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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Kaplan Meier Plotter Resource Report Resource Website 1+ mentions |
Kaplan Meier Plotter (RRID:SCR_024521) | web service, software resource, data access protocol | Web based survival analysis tool tailored for medical research. Used to assess correlation between expression of all genes (mRNA, miRNA, protein) and survival in samples from tumor types including breast, ovarian, lung, gastric, colon cancer, AML, and myeloma. | survival analysis, assess correlation between expression of genes and survival, tumor samples, | is listed by: SoftCite | PMID:34309564 | Free, Freely available | http://kmplot.com/analysis/index.php?p=service&cancer=custom_plot | SCR_024521 | Kaplan-Meier Plotter, KM Plotter | 2026-08-11 09:44:36 | 6 | |||||||
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ProgRes Capture Pro Resource Report Resource Website 10+ mentions |
ProgRes Capture Pro (RRID:SCR_024489) | software application, data acquisition software, data processing software, software resource | Software tool for image acquisition.Supports ProgRes microscope cameras and delivers optimal image quality and reproducible results.Included with all of Jenoptik ProgRes microscope cameras. | image acquisition, Jenoptik ProgRes microscope cameras, Jenoptik, | is listed by: SoftCite | PMID:34520656 | Free, Available for download, Freely available | SCR_024489 | Jenoptic ProgRes Capture Pro | 2026-08-11 09:44:52 | 12 | ||||||||
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MADOKA Resource Report Resource Website 1+ mentions |
MADOKA (RRID:SCR_024522) | web service, software resource, data access protocol | Web server as ultra fast approach for large scale protein structure similarity searching.The upload protein structure file should be in PDB format. Used for searching similar protein structures by aligning input structure with the whole PDB library. | large scale protein structure similarity searching, searching similar protein structures, aligning input structure with whole PDB library, | is listed by: SoftCite | PMID:31870277 | Free, Freely available | SCR_024522 | 2026-08-11 09:44:53 | 1 | |||||||||
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Partnership for Interdisciplinary Studies of Coastal Oceans Resource Report Resource Website 1+ mentions |
Partnership for Interdisciplinary Studies of Coastal Oceans (RRID:SCR_024637) | PISCO | portal, consortium, data or information resource, organization portal | Academic consortium that conducts research to advance understanding of the coastal ocean within the California Current Large Marine Ecosystem and inform management and policy. | coastal ocean research, California Current Large Marine Ecosystem, management and policy, |
is listed by: DataCite has parent organization: University of California; California; USA |
Free, Freely available | https://api.datacite.org/dois?prefix=10.6085 | SCR_024637 | Partnership for Interdisciplinary Studies of Coastal Oceans (PISCO) | 2026-08-11 09:44:54 | 2 | |||||||
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GQuery Resource Report Resource Website 100+ mentions |
GQuery (RRID:SCR_001455) | Entrez | data or information resource, portal, database, organization portal | Search engine for the National Library of Medicine and the National Institutes of Health. It contains databases such as PubMed, EST, and BioSystems. | search engine, national library of medicine, nih, national institutes of health | has parent organization: NCBI | Free, Freely Available | nif-0000-08510 | SCR_001455 | NCBI Entrez, Entrez - The Life Sciences Search Engine | 2026-08-11 09:40:21 | 143 | |||||||
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Center for the Neural Basis of Cognition Resource Report Resource Website 10+ mentions |
Center for the Neural Basis of Cognition (RRID:SCR_002301) | data or information resource, portal, organization portal | CNBC is joint venture of University of Pittsburgh and Carnegie Mellon University. Our center leverages the strengths of the University of Pittsburgh in basic and clinical neuroscience and those of Carnegie Mellon in cognitive and computational neuroscience to support a coordinated cross-university research and educational program of international stature. In addition to our Ph.D. program in Neural Computation, we sponsor a graduate certificate program in cooperation with a wide variety of affiliated Ph.D. programs. | brain, cognition, cognitive abilities, development, disorders, human, human thought, learning, mind, multidisciplinary, neural activity, neural mechanisms, neurobasis, normal, training | has parent organization: Carnegie Mellon University; Pennsylvania; USA | nif-0000-00370 | SCR_002301 | CNBC | 2026-08-11 09:40:30 | 16 | |||||||||
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DPARSF Resource Report Resource Website 500+ mentions |
DPARSF (RRID:SCR_002372) | DPARSF | software toolkit, data processing software, software resource, software application | A MATLAB toolbox forpipeline data analysis of resting-state fMRI that is based on Statistical Parametric Mapping (SPM) and a plug-in software within DPABI. After the user arranges the Digital Imaging and Communications in Medicine (DICOM) files and click a few buttons to set parameters, DPARSF will then give all the preprocessed (slice timing, realign, normalize, smooth) data and results for functional connectivity, regional homogeneity, amplitude of low-frequency fluctuation (ALFF), fractional ALFF, degree centrality, voxel-mirrored homotopic connectivity (VMHC) results. DPARSF can also create a report for excluding subjects with excessive head motion and generate a set of pictures for easily checking the effect of normalization. In addition, users can also use DPARSF to extract time courses from regions of interest. DPARSF basic edition is very easy to use while DPARSF advanced edition (alias: DPARSFA) is much more flexible and powerful. DPARSFA can parallel the computation for each subject, and can be used to reorient images interactively or define regions of interest interactively. Users can skip or combine the processing steps in DPARSF advanced edition freely. | magnetic resonance, fmri, resting-state fmri, matlab, analysis, brain |
is used by: DPABI is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Beijing Normal University; Beijing; China has parent organization: RFMRI.ORG |
PMID:20577591 | GNU General Public License | nlx_155735 | http://www.nitrc.org/projects/dparsf | SCR_002372 | Data Processing Assistant for Resting-State fMRI | 2026-08-11 09:40:35 | 696 | |||||
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NiftyRec Resource Report Resource Website 1+ mentions |
NiftyRec (RRID:SCR_002499) | NiftyRec | software application, data processing software, software resource, software toolkit | Software toolbox that includes reconstruction tools for emission and transmission imaging modalities, including Single Photon Emission Computed Tomography (SPECT), Positron Emission Tomography (PET), cone-beam X-Ray CT and parallel-beam X-Ray CT. At the core of NiftyRec are efficient, GPU accelerated, projection, back-projection and iterative reconstruction algorithms. The easy to use Matlab and Python interfaces of NiftyRec enable fast prototyping and development of reconstruction algorithms. NiftyRec includes standard iterative reconstruction algorithms such as Maximum Likelihood Expectation Maximisation (MLEM), Ordered Subsets Expectation Maximisation (OSEM) and One Step Late Maximum A Posteriori Expectation Maximisation (OSL-MAPEM), for multiple imaging modalities. | computed tomography, pet, spect |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University College London; London; United Kingdom |
BSD License | nlx_155898 | http://www.nitrc.org/projects/niftyrec | SCR_002499 | NiftyRec Tomography Toolbox, NiftyRec Open Source Tomography Toolbox | 2026-08-11 09:40:36 | 2 | ||||||
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Addiction Research GPCR Assay Bank Resource Report Resource Website 1+ mentions |
Addiction Research GPCR Assay Bank (RRID:SCR_002895) | biomaterial supply resource, cell repository, material resource | Describes data from and access to permanent cell lines containing beta-arrestin fluorescent protein biosensors. This assay Bank provides plasmids, cells lines, and resulting data to the NIDA/NIH funded research community in order to better understand and combat addiction. | fluorescent, addiction, assay, beta-arrstin, biology, biosensor, cell, data, g protein, g-protein coupled receptor, ligand, plasmid, protein, receptor, catalog, protein supplier, supplier |
is listed by: One Mind Biospecimen Bank Listing has parent organization: Duke University; North Carolina; USA |
Addiction | NIDA | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-25722 | SCR_002895 | GPCR Assay Bank | 2026-08-11 09:40:46 | 1 | ||||||
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MutPred Splice Resource Report Resource Website 1+ mentions |
MutPred Splice (RRID:SCR_000594) | MutPred Splice | service resource, production service resource, analysis service resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 6,2023. Tool for identifying coding region variants which disrupt pre-mRNA splicing and the underlying mechanism. | exonic variant, splicing, mrna, next generation sequencing, coding region substitution |
is listed by: OMICtools has parent organization: Cardiff University; Wales; United Kingdom has parent organization: Buck Institute; California; USA |
PMID:24451234 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02257 | SCR_000594 | 2026-08-11 09:40:11 | 1 | |||||||
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Statistical non-Parametric Mapping Resource Report Resource Website 50+ mentions |
Statistical non-Parametric Mapping (RRID:SCR_002092) | SnPM | software toolkit, data processing software, software resource, software application | A toolbox for Statistical Parametric Mapping (SPM) that provides an extensible framework for voxel level non-parametric permutation/randomization tests of functional Neuroimaging experiments with independent observations. SnPM uses the General Linear Model to construct pseudo t-statistic images, which are then assessed for significance using a standard non-parametric multiple comparisons procedure based on randomization/permutation testing. It is most suitable for single subject PET/SPECT analyses, or designs with low degrees of freedom available for variance estimation. In these situations the freedom to use weighted locally pooled variance estimates, or variance smoothing, makes the non-parametric approach considerably more powerful than conventional parametric approaches, as are implemented in SPM. Further, the non-parametric approach is always valid, given only minimal assumptions. The SnPM toolbox provides an alternative to the Statistics section of SPM. | analyze, linear, linux, macos, matlab, microsoft, magnetic resonance, nifti, posix/unix-like, regression, statistical operation, sunos/solaris, windows, statistical parametric mapping, pet, spect |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is affiliated with: SPM has parent organization: University of Michigan; Ann Arbor; USA has parent organization: University of Warwick; Coventry; United Kingdom |
Human Brain Project | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-00342 | http://www.nitrc.org/projects/snpm | SCR_002092 | SnPM: Statistical nonParametric Mapping, SnPM - Statistical NonParametric Mapping - A toolbox for SPM, Statistical nonParametric Mapping | 2026-08-11 09:40:32 | 95 | |||||
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Islet Cell Resource Centers Resource Report Resource Website 100+ mentions |
Islet Cell Resource Centers (RRID:SCR_002806) | ICR | biomaterial supply resource, cell repository, material resource | Group of 10 academic laboratories provide pancreatic islets of cGMP-quality to eligible investigators for use in FDA approved, IRB-approved transplantation protocols in which isolated human islets are transplanted into qualified patients afflicted with type 1 diabetes mellitus; optimize the harvest, purification, function, storage, and shipment of islets while developing tests that characterize the quality and predict the effectiveness of islets transplanted into patients with diabetes mellitus; and provide pancreatic islets for basic science studies. The centers are electronically linked through an Administrative and Bioinformatics Coordinating Center (ABCC). The ABCC manages a system with objectively defined criteria that establishes the order of priority for islet distribution. It also provides database and other informatics to track the utilization of pancreata and all distributed clinical grade islets for transplant and basic research, and supports the Islet Cell Resource Centers Consortium so that the research community has a single entry point to the program. Qualified researchers from domestic institutions may request islets by submitting a written application to the director of the ABCC. The ICRs will distribute Islets as appropriate for either clinical or basic science protocol use to eligible investigators who have received a favorable review and subsequent approval by the ICR Steering Committee (SC). The Administrative and Bioinformatics Coordinating Center (ABCC) manages the distribution according to a priority list. The ABCC will give preference to investigators who have peer-reviewed, NIH-funded research support. | pancreatic islet, clinical |
is listed by: One Mind Biospecimen Bank Listing is related to: One Mind Biospecimen Bank Listing is related to: NIDDK Information Network (dkNET) |
Type 1 diabetes, Diabetes | NIDDK ; Juvenile Diabetes Research Foundation International ; NCRR 1 U42 RR17673 |
Free, Freely available, Available for download | nif-0000-25418 | SCR_002806 | 2026-08-11 09:40:37 | 123 | ||||||
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Plant Metabolic Network Resource Report Resource Website 100+ mentions |
Plant Metabolic Network (RRID:SCR_002888) | data or information resource, project portal, portal | Collaborative project to bring together biochemical pathway databases and research communities focused on plant metabolism. Used to build broad network of plant metabolic pathway databases. Central feature of PMN is PlantCyc, comprehensive plant biochemical pathway database, containing curated information from literature and computational analyses about genes, enzymes, compounds, reactions, and pathways involved in primary and secondary metabolism. | e. coli, gene, arabidopsis, barley, coffee, database, genome, grass, homolog, maize, medicago, oats, pathway, pepper, plant, potato, rice, rye, sorghum, species, taxonomy, tomato, wheat, ontology | lists: PlantCyc | nif-0000-25602, SCR_003778, nlx_15806 | SCR_002888 | Plant Biochemical Pathway Databases | 2026-08-11 09:40:46 | 162 | |||||||||
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Tissue Engineering Resource Center Resource Report Resource Website 1+ mentions |
Tissue Engineering Resource Center (RRID:SCR_000103) | TERC | data or information resource, portal, organization portal | Biomedical technology research center designed to advance basis and clinical aspects of tissue engineering, to provide training for investigators and dissemination of scientific findings and new techniques. Expertise and facilities are focused on research, problem solving and training for biomedical community through integrated systems approach to challenges in tissue engineering. Mission for TERC is to engineer human tissues for medical impact. Includes Functional human tissue grafts: human tissues for application in regenerative medicine;Human disease models in vitro: in vitro models of human disease to provide new experimental tools to understand progression of disease, effects and mechanisms of drug action; Biological materials research: bioengineering tools for cell biology studies in context of tissue development, regeneration and disease. | tissue engineering, stem cell, tissue graft, tissue development, regeneration, human disease, regenerative medicine, in vitro, disease model, bioengineering |
is listed by: National Institute of Biomedical Imaging and Bioengineering has parent organization: Tufts University; Massachusetts; USA has parent organization: Columbia University; New York; USA |
nlx_152637 | SCR_000103 | TERC: Tissue Engineering Resource Center | 2026-08-11 09:40:06 | 8 | ||||||||
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Wavelet-based Image Fusion Resource Report Resource Website 1+ mentions |
Wavelet-based Image Fusion (RRID:SCR_002007) | Wavelet-based Image Fusion | software application, data processing software, software resource, software toolkit | Matlab toolbox that implements the wavelet-based image fusion technique for orthogonal images, introduced in (Aganj et al, MRM 2012). | magnetic resonance | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | PMID:21761448 | Free, Available for download, Freely available | nlx_156018 | SCR_002007 | 2026-08-11 09:40:31 | 2 | |||||||
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Ontario Ministry of Research and Innovation; Ontario; Canada Resource Report Resource Website 1+ mentions |
Ontario Ministry of Research and Innovation; Ontario; Canada (RRID:SCR_000989) | ORFAB | funding resource, regional funding resource | Ministry that supports research, commercialization and innovation taking place across Ontario through a range of programs and services like the Ontario Research Fund, Innovation Demonstration Fund and Ontario Venture Capital Fund. | is parent organization of: Ontario Centres of Excellence | nlx_157929 | https://www.ontario.ca/ministry-research-innovation | SCR_000989 | Ontario Ministry of Research and Innovation | 2026-08-11 09:40:15 | 2 | ||||||||
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Netherlands Organization for Scientific Research Resource Report Resource Website 100+ mentions |
Netherlands Organization for Scientific Research (RRID:SCR_000988) | NWO | data or information resource, portal, funding resource, regional funding resource | Netherlands Organization for Scientific Research (NWO) is a research institute and regional funding source in the Netherlands. | nwo, the netherlands, neternlands research institute, netherlands organization, netherlands government, netherlands granting agency | nlx_151487 | SCR_000988 | Netherlands Organization for Scientific Research | 2026-08-11 09:40:15 | 221 | |||||||||
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Project Halo Resource Report Resource Website 1+ mentions |
Project Halo (RRID:SCR_000136) | Project Halo | data or information resource, portal, organization portal | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Project Halo is a staged, long-range research effort by Vulcan Inc. towards the development of a Digital Aristotlea reasoning system capable of answering novel questions and solving advanced problems in a broad range of scientific disciplines and related human affairs. The project focuses on creating two primary functions: a tutor capable of instructing and assessing students in those subjects, and a research assistant with broad, interdisciplinary skills to help scientists and others in their work. Vulcan began work towards this ambitious vision in 2003 with the Halo Pilot a six-month effort to investigate the feasibility of creating a scientific knowledge base capable of answering novel questions from the AP (1st year college level) chemistry test. Three teams SRI International, Cycorp, and Ontoprise developed knowledge bases, for a limited section of an AP-chemistry syllabus, that were able to correctly answer 40 to 50 percent of the associated questions from the AP test. Since 2004, Project Halo has worked to improve these systems, with an emphasis on enabling knowledge entry by domain experts, instead of specialists in artificial intelligence software. In 2004, Vulcan began the development of Automated User-Centered Reasoning and Acquisition System (AURA), by SRI, that enables domain experts (graduate students in Biology, Chemistry, and Physics) to enter knowledge from introductory science textbooks. In 2006, an evaluation of AURA showed that students could create AURA knowledge bases that correctly answered 40 percent of the questions on a limited AP exam. In 2008, the next evaluation demonstrated an improvement of that score to 70 percent correct. In parallel, Project Halo has sponsored Ontoprise to develop semantic extensions to MediaWiki, the software that Wikipedia runs on. Ontoprise has developed a set of Semantic MediaWiki (SMW)+ extensions to MediaWiki that provide a community-based environment for authoring ontologies and creating semantically enhanced wikis. SMW+ has been widely used and is being applied in project management, enterprise collaboration and knowledge management, business intelligence, and the management of large terminology sets. In 2007, Vulcan began a new effort, Halo Advanced Research (HalAR), to address the difficult knowledge representation and reasoning (KR) challenges that prevent the realization of Digital Aristotle. This effort has produced a new semantic rule language and reasoning system, Semantic Inferencing on Large Knowledge (SILK), which includes major advances, including for default and higher-order reasoning over the web. | project, tutor, research assistant, science, knowledge-base, semantic mediawiki, ontology, textbook, book, training material, digital book, data mining, biology | has parent organization: Stanford Research Institute International | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_144483 | SCR_000136 | 2026-08-11 09:40:06 | 1 | ||||||||
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EuMMCR Resource Report Resource Website 10+ mentions |
EuMMCR (RRID:SCR_001506) | EuMMCR | biomaterial supply resource, cell repository, material resource | Embryonic stem cell distribution unit that distributes material arising within European Conditional Mouse Mutagenesis Program consortium, currently targeting vectors and ES cells. Upon user request EUCOMM grow targeting vectors from glycerol stocks and prepare vector DNA. Identity of vector is verified by restriction mapping. Upon user request EUCOMM thaw, expand and re-freeze several aliquots of desired ES cell clone. Standard controls include PCR based assay. Upon additional request EuMMCR unit develops genotyping PCR, which can be used to genotype chimeric mice that may be generated using those ES cell clones. | embryonic stem cell, vector, experimental protocol, male, dna, genotype |
is used by: EUCOMMTOOLS is listed by: One Mind Biospecimen Bank Listing is related to: European Conditional Mouse Mutagenesis Program has parent organization: Helmholtz Center Munich |
Free, Freely available | nlx_152805 | http://www.eummcr.org/ | SCR_001506 | EuMMCR - European Mouse Mutant Cell Repository, European Mouse Mutant Cell Repository | 2026-08-11 09:40:22 | 24 | ||||||
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Ensembl Covid-19 Resource Report Resource Website 1+ mentions |
Ensembl Covid-19 (RRID:SCR_024704) | portal, topical portal, disease-related portal, data or information resource | Ensembl SARS-Cov2 data portal. | Ensembl, SARS-Cov2, Covid -19, data | is listed by: Ensembl | Covid -19 | Free, Freely available | SCR_024704 | 2026-08-11 09:44:38 | 4 |
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