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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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HAMMER Suite Resource Report Resource Website 1+ mentions |
HAMMER Suite (RRID:SCR_009583) | HAMMER Suite | software application, software toolkit, software resource, image analysis software, image processing software, data processing software | The tool is a GUI for a complete processing pipeline of brain MR images. It provides functions on skull-stripping, cerebellum removal, tissue segmentation, and HAMMER registration. | magnetic resonance, mri |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of North Carolina at Chapel Hill; North Carolina; USA |
PMID:12575879 | Free | nlx_155769 | http://www.nitrc.org/projects/hammer_suite | SCR_009583 | 2026-08-10 09:33:44 | 1 | ||||||
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BeeBase Resource Report Resource Website 50+ mentions |
BeeBase (RRID:SCR_008966) | BeeBase | data or information resource, analysis service resource, production service resource, database, data set, service resource, data analysis service | Gene sequences and genomes of Bombus terrestris, Bombus impatiens, Apis mellifera and three of its pathogens, that are discoverable and analyzed via genome browsers, blast search, and apollo annotation tool. The genomes of two additional species, Apis dorsata and A. florea are currently under analysis and will soon be incorporated.BeeBase is an archive and will not be updated. The most up-to-date bee genome data is now available through the navigation bar on the HGD Home page. | genome, gene set, sequence, bee, genomics, entomology, blast, annotation, pest, pathogen, honey, beehive, insect, bee pollen, bee product, bee culture, pollination, pollinator, bio.tools, FASEB list |
is listed by: re3data.org is listed by: Debian is listed by: bio.tools has parent organization: University of Missouri; Missouri; USA |
Texas Agricultural Experiment Station ; Golden Heritage Foods and Sioux Honey Association ; NHGRI 5-P41-HG000739-13; USDA 2008-35302-18804 |
PMID:21071397 | Open unspecified license, Acknowledgement requested, Data Usage Policy | nlx_152034, biotools:hgd, r3d100010925 | https://bio.tools/hgd, https://doi.org/10.17616/R3Z629 | SCR_008966 | Hymenoptera Genome Database | 2026-08-10 09:33:35 | 56 | ||||
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BrainMagix SPM Viewer Resource Report Resource Website 1+ mentions |
BrainMagix SPM Viewer (RRID:SCR_009537) | BrainMagix SPM Viewer | software application, data visualization software, software resource, data processing software | A free, professional viewer for SPM fMRI results. SPM (Statistical Parametric Mapping, UCL, London) is a powerful fMRI analysis software but its visualization capabilities are sometimes a limitation for the researchers. That's why Imagilys has decided to offer the neuroimaging community a free version of its commercial "BrainMagix" neuroimaging software, called "BrainMagix SPM viewer". BrainMagix SPM Viewer's Features - Professional viewer for your SPM-based fMRI activations - JAVA-programmed, cross-platform (Windows, MAC, Linux), without Matlab license, making it possible to share your results with colleagues who do not have SPM installed - Reads SPM.mat files and NIfTI images in an user-friendly way - Overlay the blobs with an atlas or any anatomical image - On the fly adjustment of threshold and cluster size - Localize your activations in an atlas - BOLD signal curves in ROIs (future feature) - Export your results as PNG images | java, magnetic resonance, nifti, os independent, visualization, statistical parametric mapping, fmri |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: SPM |
Other/Commercial license License, Free | nlx_155714 | http://www.nitrc.org/projects/bm_spm_viewer | SCR_009537 | 2026-08-10 09:33:48 | 1 | |||||||
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Pharmacology Resource Report Resource Website 100+ mentions |
Pharmacology (RRID:SCR_009017) | data or information resource, wiki, book, narrative resource | Pharmacology is a wikibook covering topics within pharmacology and pharmaceutical sciences. | has parent organization: Wikibooks | nlx_152817 | SCR_009017 | Pharmacology (wikibook) | 2026-08-10 09:33:45 | 146 | ||||||||||
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Neural Decoding Toolbox Resource Report Resource Website 10+ mentions |
Neural Decoding Toolbox (RRID:SCR_009012) | NDT | data analysis software, software application, software toolkit, software resource, data processing software | Matlab toolbox that makes it easy to apply decoding analyses to neural data. The design of the toolbox revolves around four abstract object classes which enables users to interchange particular modules in order to try different analyses while keeping the rest of the processing stream intact. The toolbox is capable of analyzing data from many different types of recording modalities, and examples are given on how it can be used to decode basic visual information from neural spiking activity and how it can be used to examine how invariant the activity of a neural population is to stimulus transformations. | population decoding, neuron, analysis, matlab, data analysis, machine learning, multivariate pattern analysis, neural decoding | has parent organization: Massachusetts Institute of Technology; Massachusetts; USA; | DARPA ; IPTO ; DSO ; AFSOR-THRL ; Adobe Systems ; Honda Research Institute USA ; King Abdullah University of Science and Technology ; NEU ; Sony ; Eugene McDermott Foundation ; NSF 0640097; NSF 0827427; NSF FA8650-05-C-7262 |
PMID:23734125 | Acknowledgement requested, Account required | nlx_152729 | SCR_009012 | 2026-08-10 09:33:45 | 19 | ||||||
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R/QTLBIM Resource Report Resource Website 1+ mentions |
R/QTLBIM (RRID:SCR_009375) | software application, software library, software toolkit, software resource | Software library for QTL Bayesian Interval Mapping that provides a Bayesian model selection approach to map multiple interacting QTL. It works on experimentally inbred lines and performs a genome-wide search to locate multiple potential QTL. The package can handle continuous, binary and ordinal traits. (entry from Genetic Analysis Software) | gene, genetic, genomic, r, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
nlx_154597, biotools:qtlbim | http://www.ssg.uab.edu/qtlbim/index.jsp, https://cran.r-project.org/src/contrib/Archive/qtlbim/, https://bio.tools/qtlbim | http://www.qtlbim.org/ | SCR_009375 | 2026-08-10 09:33:45 | 2 | ||||||||
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Clinical Outcomes Research Initiative Resource Report Resource Website 1+ mentions |
Clinical Outcomes Research Initiative (RRID:SCR_009010) | CORI | data or information resource, resource, database, service resource, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on December 5, 2022. Endoscopic Reporting Software, aggregated and individual research data and tailor-made services aimed to advance the overall practice of endoscopy. It was developed to study outcomes of gastrointestinal (GI) endoscopic procedures in real life settings, using data obtained from the CORI Endoscopic Reporting Software or from other endoscopic reporting software. Practice sites include hospitals, ambulatory care centers, private practices, universities, and Veteran''''s hospitals (VA''''s). The CORI v4 Endoscopic Reporting Software is a specialty Electronic Health Record used to document endoscopic procedures and provide reporting services to your practice. Data from participating providers is also sent to a central data repository to become part of the National Endoscopic Database (NED), which now contains data from over 2.7 million GI procedures. The CORI v4 Endoscopic Reporting Software offers significant benefits for participating practices, providers and patients, as well as for everyone who benefits from CORI''''s research efforts. You may actively participate in research with CORI. If you have ideas for research using the NED, their research team can help you evaluate those ideas, collect and analyze the data. In addition, you may choose to participate in one of the prospective research projects conducted by CORI research staff. | clinical, endoscopy, gastroenterology, gastrointestinal, endoscopic, endoscopy reporting software, outcome, report, electronic health record, aggregator |
is listed by: NIDDK Information Network (dkNET) is listed by: NIDDK Research Resources has parent organization: Oregon Health and Science University; Oregon; USA |
NIDDK | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_152692 | SCR_009010 | 2026-08-10 09:33:41 | 6 | |||||||
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IDeA Lab brain image processing suite Resource Report Resource Website 1+ mentions |
IDeA Lab brain image processing suite (RRID:SCR_009495) | IDeA Lab brain image processing suite | software application, software toolkit, software resource, image analysis software, data processing software | Suite of tools for brain image analysis. Image manipulation, 2D visualization, linear alignment, BBSI, template-based bias correction, skullstrip. GUI Image analysis tools. Now modified to read/write single file nifti (.nii) format. Other packages to be added. | analyze, c++, console (text based), csh/tcsh, image display, image-to-image, image-to-template, intermodal, intersubject, linux, magnetic resonance, nifti, nonlinear warp, posix/unix-like, quantification, registration, resampling, spatial transformation, spline interpolation, tri-linear, two dimensional display, unix shell, visualization, volume measurement, volumetric analysis, warping | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | nlx_155644 | SCR_009495 | 2026-08-10 09:33:44 | 1 | |||||||||
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HD Neuro-Informatics Resource Report Resource Website 1+ mentions |
HD Neuro-Informatics (RRID:SCR_009493) | HDNI | data or information resource, topical portal, portal | An international effort to establish resources necessary to study the application of neuroimaging measures as (surrogate) biomarkers in Huntington''s Disease (HD). The primary aims are to develop and apply software tools, imaging protocols, quality control procedures, data archiving, data distribution, and participation guidelines that will accelerate existing and prospective imaging studies. | magnetic resonance | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Huntington''s disease | BSD License | nlx_155641 | SCR_009493 | Huntington Disease Nueroimaging Initiative | 2026-08-10 09:33:47 | 2 | ||||||
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National Geophysical Data Center Resource Report Resource Website 10+ mentions |
National Geophysical Data Center (RRID:SCR_009429) | NGDC | data or information resource, organization portal, portal, service resource | National Data Center that provides scientific stewardship, products, and services for geophysical data from sea floor and solid earth environments, including Earth observations from space. Please note that routine underway geophyiscal shipboard data collected with standard equipment aboard the UNOLS fleet (e.g. bathymetry, subbottom, magnetics, gravity) are routinely transmitted to NGDC via Rolling Deck to Repository (R2R). | geophysics, sea floor, solid earth, bathymetry, subbottom, magnetics, gravity |
is listed by: CINERGI has parent organization: National Oceanic and Atmospheric Administration |
nlx_154716 | SCR_009429 | 2026-08-10 09:33:42 | 46 | |||||||||
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National Climatic Data Center Resource Report Resource Website 100+ mentions |
National Climatic Data Center (RRID:SCR_009427) | NCDC | data or information resource, data repository, database, service resource, storage service resource | National Data Center that accepts and makes available weather, climate, paleoclimate, meteorological data. | weather, climate, paleoclimate, meteorology, FASEB list |
is listed by: CINERGI has parent organization: National Oceanic and Atmospheric Administration is parent organization of: World Data Center for Paleoclimatology |
nlx_154702 | SCR_009427 | 2026-08-10 09:33:41 | 135 | |||||||||
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GRDR Resource Report Resource Website 1+ mentions |
GRDR (RRID:SCR_008978) | GRDR, RaDaR | data or information resource, data repository, database, patient registry, service resource, people resource, storage service resource | Data repository of de-identified patient data, aggregated in a standardized manner, to enable analyses across many rare diseases and to facilitate various research projects, clinical studies, and clinical trials. The aim is to facilitate drug and therapeutics development, and to improve the quality of life for the many millions of people who are suffering from rare diseases. The goal of GRDR is to enable analyses of data across many rare diseases and to facilitate clinical trials and other studies. During the two-year pilot program, a web-based template will be developed to allow any patient organization to establish a rare disease patient registry. At the conclusion of the program, guidance will be available to patient groups to establish a registry and to contribute de-identified patient data to the GRDR repository. A Request for Information (RFI) was released on February 10, 2012 requesting information from patient groups about their interest in participating in a GRDR pilot project. ORDR selected 30 patient organizations to participate in this pilot program to test the different functionalities of the GRDR. Fifteen (15) organizations with established registries and 15 organizations that do not have patient registry. The 15 patient groups, each without a registry, were selected to assist in testing the implementation of the ORDR Common Data Elements (CDEs) in the newly developed registry infrastructure. These organizations will participate in the development and promotion of a new patient registry for their rare disease. The GRDR program will fund the development and hosting of the registry during the pilot program. Thereafter, the patient registry is expected to be self-sustaining.The 15 established patient registries were selected to integrate their de-identified data into the GRDR to evaluate the data mapping and data import/export processes. The GRDR team will assist these organizations in mapping their existing registry data to the CDEs. Participating registries must have a means to export their de-identified registry data into a specified data format that will facilitate loading the data into the GRDR repository on a regular basis. The GRDR will also develop the capability to link patients'''' data and medical information to donated biospecimens by using a Voluntary Global Unique Patient Identifier (GUID). The identifier will enable the creation of an interface between the patient registries that are linked to biorepositories and the Rare Disease Human Biospecimens/Biorepositories (RD-HUB) http://biospecimens.ordr.info.nih.gov/. | clinical, common data element, global unique patient identifier, clinical trial, drug development, therapy |
is related to: Biospecimens/Biorepositories: Rare Disease-HUB (RD-HUB) is related to: NIH Data Sharing Repositories has parent organization: Office of Rare Diseases Research |
Rare disease | NIH | Public, The community can contribute to this resource | nlx_152145 | http://www.grdr.info/ | SCR_008978 | Rare Diseases Registry Program (RaDaR), Global Rare Diseases Patient Registry and Data Repository | 2026-08-10 09:33:41 | 1 | ||||
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INVIZIAN Resource Report Resource Website 1+ mentions |
INVIZIAN (RRID:SCR_009549) | INVIZIAN | software application, data visualization software, software resource, data processing software | A visualization environment that enables you, via your computer, to display and interact with hundreds of neuroimaging data sets at once ?bringing together brain image data from some of the world?s best neuroscience research teams. INVIZIAN empowers both researchers and students of neuroscience to explore and understand the human brain using a simple yet powerful user interface for neuroimaging data exploration and discovery. See a beautiful example of a cloud of individual brains tumbling around in the INVIZIAN interface in Vimeo (http://vimeo.com/67984681). Visit often to see how we are making continuing progress to make Invizian even more amazing. | magnetic resonance |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Laboratory of Neuro Imaging |
LONI Software License | nlx_155775 | http://www.nitrc.org/projects/invizian | SCR_009549 | Informatics Visualization in Neuroimaging | 2026-08-10 09:33:48 | 1 | ||||||
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Digital Ageing Atlas Resource Report Resource Website 10+ mentions |
Digital Ageing Atlas (RRID:SCR_009020) | DAA | data or information resource, data repository, database, service resource, storage service resource | Database of age-related changes covering different biological levels, including molecular, physiological, psychological and pathological age-related data, to create an interactive portal that serves as a centralized collection of human aging changes and pathologies. To facilitate integrative, system-level studies of aging, the DAA provides a centralized source for aging-related data as well as basic tools to query and visualize the data, including anatomical models. Data in the DAA is manually curated from the literature and retrieved from public databases. For more detailed analyses users are able to download the entire database. More information on how to use the DAA is available on the help page. The DAA primarily focuses on human aging, but also includes supplementary mouse data, in particular gene expression data, to enhance and expand the information on human aging. If you would like to contribute to the database yourself, for instance if you have new data on aging, please use the contribute page to submit your data. | late adult human, anatomy, gene, molecular, pathological, physiological, psychological, tissue, reference, cellualar, gene expression | has parent organization: University of Liverpool; Liverpool; United Kingdom | Aging | The community can contribute to this resource, Creative Commons Attribution License, v3 Unported | nlx_153874 | SCR_009020 | Digital Aging Atlas | 2026-08-10 09:33:45 | 15 | ||||||
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Musculoskeletal Transplant Foundation - MTF Resource Report Resource Website 1+ mentions |
Musculoskeletal Transplant Foundation - MTF (RRID:SCR_006684) | MTF | material resource, tissue bank, biomaterial supply resource | The Musculoskeletal Transplant Foundation is a non-profit service organization dedicated to providing quality allograft tissue through a commitment to excellence in education, research, recovery and care for recipients, donors and their families. We are a national consortium comprised of academic medical institutions, organ procurement organizations and tissue recovery organizations. MTF was created as a charitable organization with a mission that is dedicated to the needs of donors, donor families, patients and surgeons. We focus on respectful stewardship of the donated gift while advancing the science and practice of bone, ligament, cartilage and skin transplantation. Since our inception in 1987, MTF has recovered more than 60,000 donors and distributed more than 3 million grafts for transplantation. We also support research to expand the science of transplantation, and we encourage the efforts of our members and non-member clients to improve the understanding of donation and transplantation among the medical community and the public at large. Our policies are developed and implemented by MTF''''s Medical Board of Trustees, Donation Board of Trustees and Board of Directors, composed of physicians and recovery agency representatives who are dedicated to the mission of the Foundation. This fundamental commitment enables us to set and maintain the highest levels of safety assurance and quality control in all phases of our operations. |
is listed by: One Mind Biospecimen Bank Listing is parent organization of: International Institute for the Advancement of Medicine |
nlx_89982 | SCR_006684 | Musculoskeletal Transplant Foundation | 2026-08-10 09:32:54 | 1 | |||||||||
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MPact: Representation of Interaction Data at MIPS Resource Report Resource Website 1+ mentions |
MPact: Representation of Interaction Data at MIPS (RRID:SCR_006687) | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE, documented August 19, 2016. It provides a common access point to interaction resources at MIPS. It is designed to support the PSI-MI standard, for both downloading and uploading data. It provides the user with intuitive query forms to quickly retrieve the interactions of interest. Graphical representations allow an easy navigation through the protein interaction networks. |
is related to: Interaction Reference Index works with: IMEx - The International Molecular Exchange Consortium |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-03164 | http://mips.gsf.de/genre/proj/mpact | SCR_006687 | Mpact | 2026-08-10 09:32:59 | 2 | ||||||||
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RNase P Database Resource Report Resource Website 1+ mentions |
RNase P Database (RRID:SCR_006680) | RNase P Database | data or information resource, database | Ribonuclease P is responsible for the 5''-maturation of tRNA precursors. Ribonuclease P is a ribonucleoprotein, and in bacteria (and some Archaea) the RNA subunit alone is catalytically active in vitro, i.e. it is a ribozyme. The Ribonuclease P Database is a compilation of ribonuclease P sequences, sequence alignments, secondary structures, three-dimensional models and accessory information. The database contains information on bacterial, archaeal, and eukaryotic RNase P. The RNase P and protein sequences are available from phylogentically-arranged lists, individual sequences, or aligned in GenBank format. The database also provides secondary structures and 3D models, as well as movies, still images, and other accessory information. | ribonuclease p, ribonucleoprotein, ribozyme, sequence, sequence alignment, secondary structure, 3-d model, rnase p rna | has parent organization: North Carolina State University; North Carolina; USA | Isis Phamaceuticals ; NIGMS GM52894 |
PMID:9847214 | nif-0000-03403 | SCR_006680 | The RNase P Database, Ribonuclease P Database | 2026-08-10 09:32:59 | 8 | ||||||
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DisProt - Database of Protein Disorder Resource Report Resource Website 100+ mentions |
DisProt - Database of Protein Disorder (RRID:SCR_007097) | data or information resource, database | The Database of Protein Disorder (DisProt) is a curated database that provides information about proteins that lack fixed 3D structure in their putatively native states, either in their entirety or in part. Users can BLAST sequences, browse by protein name, or view by protein function and functional subclass. | protein, protein structure, bio.tools, FASEB list |
is listed by: bio.tools is listed by: Debian has parent organization: Temple University; Pennsylvania; USA |
nif-0000-02754, r3d100010561, biotools:disprot | https://bio.tools/disprot, https://doi.org/10.17616/R3NG75 | http://divac.ist.temple.edu/disprot | SCR_007097 | DisProt | 2026-08-10 09:33:02 | 223 | |||||||
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The Diatom EST Database Resource Report Resource Website 1+ mentions |
The Diatom EST Database (RRID:SCR_007090) | data or information resource, database | A searchable databases of diatom ESTs (expressed sequence tags) that can be used to explore diatom biology. Research has generated approximately 90,000 ESTs from P. tricornutum cells grown in a range of conditions. Here we present a database of these sequences, that can be used for digital gene expression studies to explore this organisms responses to a range of environmental conditions. Such studies should provide a foundation for interpreting the ecological success of diatoms. | est, expressed sequence tag, diatom | nif-0000-02750 | SCR_007090 | The Diatom EST Database | 2026-08-10 09:33:01 | 6 | ||||||||||
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AthaMap Resource Report Resource Website 50+ mentions |
AthaMap (RRID:SCR_006717) | data or information resource, database | Genome wide map of putative transcription factor binding sites in Arabidopsis thaliana genome.Data in AthaMap is based on published transcription factor (TF) binding specificities available as alignment matrices or experimentally determined single binding sites.Integrated transcriptional and post transcriptional data.Provides web tools for analysis and identification of co-regulated genes. Provides web tools for database assisted identification of combinatorial cis-regulatory elements and the display of highly conserved transcription factor binding sites in Arabidopsis thaliana. | gene, arabidopsis thaliana, binding site, genome, transcription factor, small rna binding site, small rna, rna, microrna, cis-regulatory element, post-transcriptional regulation, FASEB list |
is listed by: OMICtools is listed by: bio.tools has parent organization: Technical University of Braunschweig; Braunschweig; Germany |
PMID:22800758 PMID:21177332 PMID:18842622 PMID:17148485 PMID:16922688 PMID:15980498 PMID:14681436 |
Free, Freely available | nif-0000-02583, biotools:athamap, OMICS_00549, nif-0000-20814, SCR_013106 | https://bio.tools/athamap | SCR_006717 | Arabidopsis thaliana Map | 2026-08-10 09:32:55 | 50 |
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