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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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MOLEonline Resource Report Resource Website 10+ mentions |
MOLEonline (RRID:SCR_018314) | web service, data access protocol, software resource, production service resource, service resource, analysis service resource | Interactive web based tool for analyzing biomacromolecular channels, tunnels and pores. Enables two modes of calculation with one dedicated to analysis of channels and another for transmembrane pores. Can use PDB and mmCIF formats. Can analyze biomacromolecular structures stemming from NMR, X-ray and cryo-EM techniques. Interconnected with PDBe, CSA, ChannelsDB, OPM, UniProt to help setup and analysis of acquired results. Provides analytics for detection and structural characterization of channels and information about their physicochemical features. | biomacromolecular channel, analysis, biomacromolecular pore, biomacromolecular tunnel, transmembrane pore analysis, analysis, biomacromolecular sturcture, physicochemical feature |
works with: PDBe - Protein Data Bank in Europe works with: CSA - Catalytic Site Atlas works with: UniProt |
PMID:29718451 | Free, Freely available | https://mole.upol.cz/online/ | http://old.mole.upol.cz/ | SCR_018314 | MOLEonline 2.0 | 2026-08-05 10:46:59 | 30 | ||||||
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Proteomic Data Commons Resource Report Resource Website 50+ mentions |
Proteomic Data Commons (RRID:SCR_018273) | PDC | data or information resource, data repository, database, storage service resource, production service resource, service resource, analysis service resource | Portal to make cancer related proteomic datasets easily accessible to public. Facilitates multiomic integration in support of precision medicine through interoperability with other resources. Developed to advance our understanding of how proteins help to shape risk, diagnosis, development, progression, and treatment of cancer. One of several repositories within NCI Cancer Research Data Commons which enables researchers to link proteomic data with other data sets (e.g., genomic and imaging data) and to submit, collect, analyze, store, and share data throughout cancer data ecosystem. PDC provides access to highly curated and standardized biospecimen, clinical, and proteomic data, intuitive interface to filter, query, search, visualize and download data and metadata. Provides common data harmonization pipeline to uniformly analyze all PDC data and provides advanced visualization of quantitative information. Cloud based (Amazon Web Services) infrastructure facilitates interoperability with AWS based data analysis tools and platforms natively. Application programming interface (API) provides cloud-agnostic data access and allows third parties to extend functionality beyond PDC. Structured workspace that serves as private user data store and also data submission portal. Distributes controlled access data, such as patient-specific protein fasta sequence databases, with dbGaP authorization and eRA Commons authentication. | Cancer, proteomic, data, precision medicine, diagnosis, treatment, analysis, biospeciment, clinical data, metadata |
is related to: Cancer Research Data Commons has parent organization: National Cancer Institute |
cancer | Restricted | SCR_018273 | 2026-08-05 10:47:01 | 66 | ||||||||
|
Interactive Repeated Experiments Dotplot Resource Report Resource Website |
Interactive Repeated Experiments Dotplot (RRID:SCR_018328) | web service, data access protocol, software resource, production service resource, service resource, analysis service resource | Web tool for creating interactive graphics. Enables authors to create interactive graphics from data obtained with repeated independent experiments. Designed for laboratory studies with repeated experiments. | Interactive graphic, repeated independent experiment, repeated experiment data, graph, analysis, dot plot | NCATS UL1 TR000135 | PMID:28974579 | Free, Freely available | SCR_018328 | 2026-08-05 10:47:02 | 0 | |||||||||
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DichroWeb Resource Report Resource Website 50+ mentions |
DichroWeb (RRID:SCR_018125) | web service, data access protocol, software resource, data analysis service, production service resource, service resource, analysis service resource | Web server for analysis of protein circular dichroism spectra. Provides access to circular dichroism secondary structure calculation algorithms and reference databases. Used in analysis of protein secondary structures. | Analysis, protein, circular dichroism spectra, secondary structure, reference database, algorithm, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: University of London; London; United Kingdom |
BBSRC | PMID:17896349 PMID:15215473 |
Restricted | biotools:dichroweb | https://bio.tools/dichroweb | SCR_018125 | 2026-08-05 10:47:00 | 62 | ||||||
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EMBL-EBI COVID-19 Portal Resource Report Resource Website 10+ mentions |
EMBL-EBI COVID-19 Portal (RRID:SCR_018337) | data or information resource, data repository, portal, disease-related portal, topical portal, database, storage service resource, service resource | EMBL-EBI portal to enable researchers to upload, access and analyse COVID-19 related reference data and specialist datasets submitted to EMBL-EBI and other major centers for biomedical data. Used to facilitate data sharing and analysis to accelerate coronavirus research. The aim of the COVID-19 Data Portal is to facilitate data sharing and analysis, and to accelerate coronavirus research. EMBL-EBI and partners have set up the COVID-19 Data Portal, which will bring together relevant datasets submitted to EMBL-EBI and other major centres for biomedical data. The aim is to facilitate data sharing and analysis, and to accelerate coronavirus research. The COVID-19 Data Portal will enable researchers to upload, access and analyse COVID-19 related reference data and specialist datasets. The COVID-19 Data Portal will be the primary entry point into the functions of a wider project, the European COVID-19 Data Platform. | COVID-19, COVID-19 data, sequence, expression, protein sequence, protein structure, proteome, translatome, analysis, EMBL-EBI | is related to: EMBL-EBI Pathogens - COVID-19 | COVID-19 | Free, Freely available | SCR_018816 | https://www.covid19dataportal.org/, https://www.ebi.ac.uk/about/news/press-releases/embl-ebi-launches-covid-19-data-portal | SCR_018337 | EMBL-EBI COVID-19 Data Portal, COVID-19 Data Portal | 2026-08-05 10:47:02 | 10 | ||||||
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Watchdog Resource Report Resource Website 1+ mentions |
Watchdog (RRID:SCR_018355) | data processing software, data management software, software application, data analysis software, software resource | Software workflow management system for automated and distributed analysis of large scale experimental data. Implemented in Java and is thus platform independent. | Workflow management system, automated data analysis, next generation sequencing, large scale experimental data, analysis | Free, Available for download, Freely available | https://github.com/klugem/watchdog, https://anaconda.org/bioconda/watchdog-wms | SCR_018355 | 2026-08-05 10:47:03 | 2 | ||||||||||
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Big Data Processor Resource Report Resource Website 1+ mentions |
Big Data Processor (RRID:SCR_018484) | BDP | data processing software, image analysis software, software application, software resource, image processing software | Software tool for visual inspection and processing of big image data. Enables loading of Tiff and Hdf5 based image data. BDC supports cropping and saving of big image data including binning and bit depth conversion. Used for analysis of TB sized image data like light sheet microscopy or electron microscopy. | Image, image processor, data processor, data, processing, analysis, image data, microscopy | is a plug in for: Fiji | Free, Available for download, Freely available | https://github.com/embl-cba/fiji-plugin-bigDataProcessor | SCR_018484 | 2026-08-05 10:47:02 | 2 | ||||||||
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Harmony Resource Report Resource Website 10+ mentions |
Harmony (RRID:SCR_018809) | data processing software, data acquisition software, image acquisition software, software application, image analysis software, software resource | Harmony high content imaging and analysis software. Used to quantify complex cellular phenotypes. Designed for PerkinElmer high content screening systems. | Imaging, analysis, cellular phenotype quantification, PerkinElmer, high content, screening system, cell phenotypic screening, live cell imaging, | is related to: Perkin Elmer: Operetta CLS | Restricted | SCR_018809 | Harmony 4.8 | 2026-08-05 10:47:05 | 29 | |||||||||
|
RiboTaper Resource Report Resource Website 1+ mentions |
RiboTaper (RRID:SCR_018880) | software resource, data processing software, software application, data analysis software | Software tool as analysis pipeline for ribosome profiling experiments, which exploits triplet periodicity of ribosomal footprints to call translated regions. Statistical approach that identifies translated regions on basis of characteristic three nucleotide periodicity of Ribo-seq data. | Ribo-seq data, analysis, ribosome profiling experiment, triplet periodicity, ribosomal footprint, translated region, three nucleotide periodicity, data, ribosome profiling, bio.tools |
is listed by: bio.tools is listed by: Debian |
NIGMS R01 GM104962; Berlin Institute for Medical Systems Biology |
PMID:26657557 | Free, Freely available | biotools:ribotaper | https://bioconda.github.io/recipes/ribotaper/README.html, https://bio.tools/ribotaper | SCR_018880 | 2026-08-05 10:47:07 | 8 | ||||||
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IMGT/StatClonotype Resource Report Resource Website 1+ mentions |
IMGT/StatClonotype (RRID:SCR_018963) | software resource, data processing software, software application, data analysis software | Software tool to evaluate and visualize statistical significance of pairwise comparisons of IMGT clonotype (AA) diversity or expression, per variable,diversity, and joining gene of given IG or TR group, from NGS IMGT/HighV-QUEST statistical output. Antibody clonotype analysis based on NGS sequences. | T cell receptor, antibody, immunoglobulin, immunoinformatics, next generation sequencing, statistical significance, clonotype diversity, clonotype expression, pairwise comparison, gene, NGS, analysis, antybody clonotype, bio.tools |
is listed by: bio.tools is listed by: Debian |
PMID:27667992 | Free, Available for download, Freely available | biotools:IMGt_StatClonotype | https://bio.tools/IMGT_StatClonotype | SCR_018963 | IMGTStatClonotype, ImMunoGeneTics/StatClonotype | 2026-08-05 10:47:07 | 3 | ||||||
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ClinTrajAn Resource Report Resource Website 1+ mentions |
ClinTrajAn (RRID:SCR_019018) | data processing software, software application, data visualization software, data analysis software, software resource | Software Python package for analysis of trajectories in clinical datasets. | Trajectories analysis, clinical datasets, analysis, data, , bio.tools |
is listed by: bio.tools is listed by: Debian |
Free, Available for download, Freely available | biotools:clintrajan | https://bio.tools/clintrajan | SCR_019018 | 2026-08-05 10:47:08 | 1 | ||||||||
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TwoSampleMR Resource Report Resource Website 500+ mentions |
TwoSampleMR (RRID:SCR_019010) | software resource, data processing software, software application, data analysis software | Software R package for performing Mendelian randomization using genome wide association study summary data. | GWAS data, genome wide associated study data, genome data, Mendelian randomization, analysis | PMID:29846171 | Free, Available for download, Freely available | SCR_019010 | 2026-08-05 10:47:08 | 597 | ||||||||||
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BrainSuite Resource Report Resource Website 50+ mentions |
BrainSuite (RRID:SCR_006623) | BrainSuite | data processing software, image analysis software, software application, data visualization software, software resource | Suite of image analysis tools designed to process magnetic resonance images (MRI) of the human head. BrainSuite provides an automatic sequence to extract genus-zero cortical surface mesh models from the MRI. It also provides a set of viewing tools for exploring image and surface data. The latest release includes graphical user interface and command line versions of the tools. BrainSuite was specifically designed to guide its users through the process of cortical surface extraction. NITRC has written the software to require minimal user interaction and with the goal of completing the entire process of extracting a topologically spherical cortical surface from a raw MR volume within several minutes on a modern workstation. The individual components of BrainSuite may also be used for soft tissue, skull and scalp segmentation and for surface analysis and visualization. BrainSuite was written in Microsoft Visual C using the Microsoft Foundation Classes for its graphical user interface and the OpenGL library for rendering. BrainSuite runs under the Windows 2000 and Windows XP Professional operating systems. BrainSuite features include: * Sophisticated visualization tools, such as MRI visualization in 3 orthogonal views (either separately or in 3D view), and overlayed surface visualization of cortex, skull, and scalp * Cortical surface extraction, using a multi-stage user friendly approach. * Tools including brain surface extraction, bias field correction, voxel classification, cerebellum removal, and surface generation * Topological correction of cortical surfaces, which uses a graph-based approach to remove topological defects (handles and holes) and ensure a tessellation with spherical topology * Parameterization of generated cortical surfaces, minimizing a harmonic energy functional in the p-norm * Skull and scalp surface extraction | brain, magnetic resonance, image, analysis, human, topology, segmentation, visualization, cortex, cortical, mri, tissue classification, topological correction, rendering, edit, cortical surface |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Biomedical Informatics Research Network |
NIBIB R01 EB002010; NCRR P41 RR013642; NIMH RO1-MH53213 |
PMID:12045000 | nif-0000-30214 | http://www.nitrc.org/projects/brainsuite | SCR_006623 | Brain Suite | 2026-08-05 10:44:29 | 93 | |||||
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InterPro Resource Report Resource Website 5000+ mentions |
InterPro (RRID:SCR_006695) | InterPro | data or information resource, web service, data access protocol, database, software resource, data analysis service, production service resource, service resource, analysis service resource | Service providing functional analysis of proteins by classifying them into families and predicting domains and important sites. They combine protein signatures from a number of member databases into a single searchable resource, capitalizing on their individual strengths to produce a powerful integrated database and diagnostic tool. This integrated database of predictive protein signatures is used for the classification and automatic annotation of proteins and genomes. InterPro classifies sequences at superfamily, family and subfamily levels, predicting the occurrence of functional domains, repeats and important sites. InterPro adds in-depth annotation, including GO terms, to the protein signatures. You can access the data programmatically, via Web Services. The member databases use a number of approaches: # ProDom: provider of sequence-clusters built from UniProtKB using PSI-BLAST. # PROSITE patterns: provider of simple regular expressions. # PROSITE and HAMAP profiles: provide sequence matrices. # PRINTS provider of fingerprints, which are groups of aligned, un-weighted Position Specific Sequence Matrices (PSSMs). # PANTHER, PIRSF, Pfam, SMART, TIGRFAMs, Gene3D and SUPERFAMILY: are providers of hidden Markov models (HMMs). Your contributions are welcome. You are encouraged to use the ''''Add your annotation'''' button on InterPro entry pages to suggest updated or improved annotation for individual InterPro entries. | protein, classify, prediction, protein domain, genome, protein family, functional site, protein sequence, protein function, analysis, nucleic acid, amino acid, amino acid sequence, gold standard |
is listed by: re3data.org is listed by: OMICtools is related to: TIGRFAMS is related to: TIGRFAMS is related to: FlyMine is related to: GeneSpeed- A Database of Unigene Domain Organization is related to: Biomine is related to: InterProScan is related to: GeneTerm Linker is related to: Gene Ontology is related to: ProDom is related to: Algal Functional Annotation Tool has parent organization: European Bioinformatics Institute |
European Union FP7 Scientific Data Repositories 213037; BBSRC BB/F010508/1; NIGMS GM081084 |
PMID:22096229 PMID:21082426 PMID:18940856 PMID:18428686 PMID:18025686 PMID:17202162 PMID:16909843 PMID:15608177 PMID:12520011 PMID:12230031 PMID:11159333 PMID:11119311 PMID:11125043 |
Acknowledgement requested, Free, Public, The community can contribute to this resource | nif-0000-03035, OMICS_01694, r3d100010798 | https://doi.org/10.17616/R3FS61 | SCR_006695 | InterPro: protein sequence analysis & classification, InterPro protein sequence analysis and classification | 2026-08-05 10:44:30 | 7000 | ||||
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Brain Innovation: Home of the BrainVoyager Product Family Resource Report Resource Website 100+ mentions |
Brain Innovation: Home of the BrainVoyager Product Family (RRID:SCR_006660) | Brain Innovation | data or information resource, topical portal, portal, software resource | Brain Innovation B.V. is developing scientific software in the field of human and animal brain imaging, neural network simulation and computer-based experimental control. Our current major product, BrainVoyager QX, is a commercially available cross-platform neuroimaging tool, which is used in hundreds of labs across the planet. Turbo-BrainVoyager is an easy to use program for real-time data analysis, which allows to observe a subject''s or patient''s brain activity during an ongoing functional MRI scanning session. TMS Neuronavigator provides the hard- and software to navigate a TMS coil to desired anatomical or functionally defined brain regions. We also provide free software products. BrainVoyager Brain Tutor allows to learn about brain areas by clicking on rotatable 3D brain models. StimulDX is a powerful stimulation software based on Microsofts DirectX API, which we will make available for free download in the near future. | brain, imaging, human, non-human animal, brain imaging, neural network simulation, experimental control, network, simulation, experimental, analysis, anatomical, neuroimaging, tool |
is parent organization of: BrainVoyager Brain Tutor is parent organization of: BrainVoyager Brain Viewer is parent organization of: Turbo-BrainVoyager is parent organization of: BrainVoyager |
nif-0000-30213 | SCR_006660 | Brain Innovation B.V. | 2026-08-05 10:44:30 | 168 | ||||||||
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mAdb Resource Report Resource Website 10+ mentions |
mAdb (RRID:SCR_006677) | mAdb | data or information resource, data repository, storage service resource, database, data analysis service, production service resource, service resource, analysis service resource | Microarray data management and analysis system for NCI / Center for Cancer Research scientists / collaborators. Data is secured and backed up on a regular basis, and investigators can authorize levels of access privileges to their projects, allowing data privacy while still enabling data sharing with collaborators. | microarray, bioinformatics, data management, analysis, gene expression, affymetrix, image, alignment, gene array list, cdna, oligonucleotide, gene discovery, prediction, comparison, cancer, FASEB list | has parent organization: Center for Cancer Research | Center for Information Technology | PMID:14728569 | Account required, Restricted to NIH users/collaborators, The community can contribute to this resource | nif-0000-00171 | http://nciarray.nci.nih.gov/ | SCR_006677 | Mad Bee, microArray database, Micro-array Database at the National Cancer Institute, NCI/CIT microArray database | 2026-08-05 10:44:30 | 38 | ||||
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MITK Diffusion Resource Report Resource Website 1+ mentions |
MITK Diffusion (RRID:SCR_006846) | MITK-DI | data processing software, source code, image analysis software, software application, data visualization software, software toolkit, software resource, image processing software | A selection of image analysis algorithms for the processing of diffusion-weighted MR images. Features & Highlights * Tensor and q-ball reconstruction * Glyph visualization * Quantification and partial volume clustering of tensor and q-ball images * Global fiber tractography, visualization, and tract post-processing * Brain network statistics and visualization (connectomics) * Interactive exploration of Tract-based spatial statistics (TBSS) results * Intra-voxel incoherent motion (IVIM) estimation * Synthetic data generation Additional system specific requirements: * Windows: If you have problems running the Windows application, please install the Microsoft Redistributable Packages for VS 2008: 32 bit or 64 bit * Linux: the Qt framework, version 4.6.2 or later Tested systems: Windows 7, Windows Vista; Ubuntu 12.04 and newer; OS X 10.6 (Snow Leopard), OS X 10.8 (Mountain Lion) The OS X 10.6 installer is compatible with OS X 10.7 (Lion) so there is no dedicated disk image build under 10.7. The MITK Diffusion application is based on the MITK research platform and the most of it is open-source. The available code is embedded into the source code of MITK as a module and can be accessed through the public git repository. | tractography, diffusion tensor imaging, q-ball imaging, diffusion mri, data processing, analysis, visualization, connectomics, fiber tractography, tract post processing, glyph visualization, tensor reconstruction, q-ball reconstruction, scalar index, connectivity analysis, image reconstruction, modeling, quantification, segmentation, fiber tracking, macos, windows, os independent, linux, c++, dicom, nifti-1, nrrd, other format |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: Diffusion MRI of Traumatic Brain Injury has parent organization: German Cancer Research Center |
PMID:23038239 | Most of it, Simplified BSD License | nlx_153917 | http://www.nitrc.org/projects/mitk-diffusion | SCR_006846 | MITK Diffusion Imaging | 2026-08-05 10:44:33 | 3 | |||||
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eXpress Resource Report Resource Website 100+ mentions |
eXpress (RRID:SCR_006873) | eXpress | data processing software, software application, sequence analysis software, data analysis software, software resource |
THIS RESOURCE IS NO LONGER IN SERVICE. Documented January 29, 2018. From website: "Note that the eXpress software is also no longer being developed. We recommend you use kallisto instead." Kallisto can be found at http://pachterlab.github.io/kallisto/. Software for streaming quantification for high-throughput DNA/RNA sequencing. Can be used in any application where abundances of target sequences need to be estimated from short reads sequenced from them. |
quantification, high-throughput, DNA, RNA, sequencing, target, fragment, analysis |
is listed by: OMICtools is listed by: Debian has parent organization: University of California at Berkeley; Berkeley; USA |
NSF ; NHGRI R01HG006129 |
DOI:10.1038/nmeth.2251 | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_015990, OMICS_01275 | https://sources.debian.org/src/berkeley-express/ | SCR_006873 | eXpress - Streaming quantification for high-throughput sequencing, Berkeley-express | 2026-08-05 10:44:33 | 494 | ||||
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g:Profiler Resource Report Resource Website 1000+ mentions |
g:Profiler (RRID:SCR_006809) | web service, data access protocol, software resource, data analysis service, production service resource, service resource, analysis service resource | Web server for functional enrichment analysis and conversions of gene lists. Web based tool for functional profiling of gene lists from large scale experiments. Has web interface with powerful visualization. Used for analyzing data from any organism. | gene, high-throughput, genomics, visualization, statistical analysis, slimmer-type tool, term enrichment, protein interaction, functional similarity, analysis, coexpression, gene id, network enrichment analysis, orthology mapping, genomic locus, ontology or annotation visualization, other analysis, ortholog, functional profile, gene list, ontology, pathway, transcription factor, microrna, regulatory motif, protein-protein interaction, biomolecule, gene expression, gene, homology, single nucleotide polymorphism, dna polymorphism, chromosome, network analysis, disease gene, r |
is listed by: Gene Ontology Tools is listed by: OMICtools is related to: Gene Ontology is related to: Ensembl is related to: Ensembl Genomes has parent organization: BIIT - Bioinformatics Algorithmics and Data Mining Group works with: gProfiler2 |
Estonian Research Council grants ; European Regional Development Fund for CoE of Estonian ICT research EXCITE projects |
PMID:21646343 PMID:17478515 PMID:31066453 |
Free, Freely available | OMICS_02223, nif-0000-31975 | SCR_006809 | G:Profiler, g:profiler, gProfiler | 2026-08-05 10:44:32 | 2078 | ||||||
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NIMH DIRP Scientific and Statistical Computing Core Resource Report Resource Website |
NIMH DIRP Scientific and Statistical Computing Core (RRID:SCR_006958) | SSCC, NIMH DIRP SSCC | data or information resource, topical portal, portal | Scientific and Statistical Computing Core of the NIMH Intramural Research Program supporting functional neuroimaging research at the NIH. This includes development of new data analysis techniques, their implementation in the AFNI software, advising researchers on the analysis methods, and instructing them in the use of software tools. Support methods: A. Provision of software for analysis for FMRI data (AFNI package: http://afni.nimh.nih.gov) * AFNI has been developed for the last 10 years by Dr Cox, et al. (6 years in Milwaukee, 4 years at NIMH) * Formal and informal instruction in the use of AFNI, including outlines of the statistical methods used in the programs * Installation of AFNI on NIH computers (Mac OS X, Unix, Linux) approximately 120 NIH systems have used AFNI in the last month (80 NIMH, 20 NINDS, 20 other) * Realtime monitoring of FMRI data at scanners * Continuing development of new modules for AFNI to meet needs of NIH researchers B. Consulting with NIH researchers about FMRI data analysis issues, concerns, and methods | neuroimaging, functional neuroimaging, research, data analysis, analysis, software, tool, fmri, statistics, computing | has parent organization: NIMH Division of Intramural Research Programs | NIMH | nlx_144305 | SCR_006958 | NIMH DIRP Scientific Statistical Computing Core, Scientific and Statistical Computing Core, DIRP Scientific and Statistical Computing Core, Scientific Statistical Computing Core | 2026-08-05 10:44:34 | 0 |
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