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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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IFTI-Mirage Resource Report Resource Website 1+ mentions |
IFTI-Mirage (RRID:SCR_000505) | data or information resource, database, portal | A resource for information pertaining to methodologies, tools and technologies of gene expression. The website offers resources for sequence analysis, database services, and other technologies of gene expression and regulation. | bioinformatics, gene, expression, database, technology, method, tool, sequence, regulation |
is parent organization of: object-oriented Transcription Factors Database is parent organization of: TfSiteScan |
Public, Available to the research community | nlx_19877 | SCR_000505 | Institute for Transcriptional Informatics-Molecular Informatics Resource for the Analysis of Gene Expression, MIRAGE | 2026-09-05 06:30:35 | 5 | ||||||||
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NIH Office of Research Services Resource Report Resource Website |
NIH Office of Research Services (RRID:SCR_000987) | ORS, | data or information resource, funding resource, portal | The Office of Research Services (ORS) provides support to the NIH research mission by planning, directing and delivering scientific and regulatory activities, public safety, security, and services for the NIH community. | office research, ors, nih ors, nih research services, ors planning ors directing, ors public safety, ors security | has parent organization: National Institutes of Health | nlx_inv_1005067 | SCR_000987 | Office of Research Services - Serving the NIH Community, Office of Research Services | 2026-09-05 06:30:34 | 0 | ||||||||
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Franklin Resource Report Resource Website |
Franklin (RRID:SCR_024670) | data or information resource, knowledge base | Connectivity hub across medical genetics domain. Network of genomic information. Supports all vendors and workflows and thus enables any genetic professional to deliver more accurate, more actionable data insights. | medical genetics domain, genomic information network, genomic data | Restricted | SCR_024670 | 2026-09-05 06:30:33 | 0 | |||||||||||
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MapMyCells Resource Report Resource Website 50+ mentions |
MapMyCells (RRID:SCR_024672) | algorithm resource, software application, software resource, web application | MapMyCells maps single cell and spatial transcriptomics data sets to massive, high-quality, and high-resolution cell type taxonomies. It enables speeding up the creation of brain reference atlases by facilitating the integration of datasets from the scientific community with a shared reference. MapMyCells is part of the growing Brain Knowledge Platform. Its key advantage is scale: researchers can provide up to 327 million cell-gene pairs from their own data, a huge leap forward for working with whole-brain datasets. Allen Institute and its collaborators continue to add new reference taxonomies and algorithms to MapMyCells. | mapping of single cell and spatial transcriptomics data, mapping to whole mouse brain taxonomy, mapping to human brain taxonomy, correlation mapping, hierarchical mapping, label transfer |
has parent organization: Allen Institute is organization facet of: BICCN |
NIMH U24MH130918; Paul G. Allen Foundation |
Free, Freely available | https://knowledge.brain-map.org/mapmycells/process/, https://portal.brain-map.org/atlases-and-data/bkp/mapmycells/mapmycells-use-case-single-cell-genomics | SCR_024672 | Map My Cells, Allen MapMyCells | 2026-09-05 06:30:33 | 60 | |||||||
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Philips: FEI CM120 BioTwin Transmission Electron Microscope Resource Report Resource Website |
Philips: FEI CM120 BioTwin Transmission Electron Microscope (RRID:SCR_024709) | instrument resource | Transmission electron microscope with maximum acceleration voltage of 120 kv.Microscope primarily used for sample screening. | Microscope, Philips, FEI, instrument, Transmission Electron Microscope, sample screening, | Restricted | Model_Number_CM120 | SCR_024709 | , FEI CM120 Biotwin, FEI/PHILIPS CM120 TEM, Philips/FEI CM120 Bio Twin Transmission Electron Microscope, Philips CM120 Biotwin Lens | 2026-09-05 06:30:34 | 0 | |||||||||
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Grantees Meeting for NITRC Resource Report Resource Website |
Grantees Meeting for NITRC (RRID:SCR_000419) | data or information resource, portal, project portal | This project is meant for planning the NITRC Grantee meetings. A website for organizing meetings for the Neuroimaging Informatics Tools and Resources Clearinghouse, to facilitate participants meeting one another, and promote discussion of common interests and collaboration. | meeting, neuroimaging, nitrc, informatics, tools, collaboration, discussion | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Free, Freely available | nlx_155875, SCR_014081 | http://www.nitrc.org/plugins/mwiki/index.php/nihgrantees:2009Meeting | SCR_000419 | 2026-09-05 06:30:35 | 0 | ||||||||
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University of Texas Health Science at Houston Center for SUDEP Research Resource Report Resource Website |
University of Texas Health Science at Houston Center for SUDEP Research (RRID:SCR_024700) | data access protocol, data or information resource, organization portal, portal, software resource, web service | NIH funded center to provide system for sharing multimodal epilepsy data for Sudden Unexpected Death in Epilepsy. Modality Epilepsy Data Capture and Integration System (MEDCIS) is cross cohort query interface for SUDEP (Sudden Unexpected Death in EPilepsy) research. | sharing multimodal epilepsy data, sudden unexpected death, epilepsy, MEDCIS, Modality Epilepsy Data Capture and Integration System, cross cohort query interface, | epilepsy | NINDS R01NS116287; NINDS R01NS126690; NINDS U01NS090405; NINDS U01NS090408 |
PMID:25954436 PMID:36059922 |
Restricted | SCR_024700 | , Center for SUDEP Research, Center for Sudden Unexpected Death in Epilepsy Research | 2026-09-05 06:30:34 | 0 | |||||||
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Multitron: Incubation Shaker Resource Report Resource Website |
Multitron: Incubation Shaker (RRID:SCR_024668) | instrument resource | Shaker for cultivation of microorganisms and cell cultures provides homogeneous conditions for cultivation up to 63 liters or 23 000 batches in parallel in less than square meter of space. | Shaker, cultivation of microorganisms and cell cultures, | SCR_024668 | Multitron Standard Incubation Shaker | 2026-09-05 06:30:33 | 0 | |||||||||||
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Project Halo Resource Report Resource Website 1+ mentions |
Project Halo (RRID:SCR_000136) | Project Halo | data or information resource, organization portal, 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 | 2026-09-05 06:30:35 | 1 | ||||||||
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Ensembl Covid-19 Resource Report Resource Website 1+ mentions |
Ensembl Covid-19 (RRID:SCR_024704) | data or information resource, disease-related portal, portal, topical portal | Ensembl SARS-Cov2 data portal. | Ensembl, SARS-Cov2, Covid -19, data | is listed by: Ensembl | Covid -19 | Free, Freely available | SCR_024704 | 2026-09-05 06:30:34 | 4 | |||||||||
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PyPOLAR Resource Report Resource Website 1+ mentions |
PyPOLAR (RRID:SCR_024681) | data processing software, image analysis software, software application, software resource, standalone software | Software Python based app for analyzing polarization resolved microscopy data to measure molecular orientation and order in biological samples. | analyzing polarization resolved microscopy data, measure molecular orientation and order, biological samples, | Free, Available for download, Freely available | https://www.fresnel.fr/polarimetry | SCR_024681 | 2026-09-05 06:30:33 | 1 | ||||||||||
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SPAdes Resource Report Resource Website 100+ mentions |
SPAdes (RRID:SCR_000131) | SPAdes | software resource, software toolkit | Software package for assembling single cell genomes and mini metagenomes. Uses short read sets as input. Used for genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. Works with Illumina or IonTorrent reads and can provide hybrid assemblies using PacBio, Oxford Nanopore and Sanger reads. Intended for small genomes like bacterial or fungal., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | assembler, single, cell, small, genome, short, read, data |
is used by: shovill is listed by: OMICtools is listed by: Debian is listed by: SoftCite is related to: rnaSPAdes is related to: rnaQUAST has parent organization: Saint Petersburg Academic University; Saint Petersburg; Russia works with: Illumina: iSeq 100 Sequencing System |
Government of the Russian Federation ; NCRR P41 RR024851 |
PMID:24093227 PMID:22506599 DOI:10.1089/cmb.2012.0021 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01502 | https://sources.debian.org/src/spades/ | http://bioinf.spbau.ru/spades/ | SCR_000131 | SPAdes Genome Assembler | 2026-09-05 06:30:35 | 108 | |||
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PERFect Resource Report Resource Website 1+ mentions |
PERFect (RRID:SCR_024682) | data processing software, software application, software resource | Software R package as filtering test for microbiome data. Permutation filtering approach to address two unsolved problems in microbiome data processing: (i) define and quantify loss due to filtering by implementing thresholds and (ii) introduce and evaluate a permutation test for filtering loss to provide a measure of excessive filtering. | filtering test, microbiome data, microbiome data processing, | NIGMS 1U54GM104944; NSF |
PMID:29917060 | Free, Available for download, Freely available | SCR_024682 | Permutation Filtering Package in R | 2026-09-05 06:30:33 | 1 | ||||||||
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Rosalind Resource Report Resource Website 10+ mentions |
Rosalind (RRID:SCR_006233) | Rosalind | online course, open course, training resource | A software infrastructure, course and tool set for teaching bioinformatics, and biology through the use of models. This platform for learning bioinformatics through problem solving aims to make learning bioinformatics fun and easy. Learning bioinformatics usually requires solving computational problems of varying difficulty that are extracted from real challenges of molecular biology. Rosalind offers an array of intellectually stimulating problems that grow in biological and computational complexity; each problem is checked automatically, so that the only resource required to learn bioinformatics is an internet connection. Rosalind also promises to facilitate improvements in standard bioinformatics education by providing a vital teaching aid and a central homework resource. Rosalind is inspired by Project Euler, Google Code Jam, and the ever growing movement of free online courses. The project''s name commemorates Rosalind Franklin, whose X-ray crystallography with Raymond Gosling facilitated the discovery of the DNA double helix by Watson and Crick. We hope that Rosalind will inspire a new generation of bioinformatics students by attracting biologists who want to develop vital programming skills at their own pace in a unique environment as well as programmers who have never been exposed to some of the stimulating computational problems generated by molecular biology. | bioinformatics, biology, model, programming, teaching, course, problem solving, python, algorithm, molecular biology |
is listed by: OMICtools has parent organization: University of California at San Diego; California; USA has parent organization: Saint Petersburg Academic University; Saint Petersburg; Russia |
Howard Hughes Medical Institute ; Ministry of Education and Science of the Russian Federation ; Megagrant |
nlx_151793, OMICS_01709 | SCR_006233 | 2026-09-05 06:30:34 | 39 | ||||||||
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Drug Design Data Resource Resource Report Resource Website 1+ mentions |
Drug Design Data Resource (RRID:SCR_000497) | D3R | data or information resource, database, portal | Project portal's database of protein-ligand data sets provided by pharmaceutical partners that provide atomic details of drug mechanisms that will be used to improve computer-aided drug-design methods and thus accelerate drug discovery. The project aims to help companies release the high-quality data they have generated, which has incredible value to researchers working to improve methods of computer-aided drug discovery. Everyone stands to benefit from the ability to develop new medications more quickly and inexpensively. What computational chemists globally are trying to do is to make faster, more accurate, more predictive programs to speed up the process. Part of their mission is to engage the community in these challenges to test newly developed predictive algorithms. | computer-aided drug design, drug design, pharmaceutical, small molecule, ligand-protein interaction, protein, ligand, drug development, drug, binding, data set, affinity, computation, medicine, compound, structure |
uses: Binding MOAD uses: Protein Data Bank Bind Database is used by: NIF Data Federation is listed by: DataCite has parent organization: University of California at San Diego; California; USA has parent organization: University of California; California; USA |
NIGMS 1U01GM111528 | nlx_158375 | https://api.datacite.org/dois?prefix=10.15782 | SCR_000497 | Drug Design Data (D3R) Resource | 2026-09-05 06:30:35 | 3 | ||||||
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NCI SEER Cancer Statistics Review Resource Report Resource Website 500+ mentions |
NCI SEER Cancer Statistics Review (RRID:SCR_024685) | data or information resource, disease-related portal, portal, topical portal | Platform to report outlining trends in cancer statistics and methods to derive various cancer statistics from the Surveillance, Epidemiology, and End Results (SEER) program. Authoritative source for cancer statistics in the United States. | trends in cancer, cancer statistics, methods to derive various cancer statistics, Surveillance, Epidemiology, and End Results program, SEER program, | cancer | NCI | Free, Freely available | https://seer.cancer.gov/ | SCR_024685 | SEER Cancer Statistics Review, , National Cancer Institute SEER Cancer Statistics Review, NIH NCI Surveillance, Epidemiology, and End Results Cancer Statistics Review, NIH NCI SEER Cancer Statistics Review | 2026-09-05 06:30:33 | 760 | |||||||
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OppNet - Basic Behavioral and Social Science Opportunity Network Resource Report Resource Website 1+ mentions |
OppNet - Basic Behavioral and Social Science Opportunity Network (RRID:SCR_003522) | OppNet | data or information resource, funding resource, organization portal, portal | OppNet is a trans-NIH initiative to expand the agency's funding of basic behavioral and social sciences research (b-BSSR). Basic-BSSR studies mechanisms and processes that influence behavior at the individual, group, community and population level. Research results lead to new approaches for reducing risky behaviors and improving the adoption of healthy practices. The mission of OppNet is to pursue opportunities for strengthening basic behavioral and social science research (b-BSSR) at the NIH while innovating beyond existing investments. * OppNet advances basic behavioral and social science research through activities and initiatives that build a body of knowledge about the nature of behavior and social systems. * OppNet prioritizes activities and initiatives that focus on basic mechanisms of behavior and social processes; that are relevant to the missions and public health challenges of multiple NIH Institutes, Centers and Offices (ICOs); and that build upon existing NIH investments without replicating them. All NIH Institutes and Centers (ICs) share the mission of supporting b-BSSR. OppNet will also develop a plan for focused multi-year programs across ICs to advance priority topics within b-BSSR. | has parent organization: National Institutes of Health | nif-0000-38232 | SCR_003522 | OppNet: Basic Behavioral and Social Science Opportunity Network | 2026-09-05 06:30:34 | 1 | |||||||||
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NCI Lymphoid Neoplasm Recode 2020 Revision Definition Resource Report Resource Website |
NCI Lymphoid Neoplasm Recode 2020 Revision Definition (RRID:SCR_024686) | data or information resource, disease-related portal, portal, topical portal | Website describing International Classification of Diseases codes that corresponds to lymphomas in the Surveillance, Epidemiology, and End Results (SEER) registry. | International Classification of Diseases codes, ICD, lymphoma, Surveillance, Epidemiology, and End Results registry, SEER registry, | lymphomas | NCI | Free, Available for download, Freely available | https://seer.cancer.gov/lymphomarecode/lymphoma-2021.html | SCR_024686 | , Lymphoid Neoplasm Recode 2020 Revision Definition, National Cancer Institute Lymphoid Neoplasm Recode 2020 Revision Definition, NIH NCI Lymphoid Neoplasm Recode 2020 Revision Definition | 2026-09-05 06:30:33 | 0 | |||||||
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Emerson: Branson Digital Sonifier SFX250 Resource Report Resource Website 1+ mentions |
Emerson: Branson Digital Sonifier SFX250 (RRID:SCR_024710) | instrument resource | Branson Sonifier ultrasonic cell disruptor / homogenizers are versatile laboratory units suitable for broad range of liquid processing applications. Digital sonifier to disrupt cells, bacteria, spores, or tissue. Ideal for initiating and accelerating chemical, biochemical, and physical reactions, and for degassing liquids. Used to prepare emulsion to 0.01 micron, homogenize immiscible liquids, polymerize some materials, and depolymerize others. | Digital sonifier, Branson, instrument, sonication, sonicator, | https://raw.githubusercontent.com/SciCrunch/RRID-Instruments/refs/heads/main/PDF/SCR_024710.pdf | Model_Number_SFX250 | https://www.manualslib.com/manual/1387800/Branson-Digital-Sonifier-250.html#product-Sonifier%20450 | SCR_024710 | Branson Digital Sonifier | 2026-09-05 06:30:34 | 3 | ||||||||
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Polar Geospatial Center Resource Report Resource Website |
Polar Geospatial Center (RRID:SCR_000402) | PGC | data or information resource, organization portal, portal | Portal as data resource, map repository, and GIS service provider for federally-funded scientists conducting research in the Arctic and Antarctic. The PGC holds an extensive collection of satellite imagery and aerial photography at varying resolutions. | arctic, antarctic, geospatial, polar, mapping, gis, remote sensing, cartography, map, image collection, satellite imagery, aerial photography |
is listed by: CINERGI has parent organization: University of Minnesota Twin Cities; Minnesota; USA |
NSF | Free, Freely available | nlx_154743 | SCR_000402 | 2026-09-05 06:30:35 | 0 |
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The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant U24DK097771.
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