State University; Iowa; USA |
UniNSF DBI-0543441; NSF IOS-0922746; USDA 3625-21000-049-00D |
PMID:22084198 | biotools:plexdb, r3d100011516, nlx_149236 | https://bio.tools/plexdb, https://doi.org/10.17616/R39D13 | SCR_006963 | SciCrunch Registry | PLEXdb - Gene expression resources for plants and plant pathogens, Plant Expression Database | 2026-11-07 12:00:34 | 21 | |||||
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HDBase Resource Report Resource Website |
HDBase (RRID:SCR_007132) | HDBase | data or information resource, data set, disease-related portal, portal, topical portal | A community website for Huntington''s Disease (HD) research that currently contains Y2H and Mass spectrometry protein-protein interaction data centered around the HD protein (huntingtin) and information on therapeutic studies in mouse. Also available are raw Human and Mouse Affymetrix Microarray data. The protein interaction data is from several sources, including interactions curated from the literature by ISB staff, experimentally determined interactions produced by Bob Hughes and colleagues at Prolexys (currently password protected), and interactions reported in a recent publication by Goehler et al from Eric Wanker''s lab. Content areas that may be covered by the site include the following: * Therapeutic studies in mouse, primarily drug screens. * HD mouse models with a focus on timelines of disease progression. * Antibodies used in HD research. * Microarray gene expression studies. * Genes and proteins relevant to HD research. This includes HD itself, the growing list of proteins thought to interact directly or indirectly with huntingtin (Htt), and other genes and proteins implicated in the disease process. * Molecular pathways thought to be involved in the disease process. * Timelines of disease for Mouse models | drug, gene expression, huntingtin, mass spectrometry, microarray, protein interaction, protein-protein interaction, y2h, mouse model, treatment, disease, phenotype, brain, striatum, adipose, muscle, gene, protein, antibody, pathway |
uses: Cytoscape has parent organization: Institute for Systems Biology; Washington; USA |
Huntington''s disease, Control | Hereditary Disease Foundation | nif-0000-00153 | SCR_007132 | SciCrunch Registry | HDBase - A Community Website for Huntingtons Disease Research, HDBase - A Community Website for Huntington''s Disease Research | 2026-11-07 12:00:15 | 0 | ||||||
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Cytoseg Resource Report Resource Website 1+ mentions |
Cytoseg (RRID:SCR_009553) | Cytoseg | data processing software, image analysis software, segmentation software, software application, software resource | A tool for automatic segmentation of 3D biological datasets, with emphasis on 3D electron microscopy. It works best for 3D blob shaped objects like mitochondria, lysosomes, etc. The project is written in Python and uses the pythonxy platform (which includes scipy and ITK image processing tools). | computational neuroscience, neuropil, 3d electron microscopy, electron microscopy | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | GNU Lesser General Public License | nlx_155733 | http://www.nitrc.org/projects/cytoseg | SCR_009553 | SciCrunch Registry | 2026-11-07 12:00:17 | 1 | |||||||
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University of Arkansas for Medical Sciences Department of Pharmacology and Toxicology Resource Report Resource Website |
University of Arkansas for Medical Sciences Department of Pharmacology and Toxicology (RRID:SCR_007496) | data or information resource, department portal, organization portal, portal | THIS RESOURCE IS NO LONGER IN SERVICE, documented on January 25,2022. Department of Pharmacology and Toxicology is the professional home to 18 faculty, 11 research faculty, 22 graduate students and 3 postdoctoral fellows. They offer graduate training leading to the Ph.D. degree in Pharmacology or Interdisciplinary Toxicology. Their faculty also participate in the Interdisciplinary Biological Sciences (IBS) training programs. Trainees receive a broad-based education to prepare for a career in translational research. An emphasis on therapeutic development, identification of drug targets and mechanisms of organ injury prepare our trainees for a career in drug discovery and medical toxicology. All of our students currently receive a $24,000 yearly stipend and we pay tuition! Their 'magnet areas' for research include behavioral and drug abuse pharmacology, drug discovery and antibody therapeutics, mechanisms and therapies of organ toxicology and neurodegenerative diseases, and CNS and vascular ion channels. Extramural research funding obtained by the faculty has increased to more than 5 million annually, and the Department ranks in the top quarter of all medical school pharmacology departments in the country in NIH funding. | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-02134 | SCR_007496 | SciCrunch Registry | UAMS | 2026-11-07 12:00:38 | 0 | ||||||||||
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Michigan State University Labs and Facilities Resource Report Resource Website |
Michigan State University Labs and Facilities (RRID:SCR_012252) | MSU Labs & Facilities, MSU Labs and Facilities | access service resource, core facility, data or information resource, portal, service resource | An Portal, Core facility |
is listed by: ScienceExchange is related to: Michigan State University RTSF Genomics Core Facility is related to: MSU Comprehensive Phytopathogen Genomics Resource has parent organization: Michigan State University; Michigan; USA |
SciEx_1277 | SCR_012252 | SciCrunch Registry | Michigan State University Labs & Facilities | 2026-11-07 12:00:18 | 0 | |||||||||
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Yale School of Medicine Pharmacology Resource Report Resource Website |
Yale School of Medicine Pharmacology (RRID:SCR_010594) | data or information resource, department portal, organization portal, portal | The Department of Pharmacology at Yale University offers integrated and interdisciplinary opportunities for graduate study under the newly organized Program in Biological and Biomedical Sciences (BBS). Students entering the BBS program can take courses, participate in laboratory rotations, and perform thesis research with any of the more than 200 faculty members in the biological sciences at Yale located at the closely situated School of Medicine and Science Hill ends of campus. The faculty and students of the BBS program are organized into moderately-sized, interest-based Tracks to ensure individualized attention and maximize scientific interactions. Prospective students apply to the Track that best matches their interests, although there is complete freedom to work with faculty members in any Track or to switch Tracks after arrival at Yale. | has parent organization: Yale School of Medicine; Connecticut; USA | nlx_47908 | SCR_010594 | SciCrunch Registry | YSM Pharmacology | 2026-11-07 12:00:49 | 0 | ||||||||||
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Digital Fish Library Resource Report Resource Website |
Digital Fish Library (RRID:SCR_008338) | DFL | data or information resource, database, image collection, training resource | A database of 3D magnetic resonance (MRI) images of fish accessible to scientists, educators and the general public via the web. The Marine Vertebrate Collection at the Scripps Institution of Oceanography provides the majority of the DFL specimens. | education, fish, 3d, anatomical, magnetic resonance imaging, marine, mri, oceanography, comparative anatomy | has parent organization: University of California at San Diego; California; USA | NSF DBI-0446389 | nif-0000-24963 | SCR_008338 | SciCrunch Registry | DFL - Digital Fish Library | 2026-11-07 12:00:48 | 0 | |||||||
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Mendelspod Resource Report Resource Website |
Mendelspod (RRID:SCR_009027) | Mendelspod | blog, data or information resource, narrative resource, podcast | A collection of content, including podcasts and blogs, to advance life science research, connecting people and ideas in the life sciences. Mendelspod creates a space for probing conversations and deep insight into the topics and trends which shape the industry''s future and therefore our future as a species. The podcasts are engaging, thoughtful thirty minute shows twice a week on highly relevant topics to those working around the life sciences. Their format enables them to go in depth with scientists who are leaders in their field, or CEOs of high growth companies to explore trends and the latest technologies. At Mendelspod, they offer a front row seat to the revolution going on in biology, putting a human face on some complicated, highly technical topics. Here you can tune in to hear Steve Burrill give his ''state of the industry'' overview, or listen to George Church talk about art and science, or find out how the latest developments in NGS are helping in the war on cancer. The blogs cover the latest trends and products, and can be entertaining. Guest bloggers featured and welcomed. | genomics, personalized medicine, syn bio, biotech, pharma, health, life science, consulting, community building portal |
is used by: NIF Data Federation is used by: Integrated Blogs |
Protected by copyright, For personal, Non-commercial, Use, Or with written permission, Copyright notice must be retained | nlx_153912 | SCR_009027 | SciCrunch Registry | Mendelspod.com | 2026-11-07 12:00:17 | 0 | |||||||
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Fiber Tracking / DTI Checker Resource Report Resource Website |
Fiber Tracking / DTI Checker (RRID:SCR_007364) | data analysis software, data processing software, software application, software resource | A cross-platform system for exploring diffusion tensor images and to reconstruct fiber tracts between two regions of interest, intended for tdoctors, medical technicians or medical researchers. The Fiber-Tracking tool allows the user to load data from MRIs or similar images (like a basic 3D image viewer), load DTI datasets (7 diffusion- weighted images), calculate the fractional anisotropy (FA) and the mean diffusivity (MD) images, and also load ROIs to reconstruct fibers. | diffusion tensor imaging, tractography | has parent organization: University of North Carolina at Chapel Hill; North Carolina; USA | nif-0000-00299 | http://www.ia.unc.edu/dev/download/fibertracking/index.htm, http://www.ia.unc.edu/dev/download/dtichecker/index.htm | http://www.ia.unc.edu/dev/download/index.htm | SCR_007364 | SciCrunch Registry | Fiber Tracking | 2026-11-07 12:00:48 | 0 | |||||||
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Genetic and Rare Diseases Information Center Resource Report Resource Website 10+ mentions |
Genetic and Rare Diseases Information Center (RRID:SCR_008695) | GARD | data or information resource, disease-related portal, portal, topical portal | Genetic and Rare Diseases Information Center (GARD) is a collaborative effort of two agencies of the National Institutes of Health, The Office of Rare Diseases Research (ORDR) and the National Human Genome Research Institute (NHGRI) to help people find useful information about genetic conditions and rare diseases. GARD provides timely access to experienced information specialists who can furnish current and accurate information about genetic and rare diseases. So far, GARD has responded to 27,635 inquiries on about 7,147 rare and genetic diseases. Requests come not only from patients and their families, but also from physicians, nurses and other health-care professionals. GARD also has proved useful to genetic counselors, occupational and physical therapists, social workers, and teachers who work with people with a genetic or rare disease. Even scientists who are studying a genetic or rare disease and who need information for their research have contacted GARD, as have people who are taking part in a clinical study. Community leaders looking to help people find resources for those with genetic or rare diseases and advocacy groups who want up-to-date disease information for their members have contacted GARD. And members of the media who are writing stories about genetic or rare diseases have found the information GARD has on hand useful, accurate and complete. GARD has information on: :- What is known about a genetic or rare disease. :- What research studies are being conducted. :- What genetic testing and genetic services are available. :- Which advocacy groups to contact for a specific genetic or rare disease. :- What has been written recently about a genetic or rare disease in medical journals. GARD information specialists get their information from: :- NIH resources. :- Medical textbooks. :- Journal articles. :- Web sites. :- Advocacy groups, and their literature and services. :- Medical databases. | genetic, disease, information, genome, human, rare disease, health, physician, counselor, gene, journal, medical | has parent organization: National Institutes of Health | Office of Rare Diseases Research ; NHGRI |
nif-0000-37627 | SCR_008695 | SciCrunch Registry | Genetic Rare Diseases Information Center | 2026-11-07 12:00:35 | 16 | |||||||
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SUNY Stony Brook, Pharmacological Sciences Resource Report Resource Website |
SUNY Stony Brook, Pharmacological Sciences (RRID:SCR_007480) | data or information resource, department portal, organization portal, portal | The Department ofPharmacological Sciencesat Stony Brook offers a collegial atmosphere with one of the highest ratios of postdoctoral to predoctoral researchers of any Pharmacology Department in the country. Students in Molecular and Cellular Pharmacology work alongside students from several other graduate programs at Stony Brook, including Molecular and Cellular Biology, Neurobiology, Chemistry, Genetics, Microbiology, Structural Biology, and Physiology and Biophysics. Several students in Molecular and Cellular Pharmacology have been trainees in the NIH-funded MSTP (Medical Scientist Training Program). | nif-0000-02081 | SCR_007480 | SciCrunch Registry | SUNY Stonybrook | 2026-11-07 12:00:34 | 0 | |||||||||||
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SurfStat Resource Report Resource Website 100+ mentions |
SurfStat (RRID:SCR_007081) | SurfStat | data processing software, image analysis software, software application, software resource, software toolkit | A Matlab toolbox for the statistical analysis of univariate and multivariate surface data using linear mixed effects models and random field theory. | afni brik, analyze, linear, matlab, minc, modeling, magnetic resonance, nifti, os independent, regression, statistical operation, pet, random field theory |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: McGill University; Montreal; Canada |
Free | nlx_156000 | http://www.nitrc.org/projects/surfstat | SCR_007081 | SciCrunch Registry | 2026-11-07 12:00:34 | 260 | |||||||
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ICZN Resource Report Resource Website 10+ mentions |
ICZN (RRID:SCR_010241) | data or information resource, international standard specification, narrative resource, organization portal, portal, standard specification | An organization that acts as adviser and arbiter for the zoological community by generating and disseminating information on the correct use of the scientific names of animals. The ICZN is responsible for producing the International Code of Zoological Nomenclature - a set of rules for the naming of animals and the resolution of nomenclatural problems. | nlx_156873 | SCR_010241 | SciCrunch Registry | International Commission on Zoological Nomenclature | 2026-11-07 12:00:35 | 16 | |||||||||||
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University of Missouri Department of Medical Pharmacology and Physiology Resource Report Resource Website 1+ mentions |
University of Missouri Department of Medical Pharmacology and Physiology (RRID:SCR_007518) | data or information resource, department portal, organization portal, portal | The Department of Medical Pharmacology and Physiology has been known for outstanding programs in exercise physiology and cardiovascular physiology. The Department offers both Master of Science (MS) and Doctor of Philosophy (PhD) degree programs that provide students with excellent preparation for a variety of challenging and rewarding careers. The degrees offered are programs in Pharmacology or Physiology. The Medical Pharmacology and Physiology Department and its modern research and teaching facilities are on campus in the School of Medicine. The research laboratories of the faculty have excellent equipment and maintenance support. The award-winning Health Sciences Library, containing a wide variety of current journals and resource books, is located in the School of Medicine. Modern student computer stations are also available. Animal quarters and animal care are under the direction of qualified veterinarians. Other important University facilities include a nuclear reactor for providing short-lived radioisotopes and a campus-wide computer network. The Center for Gender Physiology manages four core facilities that provide animal models, equipment and expertise required to explore gender differences in physiological function. | nif-0000-02217 | http://mpp.missouri.edu/ | SCR_007518 | SciCrunch Registry | Missouri | 2026-11-07 12:00:48 | 9 | ||||||||||
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EpigenDx Resource Report Resource Website 100+ mentions |
EpigenDx (RRID:SCR_012624) | EpigenDx | access service resource, commercial organization, core facility, service resource | EpigenDx is a genomic and epigenomic research company specializing in disease biomarker discovery and molecular diagnosis. The company provides products related to DNA methylation analysis research. Currently available products include DNA methylation controls and validated DNA methylation assays for human, mouse, and rat. EpigenDx also provides products and laboratory services for scientific researchers from academic, government and industrial communities. Our commitment to quality comes from our desire and dedication to provide the best products and services to our customers. EpigenDx has knowledge and expertise in Pyrosequencing and its many applications. CpG methylation and allele quantification analysis are conducted using Qiagen-Pyrosequencing PSQ MD system, while short-read sequence analysis is carried out using Qiagen-Pyrosequencing PSQ ID system. | is listed by: ScienceExchange | SciEx_570 | SCR_012624 | SciCrunch Registry | 2026-11-07 12:00:18 | 121 | ||||||||||
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Computational Neurobiology and Imaging Center Resource Report Resource Website 1+ mentions |
Computational Neurobiology and Imaging Center (RRID:SCR_013317) | CNIC | data or information resource, data set, portal, software resource, topical portal | Center to advance research and training in mathematical, computational and modern imaging approaches to understanding the brain and its functions. Software tools and associated reconstruction data produced in the center are available. Researchers study the relationships between neural function and structure at levels ranging from the molecular and cellular, through network organization of the brain. This involves the development of new computational and analytic tools for imaging and visualization of 3-D neural morphology, from the gross topologic characteristics of the dendritic arbor to the fine structure of spines and their synapses. Numerical simulations of neural mechanisms based on these structural data are compared with in-vivo and in-vitro electrophysiological recordings. The group also develops new theoretical and analytic approaches to exploring the function of neural models of working memory. The goal of this analytic work is to combine biophysically realistic models and simulations with reduced mathematical models that capture essential dynamical behaviors while reproducing the functionally important features of experimental data. Research areas include: Imaging Studies, Volume Integration, Visualization Techniques, Medial Axis Extraction, Spine Detection and Classification, Applications of Rayburst, Analysis of Spatially Complex Structures, Computational Modeling, Mathematical and Analytic Studies | brain, confocal, in-vitro, in-vivo, microscopy, morphology, morphometric, multi-photon, neural, neural function, neuron, simulation, stack, structure, synapse, topologic, variable, vessel, visualization, image, neuroscience, neurobiology, reconstruction, modeling, spatial, rayburst, spine, arbor, visual, tiling, imaging |
lists: NeuronStudio lists: Rayburst Open-Source Code lists: Volume Integration and Alignment System lists: Volume Integration and Alignment System Source Code lists: Polygonized Viewer lists: NeuroGL lists: TIFF Stack Sub-Sampler is related to: NeuroMorpho.Org is related to: Rayburst Open-Source Code is related to: Polygonized Viewer is related to: NeuroGL is related to: TIFF Stack Sub-Sampler is related to: NeuronStudio is related to: Volume Integration and Alignment System is related to: Volume Integration and Alignment System Source Code has parent organization: Icahn School of Medicine at Mount Sinai; New York; USA |
Aging | Howard Hughes Medical Institute ; NIDCD ; NIA ; NIMH |
nif-0000-10200 | http://www.mssm.edu/cnic/ | SCR_013317 | SciCrunch Registry | 2026-11-07 12:00:37 | 7 | ||||||
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Gwyddion Resource Report Resource Website 1000+ mentions |
Gwyddion (RRID:SCR_015583) | data analysis software, data processing software, software application, software resource | Modular program for SPM (scanning probe microscopy) data visualization and analysis. Primarily it is intended for the analysis of height fields obtained by scanning probe microscopy techniques (AFM, MFM, STM, SNOM/NSOM) and it supports a lot of SPM data formats. However, it can be used for general height field and (greyscale) image processing, for instance for the analysis of profilometry data or thickness maps from imaging spectrophotometry. | spm data analysis, spm data visualization, height field analysis |
is listed by: Debian is listed by: OMICtools is listed by: SoftCite |
Czech Metrology Institute Department of Nanometrology | DOI:10.2478/s11534-011-0096-2 | Open source | OMICS_07548 | https://sources.debian.org/src/gwyddion/ | SCR_015583 | SciCrunch Registry | 2026-11-07 12:00:51 | 1661 | ||||||
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CalC Resource Report Resource Website 10+ mentions |
CalC (RRID:SCR_014259) | simulation software, software application, software resource | A modeling tool for simulating intracellular calcium diffusion and buffering. CalC solves continuous reaction-diffusion PDEs describing the entry of calcium into a volume through point-like channels, and its diffusion, buffering and binding to calcium receptors. Its features include: being platform-independent; being operated by simple script; combinable with MATLAB; and providing real-time views. Demos and manuals are provided on the website. | simulation software, modeling tool, intracellular calcium diffusion, intracellular calcium buffering, pde | NSF 0417416; NSF 0817703; NSF 1517085 |
Free, Acknowledgement requested | SCR_014259 | SciCrunch Registry | Calcium Calculator | 2026-11-07 12:00:50 | 31 | |||||||||
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Open MEG Archive Resource Report Resource Website 100+ mentions |
Open MEG Archive (RRID:SCR_014930) | OMEGA | data or information resource, data repository, database, service resource, storage service resource | Open data repository fully dedicated to MEG data in raw and processed form. The archive also contains anatomical MRI volumes and demographic and questionnaire information. Organized and stored as the Brain Imaging Data Structure (BIDS) with the integration of multimodal electrophysiology data. Directly readable by data-analysis software with Brainstorm. OMEGA will continue to expand, with contributions from the scientific community. | repository, meg, database, mri, data aggregation, raw meg data, processed meg data, FASEB list |
is related to: Brainstorm has parent organization: McGill University; Montreal; Canada |
Quebec Bioimaging Network | Open source, Registration required, Acknowledgement required | https://box.bic.mni.mcgill.ca/s/4qFZvf6tmgMA371/authenticate | SCR_014930 | SciCrunch Registry | OMEGA:Open MEG Archive | 2026-11-07 12:00:38 | 125 | ||||||
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NovoAlign Resource Report Resource Website 500+ mentions |
NovoAlign (RRID:SCR_014818) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software tool designed for mapping short reads onto a reference genome generated from Illumina, Ion Torrent, and 454 NGS platforms. Its features include paired end alignment, methylation status analysis, automatic base quality calibration, and in built adapter trimming and base quality trimming. | sequence analysis software, short read, map, genome, illumina, ion torrent, 454 ngs | Commercially available, Trial available by request | SCR_014818 | SciCrunch Registry | 2026-11-07 12:00:20 | 809 |
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