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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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XooNIps - Neuroinformatics Base Platform System Resource Report Resource Website 1+ mentions |
XooNIps - Neuroinformatics Base Platform System (RRID:SCR_013590) | software development tool, software resource, software application | Neuroinformatics (NI) is a new discipline that challenges the understanding of the structure and mechanism of the brain by combining neuroscience and information technology. The global collaborations in this field have been actively started with the support of the International Neuroinformatics Coordinating Facility (INCF) launched in November 2005. The Laboratory for Neuroinformatics at RIKEN Brain Science Institute (BSI) is involved in developing various cutting-edge technologies related to NI such as XooNIps. XooNIps succeeded the concept and basic feature of the vision science platform; Visiome, constructed by the NRV (i.e., Neuroinformatics Research in Vision) Project and has been developed based on a content management system (CMS); XOOPS, as infrastructure for NI databases to share different types of data on the Internet. :XooNIps has three features: :The first is the flexibility of developing databases. CMS-based XooNIps makes it easy to change the design or to extend the functions of databases by combining the different modules available on XOOPS. Therefore, even those who are not expert in computer system can develop their database on XooNIps. :The second is the diversity and extensibility of the data which can be handled by XooNIps. In order to handle different types of actual data, it provides not only the various data forms per se, but also the extension method to handle a new data form, which enables to deal easily with even a non-standardized data form. :The third is the facility to distribute metadata. XooNIps implements OAI-PMH (i.e., Open Archive Initiative-Protocol for Metadata Harvesting) which is one of the standard protocols to distribute metadata. This enables to collect information on other databases which are developed on XooNIps or to coordinate databases by exchanging metadata with other databases which implement OAI-PMH than those on XooNIps. :Since April 2007, Neuroinformatics Japan Center (NIJC) at RIKEN BSI takes charge of extending and maintaining XooNIps, and is committed to manage the documentation hereafter. :NIJC, as a national node of INCF, is developing and operating various NI platforms in neuroscience based on XooNIps to establish and facilitate NI research in Japan. XooNIps is also being applied to databases or organizational repositories in several institutions and universities, and laboratory groupware in various fields. We hope XooNIps will be of universal use in and out of Japan. :database; binary executable; software development tool; metadata; data set; : | is related to: Concierge | nif-0000-00375 | SCR_013590 | XooNIps | 2026-08-11 09:42:43 | 1 | ||||||||||
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University of Chicago Digestive Diseases Research Core Center Resource Report Resource Website 1+ mentions |
University of Chicago Digestive Diseases Research Core Center (RRID:SCR_015601) | DDRCC | data or information resource, training resource, portal, organization portal | Center whose goals include fostering collaboration among basic and clinical investigators, facilitating the use of new technologies in the study of treatment of digestive diseases, and providing education and training for improved treatment and diagnosis. | DDRCC, digestive disease, uchicago |
is listed by: NIDDK Information Network (dkNET) is parent organization of: University of Chicago Digestive Diseases Research Core Center Integrated Translational Research Core is parent organization of: University of Chicago Digestive Diseases Research Core Center Administrative Core is parent organization of: University of Chicago Digestive Diseases Research Core Center Host-Microbe Core is parent organization of: University of Chicago Digestive Diseases Research Core Center Tissue and Cell Imaging Core is parent organization of: University of Chicago Digestive Diseases Research Core Center Tissue Engineering and Cell Models Core has organization facet: University of Chicago Digestive Diseases Research Core Center Administrative Core has organization facet: University of Chicago Digestive Diseases Research Core Center Integrated Translational Research Core has organization facet: University of Chicago Digestive Diseases Research Core Center Tissue Engineering and Cell Models Core has organization facet: University of Chicago Digestive Diseases Research Core Center Host-Microbe Core has organization facet: University of Chicago Digestive Diseases Research Core Center Tissue and Cell Imaging Core is organization facet of: Digestive Disease Centers |
digestive disease | NIDDK P30 DK042086 | Available to the research community | SCR_015601 | 2026-08-11 09:43:07 | 1 | |||||||
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DistillerSR Resource Report Resource Website 10+ mentions |
DistillerSR (RRID:SCR_023078) | data management software, software resource, software application | Literature review software by DistillerSR Inc. Automates management of literature collection, screening, and assessment using AI and intelligent workflows. From systematic literature review to rapid review to living review, makes any project simpler to manage and configure to produce transparent, audit-ready, and compliant results. | DistillerSR Inc., management of literature collection, screening, and assessment, project to manage, literature review software | Restricted | SCR_023078 | 2026-08-11 09:44:24 | 11 | |||||||||||
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Musculoskeletal Knowledge Portal Resource Report Resource Website 10+ mentions |
Musculoskeletal Knowledge Portal (RRID:SCR_023171) | MSK-KP | data or information resource, topical portal, portal, disease-related portal | Portal enables browsing, searching, and analysis of human genetic and genomic information linked to musculoskeletal traits and diseases, while protecting the integrity and confidentiality of underlying data. | genomic data mining, human genetic data, genomic information, musculoskeletal traits and diseases data, DRKB | musculoskeletal disease | NIH AR085003 | PMID:34686856 | Free, Freely available | https://msk.hugeamp.org/ | SCR_023171 | 2026-08-11 09:44:30 | 26 | ||||||
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Laboratory of Systems Pharmacology program Resource Report Resource Website |
Laboratory of Systems Pharmacology program (RRID:SCR_022873) | LSP | data or information resource, portal, laboratory portal, organization portal | Research and education program in Harvard Program in Therapeutic Science at Harvard Medical School to advance science and to develop technology needed to accelerate invention of new medicines and personalization of patient care. Used to study molecular causes of disease, ways drugs exert their therapeutic and adverse effects, design and interpretation of clinical trials. | Harvard Program, Therapeutic Science, new medicines development, personalized patient care | has parent organization: Harvard Medical School; Massachusetts; USA | Free, Freely available | SCR_022873 | 2026-08-11 09:44:22 | 0 | |||||||||
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Natural Scenes Dataset Resource Report Resource Website 10+ mentions |
Natural Scenes Dataset (RRID:SCR_023648) | NSD | data or information resource, topical portal, portal, data set | Portal for large scale fMRI dataset conducted at ultra high field strength at Center of Magnetic Resonance Research at University of Minnesota. Dataset consists of whole brain, high resolution fMRI measurements of healthy adult subjects while they viewed thousands of color natural scenes over course of scan sessions. While viewing these images, subjects were engaged in continuous recognition task in which they reported whether they had seen each given image at any point in experiment. These data constitute massive benchmark dataset for computational models of visual representation and cognition, and can support wide range of scientific inquiry. | Natural scenes, vision, fMRI measurements, fMRI dataset, whole brain, healthy adult subjects, images, visual representation and cognition, benchmark, training data | has parent organization: University of Minnesota Twin Cities; Minnesota; USA | PMID:34916659 | Free,Freely available | https://github.com/cvnlab/nsdcode/ | SCR_023648 | 2026-08-11 09:44:41 | 44 | |||||||
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Global Alzheimers Association Interaction Network Resource Report Resource Website 10+ mentions |
Global Alzheimers Association Interaction Network (RRID:SCR_023699) | GAAIN | data or information resource, topical portal, portal, disease-related portal | Open access integrated research platform, which links scientists, shared data, and analysis tools to accelerate Alzheimer’s disease research, disease preventions, treatments and cure. Unites diverse and geographically distributed network of data partners to foster cohort discovery, collaboration and sharing. Researchers can discover clinical, genetic, imaging and other data collected across many independent studies. | USC Mark and Mary Stevens Neuroimaging and Informatics Institute, Alzheimer’s disease research, disease preventions, treatments and cure, network of data partners, cohort discovery, collaboration and sharing, clinical data, genetic data, imaging data, Alzheimer data discovery, | has parent organization: University of Southern California; Los Angeles; USA | Alzheimer’s disease | Alzheimer Association | Free, Freely available | SCR_023699 | 2026-08-11 09:44:37 | 30 | |||||||
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TIGER Data Portal Resource Report Resource Website 10+ mentions |
TIGER Data Portal (RRID:SCR_023626) | data or information resource, topical portal, portal, disease-related portal | Resource enables integrative exploration of genetic and epigenetic basis of development of Type 2 Diabetes, together with other associated functional, molecular and clinical data, centered in biology and role of pancreatic beta cells.The gene expression regulatory variation landscape of human pancreatic islets. | Type 2 Diabetes, genetic and epigenetic, functional data, molecular data, clinical data, pancreatic beta cells. | is related to: T2DSystems | Type 2 Diabetes | European Union Horizon 2020 ; Spanish government ; Swiss State Secretariat for Education‚ Research and Innovation ; American Diabetes Association Innovative and Clinical Translational Award ; Research England ; Wellcome Trust ; NIDDK U01 DK105535; NIDDK U01 DK085545 |
PMID:34644572 | SCR_023626 | Translational Human Pancreatic Islet Genotype Tissue-Expression Resource | 2026-08-11 09:44:28 | 23 | |||||||
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Enroll-HD Resource Report Resource Website 10+ mentions |
Enroll-HD (RRID:SCR_023300) | data or information resource, topical portal, portal, disease-related portal | Clinical research platform and longitudinal observational study for Huntington’s Disease families intended to accelerate progress towards therapeutics. Collaboration between Huntington’s disease families, clinicians, and researchers to accelerate progress toward effective treatments. | Clinical Research, clinical trails, Huntington’s Disease families, therapeutics, effective treatments, | Huntington’s disease | Cure HD Initiative Foundation | Free, Freely available | SCR_023300 | 2026-08-11 09:44:35 | 13 | |||||||||
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PROFisis Resource Report Resource Website |
PROFisis (RRID:SCR_024179) | simulation software, software resource, software application | Software tool that identifies interacting residues from sequence alone. Developed using transient protein�protein interfaces from complexes of experimentally known 3D structures. | identifies interacting residues from sequence alone, | is listed by: Debian | Free, Available for download, Freely available, | OMICS_13706 | https://sources.debian.org/src/profisis/ | SCR_024179 | profisis | 2026-08-11 09:44:34 | 0 | |||||||
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CONTRAfold Resource Report Resource Website 1+ mentions |
CONTRAfold (RRID:SCR_023994) | CONTRAfold | simulation software, software resource, software application | Software novel secondary structure prediction method based on conditional log-linear models, a flexible class of probabilistic models which generalize upon SCFGs by using discriminative training and feature-rich scoring. Used for sequence prediction. | sequence prediction, | is listed by: Debian | PMID:16873527 | Free, Available for download, Freely available | OMICS_03452 | https://sources.debian.org/src/CONTRAfold/ | SCR_023994 | CONditional TRAining for RNA Secondary Structure Prediction, contrafold | 2026-08-11 09:44:40 | 2 | |||||
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Metastudent Resource Report Resource Website |
Metastudent (RRID:SCR_024110) | simulation software, software resource, software application | Software tool to predict gene ontology terms for protein sequences through homology. | predict gene ontology terms, protein sequences, through homology, | is listed by: Debian | Free, Available for download, Freely available, | OMICS_20187 | https://sources.debian.org/src/metastudent/, https://sources.debian.org/src/metastudent-data/ | SCR_024110 | metastudent-data, metastudent | 2026-08-11 09:44:32 | 0 | |||||||
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CTSim Resource Report Resource Website |
CTSim (RRID:SCR_024004) | simulation software, software resource, software application | Software tool to simulate process of transmitting X-rays through phantom objects. Reconstructs original phantom image from projections. Has wide array of image analysis and image processing functions. | Computed tomography simulator, reconstruct original phantom image from projections, reconstruct image, | is listed by: Debian | Free, Available for download, Freely available | https://sources.debian.org/src/ctsim/ | SCR_024004 | ctsim, Open Source Computed Tomography Simulator | 2026-08-11 09:44:40 | 0 | ||||||||
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Linkage Disequilibrium Analyses for Quantitative and Discrete Traits Resource Report Resource Website 1+ mentions |
Linkage Disequilibrium Analyses for Quantitative and Discrete Traits (RRID:SCR_013365) | data or information resource, database, software resource, software application | How is association mapping going to help me find genes? During the past decade, the genes for a large number of rare mendelian traits have been identified. However, traditional linkage analyses lack power and precision when applied to complex disease. Association mapping, which compares the effects of different chromosomal variants, may be more successful at identifying genes of small effect. How does QTDT help association mapping? Association mapping can produce misleading results when the study population is not homogeneous, but includes individuals with different genetic backgrounds. Family based association tests, commonly referred to as TDTs (Transmission Disequilibrium Tests), do not produce misleading results in these circumstances. QTDT can use all the information in a pedigree to construct powerful tests of association that are robust in the presence of stratification. What does the Q stant for ? Q stands for Quantitative. Quantitative traits provide effective descriptions of many complex diseases, including asthma. For many of these conditions, all or nothing definitions of disease are arbitrary and unsatisfactory. QTDT incorporates variance components methodology in the analysis of family data and includes exact estimation of p-values for analysis of small samples and non-normal data. The QTDT abbreviation (for Quantitative Transmission Disequilibrium Tests) was first used by David Allison in his 1997 paper. This research was supported in part by the intramural program of the National Eye Institute and by National Institutes of Health Grants EY016862, EY007758, EY09859, EY012118, P30-EY014801, EY-014458, EY014467, HL084729, and HG002651, by the Foundation Fighting Blindness, the Macula Vision Research Foundation, the American Health Assistance Foundation, Research to Prevent Blindness, the Pew Charitable Trusts, the Mayo Clinic Foundation, the Casey Macular Degeneration Center Fund, the Marion W. and Edward F. Knight AMD Fund, the Harold and Pauline Price Foundation, National Genotyping Centre of Spain, and the Elmer and Sylvia Sramek Foundation. The Center for Inherited Disease Research, fully funded through a federal contract (HHSN268200782096C) from National Institutes of Health to | has parent organization: University of Michigan; Ann Arbor; USA | nif-0000-31385 | SCR_013365 | QTDT | 2026-08-11 09:42:37 | 7 | ||||||||||
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Barts and The London School of Medicine and Dentistry Labs and Facilities Resource Report Resource Website |
Barts and The London School of Medicine and Dentistry Labs and Facilities (RRID:SCR_012710) | Barts and The London School of Medicine and Dentistry Labs & Facilities | portal, service resource, data or information resource, core facility, access service resource | Barts and The London offers international levels of excellence in research and teaching while serving a population of unrivalled diversity. Through partnership with our linked trusts, notably Barts and The London NHS Trust, and our associated University Hospital Trusts _������������_ Homerton, Newham, Whipps Cross and Queen''''s (Romford) the School''''s research and teaching is informed by an exceptionally wide ranging and stimulating clinical environment. |
is listed by: ScienceExchange is related to: Queen Mary University of London Labs and Facilities is related to: Blizard Institute of Cell and Molecular Science Labs and Facilities has parent organization: Queen Mary University of London; London; United Kingdom |
SciEx_8912 | SCR_012710 | 2026-08-11 09:42:40 | 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 | portal, service resource, data or information resource, core facility, access 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 | Michigan State University Labs & Facilities | 2026-08-11 09:42:24 | 0 | |||||||||
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Phaff Yeast Culture Collection Resource Report Resource Website 1+ mentions |
Phaff Yeast Culture Collection (RRID:SCR_016781) | portal, service resource, data or information resource, database, organization portal | Collection of wild yeast in the world. Academic and industrial resarchers utilize this collection for a variety of research and applications, including pigments, enzymes, food ingredients, and hosts for protein expression. Provides contract screening and strain selection services. | yeast, strain, wild, screening, selection, service | has parent organization: University of California at Davis; California; USA | Commercially available | SCR_016781 | 2026-08-11 09:43:31 | 6 | ||||||||||
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CMMT Mouse Animal Production Service Resource Report Resource Website |
CMMT Mouse Animal Production Service (RRID:SCR_016403) | EMS, MAPS, CMMT MAPS, CMMT EMS | biomaterial supply resource, organism supplier, material resource | Supplier of mice for research purposes. The service is run by Dr. Elizabeth M. Simpson, Ph.D. and is affiliated with her lab. | mouse, strain, supply, research, repository, subject, genetic engineering, knockout, mice, gene, model | SCR_016403 | Mouse Animal Production Service (MAPS), Centre for Molecular Medicine and Therapeutics MAPS, Dr. Elizabeth M. Simpson PhD, Elizabeth M. Simpson, Mouse Animal Production Service, Centre for Molecular Medicine and Therapeutics Mouse Animal Production Service | 2026-08-11 09:43:18 | 0 | ||||||||||
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Pediatric Cancer Data Commons Resource Report Resource Website 1+ mentions |
Pediatric Cancer Data Commons (RRID:SCR_022369) | PCDC | data or information resource, topical portal, portal, disease-related portal | PCDC brings together clinical, genomic, and imaging data from institutions around the world to transform pediatric cancer research and outcomes. Headquartered at University of Chicago, PCDC works with international leaders in pediatric cancers and National Cancer Institute to develop and apply uniform data standards that facilitate collection, combination, and analysis of data from many different sources. PCDC Consortium developes common core data dictionary and common governance structure spanning pediatric cancers neuroblastoma, soft tissue sarcoma, acute myeloid leukemia, acute lymphoblastic leukemia, germ cell tumors, bone tumors, and Hodgkin lymphoma to enable innovative cross disease research as well as set standard for future cancer data commons endeavors. | pediatric cancer, clinical data, genomic data, imaging data, uniform data standards, common core data dictionary, common governance structure, | is related to: University of Chicago; Illinois; USA | pediatric cancer, neuroblastoma, soft tissue sarcoma, acute myeloid leukemia, acute lymphoblastic leukemia, germ cell tumors, bone tumors, Hodgkin lymphoma | Free, Freely available | SCR_022369 | 2026-08-11 09:44:22 | 2 | ||||||||
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TIGRFAMS Resource Report Resource Website 100+ mentions |
TIGRFAMS (RRID:SCR_005493) | JCVI TIGRFAMS, TIGRFAM | data or information resource, database, data set | Consists curated multiple sequence alignments, Hidden Markov Models (HMMs) for protein sequence classification, and associated information designed to support automated annotation of (mostly prokaryotic) proteins. Starting with release 10.0, TIGRFAMs models use HMMER3, which provides excellent search speed as well as exquisite search sensitivity. See the "TIGRFAMs Complete Listing" page to review the accession, protein name, model type, and EC number (if assigned) of all models. TIGRFAMs is a member database in InterPro. The HMM libraries and supporting files are available to download and use for free from our FTP site. | sequence alignment, hidden markov model, protein sequence, classification, protein, protein family, sequence homology, sequence, homology, function, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: InterPro is related to: InterPro has parent organization: J. Craig Venter Institute |
PMID:23197656 | Free | nif-0000-03560, OMICS_01700, biotools:tigrfams | https://bio.tools/tigrfams | http://www.tigr.org/TIGRFAMs | SCR_005493 | TIGRFAMs | 2026-08-11 09:41:17 | 142 |
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