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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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GOfetcher Resource Report Resource Website |
GOfetcher (RRID:SCR_005681) | GOfetcher | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented on June 29, 2012. We developed a web application, GOfetcher, with a very comprehensive search facility for the GO project and a variety of output formats for the results. GOfetcher has three different levels for searching the GO: Quick Search, Advanced Search, and Upload Files for searching. The application includes a unique search option which generates gene information given a nucleotide or protein accession number which can then be used in generating gene ontology information. The output data in GOfetcher can be saved into several different formats; including spreadsheet, comma-separated values, and the Extensible Markup Language (XML) format. Platform: Online tool | gene, nucleotide, protein, ontology, ontology or annotation browser |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: University of Southern Mississippi; Mississippi; USA |
NSF EPS-0556308; U.S. Army ; Environmental Quality Program contract #W912HZ-05-P-0145 |
PMID:18728045 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_149124 | http://mcbc.usm.edu/gofetcher/ | SCR_005681 | GOfetcher: a database with complex searching facility for gene ontology | 2026-09-03 04:48:10 | 0 | ||||
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GoFish Resource Report Resource Website 1+ mentions |
GoFish (RRID:SCR_005682) | GoFish | analysis service resource, data analysis service, production service resource, service resource, software resource, source code | Software program, available as a Java applet online or to download, allows the user to select a subset of Gene Ontology (GO) attributes, and ranks genes according to the probability of having all those attributes., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | gene, ontology or annotation browser, java, windows, mac os x, linux, unix, bio.tools |
is listed by: Gene Ontology Tools is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: Gene Ontology has parent organization: University of Toronto; Ontario; Canada has parent organization: Harvard Medical School; Massachusetts; USA |
Aventis Pharmaceuticals ; Howard Hughes Medical Institute ; NHGRI |
PMID:12691998 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:gofish, nlx_149126, OMICS_02272 | http://llama.mshri.on.ca/Software.html, https://bio.tools/gofish | SCR_005682 | 2026-09-03 04:48:03 | 1 | |||||
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Hepatitis C Virus Database (HCVdb) Resource Report Resource Website 1+ mentions |
Hepatitis C Virus Database (HCVdb) (RRID:SCR_005718) | HCVdb, | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | The Hepatitis C Virus Database (HCVdb) is a cooperative project of several groups with the mission of providing to the scientific community studying the hepatitis C virus a comprehensive battery of informational and analytical tools. The Viral Bioinformatics Resource Center (VBRC), the Immune Epitope Database and Analysis Resource (IEDB), the Broad Institute Microbial Sequencing Center (MSC), and the Los Alamos HCV Sequence Database (HCV-LANL) are combining forces to acquire and annotate data on Hepatitis C virus, and to develop and utilize new tools to facilitate the study of this group of organisms. | hepatitis c, hepatitis c virus, genome, gene, virus, ortholog comparison, ortholog | has parent organization: VBRC | Hepatitis C virus | NIAID contract HHSN266200400036C | nlx_149175 | SCR_005718 | Hepatitis C Viral Database | 2026-09-03 04:48:04 | 4 | ||||||
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National Hellenic Research Foundation Resource Report Resource Website 1+ mentions |
National Hellenic Research Foundation (RRID:SCR_005719) | NHRF | institution | The National Hellenic Research Foundation (NHRF) is a multidisciplinary Research Centre established by Royal Decree on 9th October 1958. Its purpose is the organisation, finance and support of high-level research projects in the humanities and the natural sciences. The Humanities Institute cover a wide spectrum of study and research fields in Greek history and culture, contributing substantially and critically to the knowledge and promotion of Greek identity. The Natural Sciences Institutes perform basic and applied research in leading edge areas of science such as health, pharmaceuticals, environment, biotechnology and new materials. They develop innovative methods for solving complex problems facing Greek industry and they provide specialised services and know-how both to the public and private sector. The NHRF is governed by the Board of Directors and the Central Administration under the Director/Chairman of the Board. | humanities, natural sciences | is parent organization of: StRAnGER | ISNI: 0000 0001 2232 6894, grid.22459.38, Wikidata: Q1248816, nlx_149177 | https://ror.org/033m02g29 | SCR_005719 | National Hellenic Research Foundation | 2026-09-03 04:48:35 | 4 | |||||||
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UT Southwestern Medical Center Department of Pathology Resource Report Resource Website |
UT Southwestern Medical Center Department of Pathology (RRID:SCR_005713) | UTSW Department of Pathology | data or information resource, department portal, organization portal, portal | The Department of Pathology at UT Southwestern Medical Center is committed to its missions in diagnostics, research, teaching, and resident and fellowship training. Our facilities include approximately 54,000 square feet of lab and office space. Our Department comprises more than 100 of the most outstanding faculty in the country and more than 50 residents and fellows. We are home to more than a dozen graduate students at any given time. The Department of Pathology offers comprehensive, in-depth training in all of the various pathology disciplines, as well as a complete array of subspecialty fellowship programs. It is our view that a strong academic environment with access to state-of-the-art and newly emerging diagnostic technologies is essential to the preparation of any pathologist for professional life in the 21st century, regardless of the ultimate practice setting. Therefore, basic training in our program is enhanced by extensive exposure to modern molecular diagnostics, advanced flow cytometric analysis, and molecular cytogenetics. The Department provides diagnostic services in a variety of clinical settings that include a large county hospital (Parkland Memorial Hospital), two private University Hospitals (Zale-Lipshy and St. Paul), a tertiary care private pediatric hospital (Children''s Medical Center), a large university outpatient clinic (Aston Clinic), and the Dallas VA Medical Center, exposing our residents, fellows, and faculty to the full spectrum of human adult and pediatric disease. | pathology, child, adult, pediatric |
has parent organization: University of Texas Southwestern Medical Center; Texas; USA is parent organization of: CLASSIFI - Cluster Assignment for Biological Inference is parent organization of: MIGen |
nlx_149168 | SCR_005713 | University of Texas Southwestern Medical Center Department of Pathology | 2026-09-03 04:48:14 | 0 | ||||||||
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Maqview Resource Report Resource Website |
Maqview (RRID:SCR_005632) | MaqView | data processing software, data visualization software, software application, software resource | A graphical read alignment viewer specifically designed for the Maq alignment file and allows you to see the mismatches, base qualities and mapping qualities. It is highly efficient in speed, memory and disk usage. Maqview is based on OpenGL and is known to work on both Mac OS X and Linux. Porting to Windows is in principle easy. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
DOI:10.1101/gr.078212.108 | GNU General Public License | OMICS_00889, biotools:maqview | https://bio.tools/maqview, https://sources.debian.org/src/maqview/ | SCR_005632 | Mapping and Assembly with Qualities Viewer, M.A.Q Viewer | 2026-09-03 04:48:10 | 0 | |||||
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Stanford TMA Software Resource Report Resource Website 1+ mentions |
Stanford TMA Software (RRID:SCR_005598) | Stanford TMA | software resource | Software Tools for High-Throughput Analysis and Archiving of Immunohistochemistry Staining Data Obtained with Tissue Microarrays. | tissue microarray |
is listed by: OMICtools is related to: TMA-Combiner has parent organization: Stanford University; Stanford; California |
PMID:12414504 | OMICS_00819 | SCR_005598 | Stanford TMA Software website, Stanford Tissue Microarray Software | 2026-09-03 04:48:00 | 1 | |||||||
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OXBench Resource Report Resource Website 1+ mentions |
OXBench (RRID:SCR_005591) | OXBench | software resource | A suite of programs aimed at developers of alignment methods rather than end-users to assess the accuracy of multiple sequence alignment methods. It includes a reference database of protein multiple sequence alignments that were generated by consideration of protein three-dimensional structure. | alignment, linux, protein, sequence alignment |
is listed by: OMICtools has parent organization: University of Dundee; Scotland; United Kingdom |
PMID:14552658 | Acknowledgement requested | OMICS_00983 | http://www.compbio.dundee.ac.uk/Software/Oxbench/oxbench.html Alt. URL: http://www.compbio.dundee.ac.uk/software.html | SCR_005591 | 2026-09-03 04:48:07 | 2 | ||||||
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Solve Therapies Resource Report Resource Website |
Solve Therapies (RRID:SCR_005590) | Solve Therapies | data or information resource, portal, service resource, topical portal | Our hope and aims are to empower those affected by common life difficulties such as Anxiety, Depression, low Self-Esteem etc to overcome their obstacles and achieve their full and true potential. Our core approach is client-centred and we aim to convey to each client the ''core conditions'' of empathy, congruence and unconditional positive regard. Using Compassion focused Cognitive Behavioral Therapy (CBT), Acceptance and Commitment Therapy (ACT) among other approaches we gear all therapy treatments towards clients unique needs and goals. Passionate about research in all therapeutic and associated fields, we want to continue to keep our fingers on the pulse of developments in this area of work. We at Solve Therapies strive to empower all of our clients to choose helpful, rational thoughts and actions and to do so with less shame and self-criticism through the use of Cognitive Behavioural Therapy and Compassion-focused techniques. We offer a confidential, professional therapeutic service using Cognitive Behavioural Therapy and other forms of counseling/psychotherapy. All therapists are accredited and regulated by the British Association of Counselling & Psychotherapy (BACP) and/or British Association of Behavioural and Cognitive Psychotherapy (BABCP), the professional bodies who regulate, inform and ensure ethical practice. We also provide useful information on common difficulties and on how you can learn how to become your own therapist and manage your difficulties in the long term, with counselling venues throughout Northern Ireland including Belfast, Portrush, Antrim and Portglenone in order to provide flexibility for client appointments. ''''''S''''''olution-focused ''''''O''''''ptions ''''''L''''''ife-change ''''''V''''''alidation ''''''E''''''mpathy | cognitive behavioral therapy, counseling, psychotherapy, acceptance and commitment therapy, depression, obsessive-compulsive disorder, post-traumatic stress disorder, panic attack, phobia, grief, panic disorder, depressive disorder, social phobia, anger management, low self-esteem, hypochondriasis, therapy, psychological therapy | nlx_146216 | SCR_005590 | Solve Therapies CBT In Northern Ireland, Cognitive Behavioral Therapy in Northern Ireland - Solve Therapies, Solve Therapies Cognitive Behavioral Therapy In Northern Ireland | 2026-09-03 04:48:30 | 0 | |||||||||
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Staden Package Resource Report Resource Website 50+ mentions |
Staden Package (RRID:SCR_005629) | software resource | A fully developed set of DNA sequence assembly (Gap4 and Gap5), editing and analysis tools (Spin) for Unix, Linux, MacOSX and MS Windows. | c, unix/linux, sequence assembly, dna/protein analysis, spin, sequence alignment, genome, genome viewer, c++, fortran, tcl, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:20513662 DOI:10.1093/bioinformatics/btq268 |
BSD License | OMICS_00894, biotools:staden | https://bio.tools/staden, https://sources.debian.org/src/staden/ | SCR_005629 | Staden Package | 2026-09-03 04:48:01 | 87 | ||||||
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e-Source: Behavioral and Social Sciences Research Resource Report Resource Website |
e-Source: Behavioral and Social Sciences Research (RRID:SCR_005627) | e-Source | book, data or information resource, narrative resource, portal, topical portal, training material | Inside e-Source you will find 20 interactive chapters with authoritative answers to methodological questions on behavioral and social science research. With contributions from a team of international experts, this anthology provides the latest information on addressing emerging challenges in public health. Book contents include: Setting the Scene, Describing How, Explaining Why, What Works, Emerging Issues. Tables, Figures, Exercises and Examples are included. Login for enhanced functionality. Contents: * Appropriate Research Methods * ''Science'' in the Social Sciences * Design Decisions in Research * Theory Development * Social and Behavioral Theories * Sample Surveys * Social Survey Data Collection * Administrative Data Systems * Observational Studies * Qualitative Methods * Conversation Analysis * Software and Qualitative Analysis * Clinical Trials * Cluster Unit Randomized Trials * Ethical Challenges * Multilevel Modeling * Objective Measurement of Subjective Phenomena * Measuring Socioeconomic Status * Evaluating the Quality of Health Care * Patient-Reported Outcomes | behavioral science, social science, research, public health, methodology, health | has parent organization: Office of Behavioral and Social Sciences Research | NIH | nlx_146241 | SCR_005627 | e-Source: Behavioral & Social Science Research, e-Source: Behavioral Social Sciences Research, OBSSR e-Source, e-Source: Behavioral and Social Science Research, e-Source: Behavioral & Social Sciences Research | 2026-09-03 04:48:08 | 0 | |||||||
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All About Grants Podcast Resource Report Resource Website |
All About Grants Podcast (RRID:SCR_005621) | All About Grants | data or information resource, narrative resource, podcast, training resource | The Office of Extramural Research (OER) presents conversations with NIH staff members. Designed for investigators, fellows, students, research administrators, and others, we provide insights on grant topics from those who live and breathe the information. In mp3 and updated monthly. Transcripts are also available. So You Wanna... Keep Up with What''''s Hot? Prepare a Successful Grant Application? Suggest a Topic? Understand How Your Grant is Reviewed? Be an NIH Investigator? | grant, investigator, fellow, student, research administrator |
is related to: National Institutes of Health has parent organization: Office of Extramural Research NIH |
NIH | nlx_146239 | SCR_005621 | OER All About Grants Podcast, All About Grants at NIH | 2026-09-03 04:48:10 | 0 | |||||||
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SPOT Resource Report Resource Website 100+ mentions |
SPOT (RRID:SCR_005623) | data processing software, image analysis software, software application, software resource, software toolkit | Software package for analysis of microarray images. Microarray spot detection and characterization software package which extracts numerical information from cDNA microarrays., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | microarray, cdna microarray, cdna, image, spot detection, microarray spot detection |
is listed by: OMICtools has parent organization: Macquarie University; Sydney; Australia |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00847 | SCR_005623 | 2026-09-03 04:48:16 | 300 | |||||||||
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NIMH Resources for Research Training and Career Development Resource Report Resource Website |
NIMH Resources for Research Training and Career Development (RRID:SCR_005624) | NIMH Resources for Research Training and Career Development | data or information resource, portal, topical portal, training resource | A portal to the National Institute of Mental Health''s Research Training, Career Development, and Related Programs. Topics cover Resources for Applicants, Individual Fellowship Programs, Individual Career Development Programs, Institutional Training Programs, Additional Career Development/Training-Related Opportunities, and Training Programs to Increase Workforce Diversity. | research, career development, fellowship, training, career | has parent organization: National Institute of Mental Health | NIMH | nlx_146240 | SCR_005624 | NIMH Research Training Career Development and Related Programs, NIMH Resources for Research Training Career Development, Research Training Career Development and Related Programs | 2026-09-03 04:48:01 | 0 | |||||||
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Chromaseq Resource Report Resource Website 1+ mentions |
Chromaseq (RRID:SCR_005587) | Chromaseq | software resource | A software package in Mesquite that processes chromatograms, makes contigs, base calls, etc., using in part the programs Phred and Phrap. | chromatogram, sequence, mesquite |
is listed by: OMICtools has parent organization: Oregon State University; Oregon; USA |
NSF EF-0531754 | Acknowledgement required | OMICS_01017 | SCR_005587 | Chromaseq: a package for processing chromatograms and sequence data in Mesquite | 2026-09-03 04:48:14 | 7 | ||||||
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snp-search Resource Report Resource Website |
snp-search (RRID:SCR_005618) | snp-search | software resource | A software tool that manages SNP data and outputs useful information which can be used to test important biological hypotheses. | is listed by: OMICtools | PMID:24246037 | OMICS_00303 | SCR_005618 | 2026-09-03 04:48:08 | 0 | |||||||||
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3D Slicer Resource Report Resource Website 1000+ mentions |
3D Slicer (RRID:SCR_005619) | Slicer | data processing software, data visualization software, image analysis software, software application, software resource | A free, open source software package for visualization and image analysis including registration, segmentation, and quantification of medical image data. Slicer provides a graphical user interface to a powerful set of tools so they can be used by end-user clinicians and researchers alike. 3D Slicer is natively designed to be available on multiple platforms, including Windows, Linux and Mac Os X. Slicer is based on VTK (http://public.kitware.com/vtk) and has a modular architecture for easy addition of new functionality. It uses an XML-based file format called MRML - Medical Reality Markup Language which can be used as an interchange format among medical imaging applications. Slicer is primarily written in C++ and Tcl. | birn, diffusion, functional, na-mic (ncbc), nifti-1 support, registration, segmentation, visualization, volume, warping |
uses: 3DSlicerLupusLesionModule uses: ShapePopulationViewer uses: Joint Anisotropic LMMSE Filter for Stationary Rician noise removal in DWI uses: Joint Anisotropic LMMSE Filter for Stationary Rician noise removal in DWI is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Biositemaps is related to: Slicer3 Example Modules is related to: Stereoscopic Atlas of Intrinsic Brain Networks is related to: VMTK in 3D Slicer is related to: Diffusion Tractography with Kalman Filter is related to: Fast Nonlocal Means for MRI denoising is related to: SpineSegmentation module for 3DSlicer is related to: BioImage Suite is related to: NA-MIC Kit is related to: Hammer And WML Modules for 3D Slicer is related to: ABC (Atlas Based Classification) is related to: ARCTIC is related to: Finsler tractography module for Slicer is related to: GAMBIT is related to: GPU based affine registration is related to: GTRACT is related to: LEAD-DBS has parent organization: Harvard University; Cambridge; United States is parent organization of: Level-set Segmentation for Slicer3 is parent organization of: Slicer3 Module Rician noise filter has plug in: MultiXplore works with: UManitoba - JHU Functionally Defined Human White Matter Atlas works with: SlicerMorph |
NIH ; NCRR ; NIBIB ; NCI ; US Army ; Telemedicine and Advanced Technology Research Center |
3D Slicer License | nif-0000-00256 | http://www.nitrc.org/projects/slicer | SCR_005619 | Slicer, 3D Slicer: A multi-platform free and open source software package for visualization and medical image computing, 3D Slicer, 3DSlicer | 2026-09-03 04:48:01 | 3187 | |||||
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BrainStars Resource Report Resource Website 10+ mentions |
BrainStars (RRID:SCR_005810) | B* | data access protocol, data or information resource, database, software resource, web service | BrainStars (or B*) is a quantitative expression database of the adult mouse brain. The database has genome-wide expression profile at 51 adult mouse CNS regions. For 51 CNS regions, slices (0.5-mm thick) of mouse brain were cut on a Mouse Brain Matrix, frozen, and the specific regions were punched out bilaterally with a microdissecting needle (gauge 0.5 mm) under a stereomicroscope. For each region, we took samples every 4 hours, starting at ZT0 (Zeitgaber time 0; the time of lights on), for 24 hours (6 time-point samples for each region), and we pooled the samples from the different time points. We independently sampled each region twice (n=2). These samples were purified their RNA, and measured with Affymetrix GeneChip Mouse Genome 430 2.0 arrays. Expression values were then summarized with the RMA method. After several analysis with the expression data, the data and analysis results were stored in the BrainStars database. The database has a REST-like Web API interface for accessing from your Web applications. This document shows how to access the database via our Web API. | mouse, brain, adult, expression profile, affymetrix genechip mouse genome 430 2.0 array, rna, central nervous system, gene expression, gene |
is related to: Allen Mouse Brain Reference Atlas is related to: Allen Institute for Brain Science has parent organization: RIKEN has parent organization: Kindai University School of Medicine; Osaka; Japan |
Japanese Ministry of Education Culture Sports Science and Technology MEXT | PMID:21858037 | BrainStars data, Images and texts (excluding ABA data and images) are licensed under a Creative Commons Attribution 2.1 Japan License. | nlx_149301 | SCR_005810 | BrainStars Database, BrainStars (B*) | 2026-09-03 04:48:16 | 15 | |||||
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GARBAN Resource Report Resource Website |
GARBAN (RRID:SCR_005778) | GARBAN | analysis service resource, data analysis service, production service resource, service resource, software resource, source code | THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 12, 2012. GARBAN is a tool for analysis and rapid functional annotation of data arising from cDNA microarrays and proteomics techniques. GARBAN has been implemented with bioinformatic tools to rapidly compare, classify, and graphically represent multiple sets of data (genes/ESTs, or proteins), with the specific aim of facilitating the identification of molecular markers in pathological and pharmacological studies. GARBAN has links to the major genomic and proteomic databases (Ensembl, GeneBank, UniProt Knowledgebase, InterPro, etc.), and follows the criteria of the Gene Ontology Consortium (GO) for ontological classifications. Source may be shared: e-mail garban (at) ceit.es. Platform: Online tool | cdna microarray, proteomics, cdna, microarray, statistical analysis, gene, est, protein, genomic, gene ontology |
is listed by: Gene Ontology Tools is related to: Gene Ontology |
PMID:14594726 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_149247 | http://garban.tecnun.es | SCR_005778 | Genomic Analysis and Rapid Biological ANnotation, University of Navarra; Pamplona; Spain | 2026-09-03 04:48:37 | 0 | |||||
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Burroughs Wellcome Fund Resource Report Resource Website 100+ mentions |
Burroughs Wellcome Fund (RRID:SCR_005772) | BWF | institution | The Burroughs Wellcome Fund is an independent private foundation dedicated to advancing the biomedical sciences by supporting research and other scientific and educational activities. Within this broad mission, BWF has two primary goals: * To help scientists early in their careers develop as independent investigators * To advance fields in the basic biomedical sciences that are undervalued or in need of particular encouragement BWF''s financial support is channeled primarily through competitive peer-reviewed award programs. * BWF''s endowment: $586.8 million at the end of FY 2009 * BWF approved $26.4 million in grants during FY 2009 BWF makes grants primarily to degree-granting institutions on behalf of individual researchers, who must be nominated by their institutions. To complement these competitive award programs, BWF also makes grants to nonprofit organizations conducting activities intended to improve the general environment for science. A Board of Directors comprising distinguished scientists and business leaders governs BWF. BWF was founded in 1955 as the corporate foundation of the pharmaceutical firm Burroughs Wellcome Co. In 1993, a generous gift from the Wellcome Trust in the United Kingdom, enabled BWF to become fully independent from the company, which was acquired by Glaxo in 1995. BWF has no affiliation with any corporation. | biomedical sciences, research, science, education | Wellcome Trust | nlx_149371, grid.427464.7, Wikidata: Q5000488, ISNI: 0000 0000 8727 8697, Crossref funder ID: 100000861 | https://ror.org/01d35cw23 | SCR_005772 | 2026-09-03 04:48:22 | 115 |
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