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Resource Name Proper Citation Abbreviations Resource Type Description Keywords Resource Relationships Related Condition Funding Defining Citation Availability Specification URL Alternate IDs Alternate URLs Old URLs Parent Organization Resource ID Synonyms Record Last Update Mentions Count
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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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