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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Heatmapper Resource Report Resource Website 100+ mentions |
Heatmapper (RRID:SCR_016974) | data access protocol, data processing software, software application, software resource, web service | Software tool to create and provide heat maps through a graphical interface. Allows to create an expression, pairwise comparison, image overlay, geomap, and geocoordinate heat maps for different data types and applications. Used to interactively visualize data. | expression, based, heat, map, pairwise, comparison, distance, correlation, image, overlay, latitude, longitude, geomap, geopolitical, geocoordinate, choropleth, data, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: R Project for Statistical Computing has parent organization: Wishart Research Group is provided by: University of Alberta; Alberta; Canada |
Canadian Institutes of Health Research ; Genome Alberta |
PMID:27190236 | Freely available, Free, Acknowledgement requested | OMICS_12077, biotools:heatmapper | http://www.heatmapper.ca, https://github.com/WishartLab/heatmapper, https://bio.tools/heatmapper | SCR_016974 | Heatmapper, HeatMapper, heat mapper | 2026-09-12 12:58:46 | 252 | |||||
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Keyence: BZ-X700 microscope Resource Report Resource Website 10+ mentions |
Keyence: BZ-X700 microscope (RRID:SCR_016979) | instrument resource | Fluorescence microscope of BZ-X series by KEYENCE CORPORATION of America. Captures high resolution images without the blurring caused by out of focus fluorescent signals. Optical sectioning allows the user to obtain images comparable to those captured on a laser confocal microscope, but in a fraction of the time and without the damaging effects of a laser., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | Fluorescence, microscope, confocal, imaging, KEYENCE CORPORATION of America | THIS RESOURCE IS NO LONGER IN SERVICE | https://www.keyence.com/landing/microscope/lp_bzx_micro.jsp | SCR_016979 | 2026-09-12 12:58:46 | 22 | ||||||||||
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Prism Clinical Imaging Resource Report Resource Website 1+ mentions |
Prism Clinical Imaging (RRID:SCR_016977) | Prism Clinical Imaging, Inc. | commercial organization, data or information resource, service resource, software resource, training service resource | Provides Prism softwares and services that integrate advanced imaging into the clinical workflow for brain mapping from acquisition through processing, visualization, and export to PACS. Prism integrates functional MRI, diffusion MRI, perfusion, MR spectroscopy, and PET/CT into a unified workflow for diagnosis and treatment planning in brain disorders. Processing is also available as a cloud deployed service, Prism Serve. Research support includes import/export for imaging and derived quantitative data in both DICOM and research formats such as AFNI and Trackviz. | Commercial, organization, advance, imaging, diagnosis, treatment, brain, disorder, processing, clinical, support | SCR_016977 | 2026-09-12 12:58:46 | 4 | |||||||||||
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Collaborative Computing Project for NMR Resource Report Resource Website 10+ mentions |
Collaborative Computing Project for NMR (RRID:SCR_016983) | CCPN | data or information resource, discussion, forum, narrative resource, portal, project portal | Project provides tools and knowledge to maximize the impact of the biological NMR studies. CCPN software facilitates data analysis and software integration. Project promotes the exchange of knowledge and provides training and best practices for the NMR community and has leading role in the development of NMR data sharing standard and coordination of NMR instrumentation proposals. Includes CCPN Data Model for macromolecular NMR and related areas, CcpNmr suite of programs like Analysis for spectrum visualization, resonance assignment and analysis, ChemBuild to create chemical structure templates in an NMR aware manner, FormatConverter for data exchange with common textual NMR formats and SpecView for swift, format independent peak and spectrum visualization. | collaborative, computing, project, NMR, software, data, standard, protein, molecule, spectroscopy, global |
is related to: University of Leicester; Leicester; United Kingdom is related to: CCPN Analysis is parent organization of: CCPN Data Model |
Astra-Zeneca ; BBSRC ; Dupont Pharma ; Genentech ; GlaxoSmithKline ; Medical Research Council |
PMID:15613391 | Free for non profit, Public, Acknowledgement requested | https://sourceforge.net/projects/ccpn/ | SCR_016983 | CCPN, Collaborative Computing Project for NMR, The Collaborative Computing Project for NMR | 2026-09-12 12:58:46 | 23 | |||||
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BinPacker Resource Report Resource Website 10+ mentions |
BinPacker (RRID:SCR_017038) | data analysis software, data processing software, software application, software resource | Software tool as de novo trascriptome assembler for RNA-Seq data. Used to assemble full length transcripts by remodeling problem as tracking set of trajectories of items over splicing graph. Input RNA-Seq reads in fasta or fastq format, and ouput all assembled candidate transcripts in fasta format. Operating system Unix/Linux. | de novo, transcriptome, assembler, RNAseq, data, full, length, transcript, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
National Natural Science Foundation of China ; NCRR P20 RR01 6460; NIGMS P20 GM103429; NSF 1553680 |
PMID:26894997 | Free, Available for download, Freely available | OMICS_11199, biotools:binpacker | http://sourceforge.net/projects/transcriptomeassembly/files/BinPacker_1.0.tar.gz/download, http://sourceforge.net/projects/transcriptomeassembly/files/BinPacker_binary.tar.gz/download, https://bio.tools/binpacker | SCR_017038 | 2026-09-12 12:58:47 | 10 | ||||||
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CCPN Data Model Resource Report Resource Website |
CCPN Data Model (RRID:SCR_016982) | data or information resource, data processing software, data repository, data storage software, database, service resource, software application, software resource, storage service resource | Model to cover data for macromolecular NMR spectroscopy from the initial experimental data to the final validation. Used for the large scale data deposition, data mining and program interoperability. Enables movement from one software package to another without difficulties with data conversion or loss of information. Works with CcpNmr Analysis software for analysis and interactive display, CcpNmr FormatConverter for allowing transfer of data from programs used in NMR to and from the Data Model, and the CLOUDS software for automated structure calculation and assignment. Used within the CCPN software suite for NMR spectroscopy and at the BioMagResBank for converting existing deposited restraint lists to a standard IUPAC nomenclature. | data, macromolecular, NMR, spectroscopy, deposition, mining, interoperability, conversion |
is related to: Biological Magnetic Resonance Data Bank (BMRB) has parent organization: Collaborative Computing Project for NMR works with: CCPN Analysis works with: CCPN Analysis |
BBSRC ; EU ; NIGMS GM67965; NLM P41 LM005799 |
PMID:15815974 PMID:15613391 PMID:21953355 |
Free, Public | SCR_016982 | The CCPN Data Model | 2026-09-12 12:58:46 | 0 | |||||||
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Zeiss: Axio Zoom.V16 for Materials��� Resource Report Resource Website 10+ mentions |
Zeiss: Axio Zoom.V16 for Materials��� (RRID:SCR_016980) | instrument resource | ZEISS Axio Zoom.V16 microscope system includes high resolution zoom microscope for large fields. Focuses on reflected light microscopy of materials. Uses optical components to manage reflected light from specimen surface. Designed for observing surface properties and structures of materials using reflected light. System focuses on providing high resolution image quality and contrast for reflected light microscopy of solid materials., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | Reflected Light Microscopy, microscope, zoom, Zeiss, stereo, motorized, materials, reflected light microscopy of solid materials, | THIS RESOURCE IS NO LONGER IN SERVICE | https://raw.githubusercontent.com/SciCrunch/RRID-Instruments/refs/heads/main/PDF/SCR_016980.pdf | https://www.binran.ru/files/ckp/fluorestsentnaya-mikroskopiya/Operating-manual_Axio-Zoom.V16.pdf | https://www.zeiss.com/microscopy/int/products/stereo-zoom-microscopes/axio-zoom-v16.html | SCR_016980 | ZEISS Axio Zoom.V16 for Materials system | 2026-09-12 12:58:46 | 10 | |||||||
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Maize Database of Images and Genomes Resource Report Resource Website 1+ mentions |
Maize Database of Images and Genomes (RRID:SCR_016987) | MaizeDIG | analysis service resource, data or information resource, database, production service resource, service resource | Genotype and phenotype database for maize images based on BioDIG. Supports multiple reference genomes and has been integrated with the MaizeGDB Genome Browser to make custom tracks showing mutant phenotypes within their genomic context. Allows for custom tagging of images to highlight regions related to the phenotypes. This is accomplished through an interface allowing users to create links from images to genomic coordinates and to curate and search images by gene model ID, gene symbol, and gene name. | genotype, phenotype, collection, maize, image, reference, genome | works with: MaizeGDB | Free, Freely available | SCR_016987 | Maize Dig, MaizeDatabase of Images and Genomes, MaizeDig, MaizeDIG | 2026-09-12 12:58:46 | 5 | ||||||||
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CCPN Analysis Resource Report Resource Website 10+ mentions |
CCPN Analysis (RRID:SCR_016984) | CcpNmr Analysis | data analysis software, data processing software, data visualization software, software application, software resource | Software package for interactive NMR spectrum visualization, resonance assignment and data analysis. Graphical elements allow to enter information and to view status of data and library functions manipulate the CCPN data model objects to record the scientific information. Software is cross platform and works on Linux, Mac OSX, Windows and Unix. | interactive, NMR, specturm, visualization, resonance, data, analysis |
is related to: University of Cambridge; Cambridge; United Kingdom is related to: Python Programming Language is related to: Collaborative Computing Project for NMR works with: CCPN Data Model works with: CCPN Data Model |
Biotechnology and Biological Sciences Research Council (UK) ; Deutsche Forschungsgemeinschaft |
PMID:21953355 PMID:15815974 |
Public, Available for download, Free of charge for non profit institutions, Tutorial available | SCR_016984 | CcpNmr Analysis, CCPN Analysis v2, CCPN Analysis v3 | 2026-09-12 12:58:46 | 48 | ||||||
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MITE-Tracker Resource Report Resource Website 1+ mentions |
MITE-Tracker (RRID:SCR_017030) | MITE Tracker | data analysis software, data processing software, sequence analysis software, software application, software resource | Open source software tool for identifying miniature inverted repeat transposable elements in large genomes. Used to process large scale genomes, to find and classify MITEs using an efficient alignment strategy to retrieve nearby inverted repeat sequences. | genomic, sequence, discover, miniature, inverted, repeat, transposable, element, clustering, cdhit |
uses: NCBI BLAST is listed by: OMICtools is related to: Python Programming Language |
National Council for Science and Technology ; Argentina ; National Institute of Agricultural Technology |
DOI:10.1186/s12859-018-2376-y | Free, Available for download, Freely available | OMICS_32242 | SCR_017030 | MITE Tracker, Miniature Inverted repeats Transposable Elements Tracker | 2026-09-12 12:58:47 | 4 | |||||
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PS-Plant Framework Resource Report Resource Website 1+ mentions |
PS-Plant Framework (RRID:SCR_017032) | PS-Plant | 2d spatial image, 3d time-series analysis software, 3d visualization software, code testing framework, data analysis software, data or information resource, data processing software, data visualization software, image, image analysis software, segmentation software, software application, software development tool, software resource, time-series analysis software, workflow software | Software tool as end to end software for data acquisition, processing, and result extraction of Arabidopsis thaliana growth. Framework uses photometric stereo based 3D imaging system with computer vision and deep learning for tracking and quantifying both plant growth and movement parameters. | photometric, 3D, imaging, tracking, plant, growth, arabidopsis, thaliana, leaf, angle, segmentation, machine, learning, near-infrared, (NIR), LED, photomorphogenesis, thermomorphogenesis, bio.tools |
uses: Python Programming Language is listed by: bio.tools is listed by: Debian |
BBSRC BB/M025551/1; BBSRC BB/N005147/1; BBSRC BB/N02334X/1 |
Free, Available for download, Freely available | biotools:PS-Plant | https://bio.tools/PS-Plant | SCR_017032 | 2026-09-12 12:58:47 | 1 | ||||||
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Onyx Pharmaceuticals Resource Report Resource Website 1+ mentions |
Onyx Pharmaceuticals (RRID:SCR_003782) | Onyx, ONXX | commercial organization | November 2020, Onyx merged with Legacy Acquisition Corp. to form PARTS iD, Inc. Our data intelligence, integrated platforms, product cataloging, digital marketing expertise, and virtual warehousing have ensured our continued leadership in the competitive marketplace. | drug, pharmaceutical, biotechnology | nlx_158070 | https://www.biospace.com/employer/540942/onyx-pharmaceuticals-inc-/ | SCR_003782 | Onyx Pharmaceuticals Inc. | 2026-09-12 12:56:02 | 5 | ||||||||
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Sciencewise Resource Report Resource Website |
Sciencewise (RRID:SCR_003780) | Sciencewise | knowledge environment | Sciencewise-ERC is the UK's national center for public dialogue in policy making involving science and technology issues. It provides co-funding and specialist advice and support to Government departments and agencies to develop and commission public dialogue activities in emerging areas of science and technology. It consists of a comprehensive online resource of information, advice and guidance together with a wide range of support services aimed at policy makers and all the different stakeholders involved in science and technology policy making, including the public. Sciencewise-ERC works with central Government and its agencies, and executive, advisory and non-departmental public bodies. Some of the Government departments include the Department for Environment, Food and Rural Affairs (Defra), the Department of Energy and Climate Change (DECC) and most recently HM Treasury. | public dialogue | Department for Business Innovation and Skills BIS UK Gov | nlx_143528 | SCR_003780 | Sciencewise - ERC, Sciencewise Expert Resource Center, Sciencewise Expert Resource Centre for Public Dialogue In Science and Innovation, Sciencewise Expert Resource Centre, Sciencewise-ERC | 2026-09-12 12:56:02 | 0 | ||||||||
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European Federation of Pharmaceutical Industries and Associations Resource Report Resource Website 10+ mentions |
European Federation of Pharmaceutical Industries and Associations (RRID:SCR_003820) | EFPIA | institution | Federation representing the pharmaceutical industry operating in Europe. Through its direct membership of 33 national associations and 40 leading pharmaceutical companies, it is the voice on the EU scene of 1,900 companies committed to researching, developing and manufacturing new medical treatments. In addition, it is active in partnering in EU Research programmes, such as the IMI (Innovative Medicines Initiative), Europe's largest public-private partnerships. They also work on corporate social responsibility initiatives with others healthcare stakeholders, such as patient groups and healthcare professionals. EFPIA has specialized committees and task forces focused on key areas of activity. EFPIA also includes two specialized groups focusing on vaccines and biotechnology, respectively: * Vaccines Europe (formerly European Vaccine Manufacturers, EVM) produces approximately 80% of vaccines used worldwide * European Biopharmaceutical Enterprises (EBE) harness biotechnology to develop approximately one-fifth of new medicines | pharmaceutical, medicine, vaccine, biotechnology, manufacturing, corporate |
is affiliated with: Merck is affiliated with: Roche is related to: Innovative Medicines Initiative is parent organization of: Innovative Medicines Initiative |
grid.484123.8, nlx_158124, ISNI: 0000 0000 9246 8110, Wikidata: Q1376562 | https://ror.org/00g1x4v36 | SCR_003820 | 2026-09-12 12:56:03 | 20 | ||||||||
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Avid Radiopharmaceuticals Resource Report Resource Website |
Avid Radiopharmaceuticals (RRID:SCR_003786) | commercial organization | Subsidiary of Eli Lilly and Company who develops new molecular imaging agents capable of changing the medical management of significant, chronic human diseases by identifying the first stages of pathological change, potentially assisting in earlier diagnosis, and better management and development of new therapies. The company has developed a radioactive tracer called florbetapir (18F). Florbetapir can be used to detect beta amyloid plaques in patients with memory problems using positron emission tomography (PET) scans, making the company the first to bring to market an FDA-approved method that can directly detect this hallmark pathology of Alzheimer's disease. | molecular imaging agent, beta amyloid plaque, pet | Alzheimer's disease | nlx_158076 | SCR_003786 | Avid Radiopharmaceuticals Inc. | 2026-09-12 12:56:02 | 0 | |||||||||
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BioSHaRE Resource Report Resource Website 10+ mentions |
BioSHaRE (RRID:SCR_003811) | BIOSHARE-EU | consortium, data or information resource, narrative resource, organization portal, portal, standard specification | A consortium of leading biobanks and international researchers from all domains of biobanking science to ensure the development of harmonized measures and standardized computing infrastructures enabling the effective pooling of data and key measures of life-style, social circumstances and environment, as well as critical sub-components of the phenotypes associated with common complex diseases. The overall aim is to build upon tools and methods available to achieve solutions for researchers to use pooled data from different cohort and biobank studies. This, in order to obtain the very large sample sizes needed to investigate current questions in multifactorial diseases, notably on gene-environment interactions. This aim will be achieved through the development of harmonization and standardization tools, implementation of these tools and demonstration of their applicability. BioSHaRE researchers are collaborating with P3G, the Global Alliance for Genomics and Health, IRDiRC (International Rare Diseases Research Consortium), H3Africa and other organizations on the development of an International Code of Conduct for Genomic and Health-Related Data Sharing. A draft version is available for external review. Generic documents have been prepared covering areas of biobanking that are of major importance. SOPs have been finalized for blood withdrawal (SOPWP5001blood withdrawal), manual blood processing (SOPWP5002blood processing), shipping of biosamples (SOPWP5003shipping) and withdrawal, processing and storage of urine samples (SOPWP5004urine). | gene-environment interaction, life-style, social circumstance, environment, phenotype, disease, biobank, socio-economic factor, data sharing, gene, clinical |
is listed by: Consortia-pedia has parent organization: University of Groningen; Groningen; Netherlands is parent organization of: BioResource Impact Factor |
European Union FP7 | nlx_158110 | SCR_003811 | Biobank Standardisation and Harmonisation for Research Excellence, Biobank Standardisation and Harmonisation for Research Excellence in the European Union | 2026-09-12 12:56:03 | 22 | |||||||
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Olink Bioscience Resource Report Resource Website 100+ mentions |
Olink Bioscience (RRID:SCR_003899) | Olink | commercial organization | Commercial organization that produces products for biomarker research and development. Their goal is to help customers and collaborators to improve clinical decisions through the use of molecular biomarkers. Their tools bring new insights into disease processes, improve disease detection, and contribute to a better understanding of biology. | biomarker, disease | is related to: READNA | nlx_158232 | SCR_003899 | 2026-09-12 12:56:04 | 342 | |||||||||
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Asthma UK Resource Report Resource Website 10+ mentions |
Asthma UK (RRID:SCR_003815) | Asthma UK | institution | Charity that aims to significantly reduce the number of asthma deaths, hospitalizations and living lives compromised by asthma helping over five million people with asthma in the UK through research, campaigning, health promotion and engagement with the asthma community. Asthma UK is a significant investor in asthma research within the UK and to date has invested over 50 million pounds into research for better treatments and ultimately a cure for asthma. | lung, treatment | is parent organization of: EARIP | Asthma | Crossref funder ID: 501100000362, ISNI: 0000 0000 9981 854X, nlx_158172, grid.453156.0 | https://ror.org/03z7xev21 | SCR_003815 | 2026-09-12 12:56:03 | 13 | |||||||
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EURORDIS Resource Report Resource Website 10+ mentions |
EURORDIS (RRID:SCR_003814) | EURORDIS | nonprofit organization | EURORDIS is a non-governmental patient-driven alliance of patient organizations and individuals active in the field of rare diseases, dedicated to improving the quality of life of all people living with rare diseases in Europe. It is a not-for-profit organization and represents more than 479 rare disease organizations in 45 different countries (of which 25 are EU Member States), covering more than 4,000 rare diseases. It is therefore the voice of the 30 million patients affected by rare diseases throughout Europe. EURORDIS aims at improving the quality of life of people living with rare diseases in Europe through advocacy at the European level, support for research and drug development, networking patient groups, raising awareness and other actions designed to fight against the impact of rare diseases on the lives of patients and family. EURORDIS' training programs and resources are designed to strengthen the capacity of rare disease patients' representatives. Training empowers patients' representatives to advocate effectively for rare diseases at both the local and EU level. Key issues affecting patients of Rare Diseases on which we actively work: * Sustaining rare diseases as an EU public health priority * Making Rare Diseases A Public Health Priority In All Member States * Rare Diseases: An International Public Health Priority * Improving Access To Orphan Drugs * Improving Access To Quality Care * Promoting cross-border healthcare and patient mobility * Bridging Patients And Research * Genetic testing and newborn screening | French Muscular Dystrophy Association ; European Union ; members ; corporate foundations ; health industry |
Wikidata: Q5412882, grid.433753.5, nlx_143535 | https://ror.org/019w4mg02 | SCR_003814 | EURORDIS - Rare Diseases Europe | 2026-09-12 12:56:03 | 40 | ||||||||
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COMPACT Resource Report Resource Website 50+ mentions |
COMPACT (RRID:SCR_003850) | COMPACT | consortium, data or information resource, organization portal, portal | Consortium to reduce delivery and targeting bottlenecks for developing novel innovative biopharmaceutical based medicines. The project aims to shed new light on the obstacles biopharmaceuticals (medicines based on biological molecules such as proteins, peptides or nucleic acids) need to overcome to get to where they are needed in the body. The team will then use this information to develop and validate biopharmaceutical formulations to deliver these novel drugs to their targets. By finding more effective ways of administering these biopharmaceutical drugs, and improving their ability to travel through the body to where they are needed, COMPACT will allow more patients to benefit from biopharmaceuticals. Furthermore, designing less invasive administration routes and reducing the dose (and therefore the side effects) and frequency of administration will help to improve patient compliance with treatments. | drug, biopharmaceutical, drug delivery, drug target, drug development |
is listed by: Consortia-pedia has parent organization: Utrecht University; Utrecht; Netherlands |
Innovative Medicines Initiative ; EFPIA |
nlx_158164 | SCR_003850 | Collaboration on the optimisation of macromolecular pharmaceutical access to cellular targets, Collaboration on the Optimization of Macromolecular Pharmaceutical Access to Cellular Targets | 2026-09-12 12:56:03 | 57 |
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