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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Northern Ireland Virtual Tissue Archive Resource Report Resource Website |
Northern Ireland Virtual Tissue Archive (RRID:SCR_004452) | NIVTA | image collection, narrative resource, data or information resource, training material | THIS RESOURCE IS NO LONGER IN SERVICE, documented August 29, 2016. A pan European network for virtual tissue archiving aimed at supporting clinical trials, biomarker research, tissue microarray analysis and virtual slide based education. NIVTA has state-of-the-art digital scanning systems including an Aperio CS system, Aperio OS system (one of only two currently available in Europe) and a Hamamatsu system with fluorescent scanning capability. | clinical trial, biomarker research, tissue microarray, analysis, virtual slide, tissue, archive, data resource | has parent organization: Queens University Belfast; Ireland; United Kingdom | Queen's University Belfast; Ireland; United Kingdom ; Hewlett-Packard |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_44619 | SCR_004452 | 2026-08-04 09:41:09 | 0 | |||||||
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Stem Cell Discovery Engine Resource Report Resource Website 50+ mentions |
Stem Cell Discovery Engine (RRID:SCR_004453) | SCDE | source code, analysis service resource, storage service resource, software resource, data repository, production service resource, service resource, database, data or information resource | An online database of curated cancer stem cell (CSC) experiments coupled to the Galaxy analytical framework. Driven by a need to improve our understanding of molecular processes that are common and unique across cancer stem cells (CSCs), the SCDE allows users to consistently describe, share and compare CSC data at the gene and pathway level. The initial focus has been on carefully curating tissue and cancer stem cell-related experiments from blood, intestine and brain to create a high quality resource containing 53 public studies and 1098 assays. The experimental information is captured and stored in the multi-omics Investigation/Study/Assay (ISA-Tab) format and can be queried in the data repository. A linked Galaxy framework provides a comprehensive, flexible environment populated with novel tools for gene list comparisons against molecular signatures in GeneSigDB and MSigDB, curated experiments in the SCDE and pathways in WikiPathways. Investigation/Study/Assay (ISA) infrastructure is the first general-purpose format and freely available desktop software suite targeted to experimentalists, curators and developers and that: * assists in the reporting and local management of experimental metadata (i.e. sample characteristics, technology and measurement types, sample-to-data relationships) from studies employing one or a combination of technologies; * empowers users to uptake community-defined minimum information checklists and ontologies, where required; * formats studies for submission to a growing number of international public repositories endorsing the tools, currently ENA (genomics), PRIDE (proteomics) and ArrayExpress (transcriptomics). Galaxy allows you to do analyses you cannot do anywhere else without the need to install or download anything. You can analyze multiple alignments, compare genomic annotations, profile metagenomic samples and much much more. Best of all, Galaxy''''s history system provides a complete analyses record that can be shared. Every history is an analysis workflow, which can be used to reproduce the entire experiment. The code for this Galaxy instance is available for download from BitBucket. | stem cell, analysis, cancer stem cell, galaxy, gene, pathway, molecular signature, tissue, bio.tools, FASEB list |
is listed by: Debian is listed by: bio.tools is related to: Galaxy is related to: Galaxy is related to: ISA Infrastructure for Managing Experimental Metadata has parent organization: Harvard T.H. Chan School of Public Health |
Cancer | NCI 1RC2CA148222-01 | PMID:22121217 | Free, The community can contribute to this resource | biotools:scde_discovery, nlx_44656 | https://bio.tools/scde_discovery | SCR_004453 | Harvard Stem Cell Discovery Engine, SCDE - Stem Cell Discovery Engine | 2026-08-04 09:41:08 | 57 | |||
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Tree and reticulogram REConstruction Resource Report Resource Website 10+ mentions |
Tree and reticulogram REConstruction (RRID:SCR_004497) | T-REX | data analysis service, analysis service resource, software resource, production service resource, service resource | A web server dedicated to the reconstruction of phylogenetic trees, reticulation networks and to the inference of horizontal gene transfer (HGT) events. | phylogenetic tree, analysis, visualization, network, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: University of Quebec in Montreal; Quebec; Canada |
PMID:22675075 | biotools:t-rex, OMICS_04264 | https://bio.tools/t-rex | SCR_004497 | Trex-online | 2026-08-04 09:41:09 | 32 | ||||||
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FieldTrip Resource Report Resource Website 1000+ mentions |
FieldTrip (RRID:SCR_004849) | data processing software, data analysis software, software resource, software application, software toolkit | Software toolbox for analysis of MEG, EEG, and other electrophysiological data. Used by experimental neuroscientists. | MEG, EEG, iEEG, analysis, data, time, frequency, source, reconstruction, dipole, beamformers, non parametric, statistical, testing |
uses: MATLAB is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: Human Connectome Coordination Facility has parent organization: Radboud University; Nijmegen; The Netherlands works with: CoSMoMVPA works with: SleepTrip works with: EEGLAB works with: SPM |
Human Connectome project ; NIH Blueprint for Neuroscience Research ; Netherlands Ministry of Economic Affairs ; Netherlands Ministry of Education Culture and Science |
PMID:21253357 | Free, Available for download, Freely available, Tutorial available | nlx_143928 | http://www.nitrc.org/projects/fieldtrip | SCR_004849 | 2026-08-04 09:41:14 | 3073 | ||||||
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CCP4 Resource Report Resource Website 1000+ mentions |
CCP4 (RRID:SCR_007255) | CCP4 | simulation software, data processing software, portal, data analysis software, software resource, software application, service resource, data or information resource | Portal for Macromolecular X-Ray Crystallography to produce and support an integrated suite of programs that allows researchers to determine macromolecular structures by X-ray crystallography, and other biophysical techniques. Used in the education and training of scientists in experimental structural biology for determination and analysis of protein structure. | macromolecular, x-ray, crystallography, biophysical, technique, structural, biology, analysis, protein, Research Complex at Harwell, computational, collaborative, project |
is used by: MoRDa is used by: PDB-REDO is listed by: SoftCite is related to: BALBES is related to: CCP4mg is related to: fragon is related to: ConPlot has parent organization: Science and Technology Facilities Council |
Science and Technology Facilities Council | Free, Available for download, Freely available, Tutorial available | SCR_016709, nif-0000-30238 | SCR_007255 | The Collaborative Computational Project Number 4 in Protein Crystallography, Collaborative Computational Project Number 4 | 2026-08-04 09:41:49 | 4740 | ||||||
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BioEdit Resource Report Resource Website 10000+ mentions |
BioEdit (RRID:SCR_007361) | data processing software, alignment software, data analysis software, software resource, sequence analysis software, software application, image analysis software | Software tool as biological sequence alignment editor written for Windows 95/98/NT/2000/XP/7 and sequence analysis program. Provides sequence manipulation and analysis options and links to external analysis programs to view and manipulate sequences with simple point and click operations., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | sequence, alignment, editor, analysis, program | is listed by: SoftCite | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_156845 | SCR_007361 | 2026-08-04 09:41:50 | 13339 | |||||||||
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Harvard Medical School, Department of Systems Biology: The Megason Lab -GoFigure Software Resource Report Resource Website 1+ mentions |
Harvard Medical School, Department of Systems Biology: The Megason Lab -GoFigure Software (RRID:SCR_008037) | portal, data processing software, topical portal, software resource, software application, data visualization software, data or information resource | GoFigure is a software platform for quantitating complex 4d in vivo microscopy based data in high-throughput at the level of the cell. A prime goal of GoFigure is the automatic segmentation of nuclei and cell membranes and in temporally tracking them across cell migration and division to create cell lineages. GoFigure v2.0 is a major new release of our software package for quantitative analysis of image data. The research focuses on analyzing cells in intact, whole zebrafish embryos using 4d (xyzt) imaging which tends to make automatic segmentation more difficult than with 2d or 2d+time imaging of cells in culture. This resource has developed an automatic segmentation pipeline that includes ICA based channel unmixing, membrane nuclear channel subtraction, Gaussian correlation, shape models, and level set based variational active contours. GoFigure was designed to meet the challenging requirements of in toto imaging. In toto imaging is a technology that we are developing in which we seek to track all the cell movements and divisions that form structures during embryonic development of zebrafish and to quantitate protein expression and localization on top of this digital lineage. For in toto imaging, GoFigure uses zebrafish embryos in which the nuclei and cell membranes have been marked with 2 different color fluorescent proteins to allow cells to be segmented and tracked. A transgenic line in a third color can be used to mark protein expression and localization using a genetic approach that this resource developed called FlipTraps or using traditional transgenic approaches. Embryos are imaged using confocal or 2-photon microscopy to capture high-resolution xyzt image sets used for cell tracking. The GoFigure GUI will provide many tools for visualization and analysis of bioimages. Since fully automatic segmentation of cells is never perfect, GoFigure will provide easy to use tools for semi-automatically and manually adding, deleting, and editing traces in 2d (figures-xy, xz, or yz), 3d (meshes- xyz), 4d (tracks- xyzt) and 4d+cell division (lineages). GoFigure will also provide a number of views into complex image data sets including 3d XYZ and XYT image views, tabular list views of traces, histograms, and scattergrams. Importantly, all these views will be linked together to allow the user to explore their data from multiple angles. Data will be easily sorted and color-coded in many ways to explore correlations in higher dimensional data. The GoFigure architecture is designed to allow additional segmentation, visualization, and analysis filters to be plugged in. Sponsors: GoFigure is developed by Harvard University., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | embryo, expression, fluorescent, gaussian, genetic, 2d, 2-photon, 4d, analysis, bioimage, cell, cell membrane, cell movement, channel, confocal, contour, culture, data, dimensional, high-resolution, histogram, in vivo, localization, microscopy, model, nuclear, nucleus, protein, scattergram, segmentation, shape, software, technology, toto imaging, tracking, transgenic, visualization, zebrafish, image | has parent organization: Harvard University; Cambridge; United States | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-10243 | SCR_008037 | GoFigure | 2026-08-04 09:42:01 | 5 | ||||||||
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Max Planck Institute for Biological Intelligence Circuits - Computation – Models Resource Report Resource Website |
Max Planck Institute for Biological Intelligence Circuits - Computation – Models (RRID:SCR_008048) | portal, organization portal, data or information resource, department portal | Merger of the Max Planck Institute of Neurobiology and the Max Planck Institute of Ornithology and has been renamed to Circuits - Computation – Models. Department devoted to the study of how the brain computes to understand neural information processing at the level of individual neurons and small neural circuits. | drosophila melanogaster, experimental, expression, flight control, fly, fruitfly, genetic, activity in collaboration with winfried denk (mpi for medical research, analysis, animal, blow fly, brightness, cappiphora vicina, computed, heidelberg), indicator, intracellular, medulla, membrane, motion, natural, nervous, network, neural optic flow, neuron, pharmacology, property, retinal, specie, technique, the knowledge about the fly motion vision system goes into the development of miniature airborne vehicles (internrobofly). t, theoretical, this resource also try to fully reconstruct important parts of the optic lobes of both species at the ultrastructural level using his recently developed serial block face scanning electron microscope (internbluefly). biophysically realistic compartmental models of individual neurons obtained from 2p-image stacks allow us to reconstitute the network of motion processing neurons in computer simulations (internmodelfly). as a joint project with martin bussand kolja kuehnlenz, tissue, vector, visual system, image |
has parent organization: Max-Planck-Gesellschaft has parent organization: Max Planck Institute for Biological Intelligence |
nif-0000-10288 | http://www.neuro.mpg.de/borst, http://www.neuro.mpg.de/english/rd/scn/research/Theory_and_modeling_of_motion_vision/Compartmental_Modeling/Tanbase_-_Download/index.html | SCR_008048 | , Max Planck Institute of Neurobiology Systems and Computational Neurobiology, Circuits - Computation – Models, MPI S&C Neurobiology | 2026-08-04 09:42:01 | 0 | ||||||||
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ConnectomeViewer: Multi-Modal Multi-Level Network Visualization and Analysis Resource Report Resource Website |
ConnectomeViewer: Multi-Modal Multi-Level Network Visualization and Analysis (RRID:SCR_008312) | ConnectomeViewer | data processing software, rendering software, d visualization software, data analysis software, software resource, software application, data visualization software, network analysis software, network graph visualization software | Extensible, scriptable, pythonic software tool for visualization and analysis in structural neuroimaging research on many spatial scales. Employing the Connectome File Format, diverse data such as networks, surfaces, volumes, tracks and metadata are handled and integrated. The field of Connectomics research benefits from recent advances in structural neuroimaging technologies on all spatial scales. The need for software tools to visualize and analyze the emerging data is urgent. The ConnectomeViewer application was developed to meet the needs of basic and clinical neuroscientists, as well as complex network scientists, providing an integrative, extensible platform to visualize and analyze Connectomics data. With the Connectome File Format, interlinking different datatypes such as hierarchical networks, surface data, volumetric data is easy and might provide new ways of analyzing and interacting with data. Furthermore, ConnectomeViewer readily integrates with: * ConnectomeWiki: a semantic knowledge base representing connectomics data at a mesoscale level across various species, allowing easy access to relevant literature and databases. * ConnectomeDatabase: a repository to store and disseminate Connectome files. | extensible, analysis, clinical, data, diverse, metadata, network, neuroscience, neuroscientist, pythonics, research, scriptable, software, structural, surface, technology, tool, track, visualization, volume, neuroimaging |
has parent organization: Ecole Polytechnique Federale de Lausanne; Lausanne; Switzerland has parent organization: University of Lausanne; Lausanne; Switzerland |
nif-0000-24442 | SCR_008312 | 2026-08-04 09:42:06 | 0 | |||||||||
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Protein Databank Fun Resource Report Resource Website 1+ mentions |
Protein Databank Fun (RRID:SCR_008226) | data processing software, software application, software resource, data analysis software | THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. PDBfun is a web server for structural and functional analysis of proteins at the residue level. pdbFun gives fast access to the whole Protein Data Bank (PDB) organized as a database of annotated residues. The available data (features) range from solvent exposure to ligand binding ability, location in a protein cavity, secondary structure, residue type, sequence functional pattern, protein domain and catalytic activity. PDBfun is an integrated web tool for querying the PDB at the residue level and for local structural comparison. It integrates knowledge on single residues in protein structures coming from other databases or calculated with available or in-house developed instruments for structural analysis. Each set of different annotations represents a feature. Features are listed in PDBfun main page in orange. Features can be used for building residues selections. | functional, 2d, ability, activity, analysis, binding, catalytic, cavity, chain, cleft, domain, ligand, location, motif, protein, protein structure databases, residue, secondary, sequence, size, solvent, structural, structure, surface | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-21315 | SCR_008226 | PDBfun | 2026-08-04 09:42:07 | 2 | |||||||||
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Berkeley Drosophila Transcription Network Project Resource Report Resource Website 10+ mentions |
Berkeley Drosophila Transcription Network Project (RRID:SCR_008640) | topical portal, portal, data or information resource | The goal of this project is to decipher the transcriptional information contained in the extensive cis-acting DNA sequences that direct the patterns of gene expression that underlie animal development. Using the early embryo of the fruitfly Drosophila melanogaster as a model, these researchers are developing experimental and computational methods to systematically characterize and dissect the complex expression patterns and regulatory interactions already present prior to gastrulation. They have identified 37 principal regulatory factors within this network for initial analysis together with their target genes. Sponsors: This project is chiefly funded by a grant from NIGMS and NHGRI, R01 GM070444. Additional funding comes from grants to Michael Eisen, Sue Celniker, and Bernd Hamann. | embryo, experimental, expression, gastrulation, gene, analysis, animal, cis-acting, computational, development, dna, information, interaction, regulatory, target, transcriptional | has parent organization: Lawrence Berkeley National Laboratory | nif-0000-32986 | SCR_008640 | BDTNP | 2026-08-04 09:42:10 | 11 | |||||||||
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GeneCluster 2: An Advanced Toolset for Bioarray Analysis Resource Report Resource Website 10+ mentions |
GeneCluster 2: An Advanced Toolset for Bioarray Analysis (RRID:SCR_008446) | data processing software, data analysis software, software resource, software application, software toolkit | THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 17, 2013. A software package for analyzing gene expression and other bioarray data, giving users a variety of methods to build and evaluate class predictors, visualize marker lists, cluster data and validate results. GeneCluster 2.0 greatly expands the data analysis capabilities of GeneCluster 1.0 by adding supervised classification, gene selection, class discovery and permutation test methods. It includes algorithms for building and testing supervised models using weighted voting (WV) and k-nearest neighbor (KNN) algorithms, a module for systematically finding and evaluating clustering via self-organizing maps, and modules for marker gene selection and heat map visualization that allow users to view and sort samples and genes by many criteria. It enhances the clustering capabilities of GeneCluster 1.0 by adding a module for batch SOM clustering, and also includes a marker gene finder based on a KNN analysis and a visualization module. GeneCluster 2.0 is a stand-alone Java application and runs on any platform that supports the Java Runtime Environment version 1.3.1 or greater. | gene, cluster, software, analysis, expression, bioarray, data, class, predictor, visualization, marker, classification, algorithm, module, java, environment | has parent organization: Broad Institute | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-30293 | SCR_008446 | GeneCluster 2 | 2026-08-04 09:42:08 | 39 | ||||||||
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BRAID Resource Report Resource Website 10+ mentions |
BRAID (RRID:SCR_008702) | BRAID | source code, software resource, image, database, data or information resource | Large-scale archive of normalized digital spatial and functional data with an analytical query mechanism. One of its many applications is the elucidation of brain structure-function relationships. BRAID stores spatially defined data from digital brain images which have been mapped into normalized Cartesian coordinates, allowing image data from large populations of patients to be combined and compared. The database also contains neurological data from each patient and a query mechanism that can perform statistical structure-function correlations. The project is developing database technology for the manipulation and analysis of 3-dimensional brain images derived from MRI, PET, CT, etc. BRAID is based on the PostgreSQL server, an object/relational DBMS, which allows a standard relational DBMS to be augmented with application-specific datatypes and operators. The BRAID project is adding operations and datatypes to support querying, manipulation and analysis of 3D medical images, including: * Image Datatypes: BRAID supports a family of 3D image datatypes, each having an abstract type and an implementation type. Abstract types include boolean (for regions of interest), integer, float, vector (for representing morphological changes), tensor (for representing derivatives and standard deviations of vector images) and color. Implementation types at present include line-segment format and voxel array. * Image Operators: BRAID supports addition of images, multiplication (which is interpreted as intersection for boolean images), coercion of an image''s abstract or implementation type to another value, and determination of volumes of regions of interest. * Statistical Operators: A chi-squared test has been added to SQL as an aggregate operator on pairs of boolean values. * Web Interface: A general-purpose Web gateway allows the results of queries that return computed images to be displayed. You can download the BRAID source code 2.0. This version is developed under postgreSQL 7.3.4., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | brain image, data mining, brain, magnetic resonance, analysis, image display, mri, pet, ct, structure, function, brain | has parent organization: University of Pennsylvania; Philadelphia; USA | Aging | NIA R01 AG13743 | PMID:18467275 PMID:11191696 PMID:9874539 |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_143545, r3d100010227 | https://doi.org/10.17616/R3F88M | SCR_008702 | BRAID: Brain Image Database, Brain Image Database | 2026-08-04 09:42:11 | 11 | |||
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Rat Genome Database: Neurological Disease Portal Resource Report Resource Website 10+ mentions |
Rat Genome Database: Neurological Disease Portal (RRID:SCR_008685) | topical portal, portal, data or information resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 12,2023. Portal that provides researchers with easy access to data on rat genes, QTLs, strain models, biological processes and pathways related to neurological diseases. This resource also includes dynamic data analysis tools. | gene, analysis, biological, data, database, disease, genome, model, neurological, neuroscience, pathway, phenotype, qtl, rat, research | has parent organization: Medical College of Wisconsin; Wisconsin; USA | Neurological disease | RGD ; NINDS |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-33773 | http://rgd.mcw.edu | SCR_008685 | RGD Neurological Disease Portal | 2026-08-04 09:42:12 | 14 | |||||
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Neurostruct Resource Report Resource Website 1+ mentions |
Neurostruct (RRID:SCR_008861) | Neurostruct | segmentation software, data processing software, software resource, software application, image analysis software | THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 16, 2013. A built-in toolbox for the tracing and analysis of neuroanatomy from nanoscale (high-resolution) imaging. It is a project under ongoing development. The name is originating by merging the words Neuron + reconstruct. The working concept is organized in filters applied successively on the image stack to be processed (pipeline). Currently, the focus of the software is the extraction of detailed neuroanatomical profiles from nanoscale imaging techniques, such as the Serial Block-Face Scanning Electron Microscopy (SBFSEM). The techniques applied, however, may be used to analyze data from various imaging methods and neuronal versatility. The underlying idea of Neurostruct is the use of slim interfaces/filters allowing an efficient use of new libraries and data streaming. The image processing follows in voxel pipelines by using the CUDA programming model and all filters are programmed in a datasize-independent fashion. Thus Neurostruct exploits efficiency and datasize-independence in an optimal way. Neurostruct is based on the following main principles: * Image processing in voxel pipelines using the general purpose graphics processing units (GPGPU) programming model. * Efficient implementation of these interfaces. Programming model and image streaming that guarantees a minimal performance penalty. * Datasize-independent programming model enabling independence from the processed image stack. * Management of the filters and IO data through shell scripts. The executables (filters) are currently managed through shell scripts. The application focuses currently in the tracing of single-biocytin filled cells using SBFSEM imaging. : * Extraction of neuroanatomical profiles: 3D reconstrution and 1D skeletons of the imaged neuronal structure. * Complete tracing: Recognition of the full neuronal structure using envelope techniques, thereby remedying the problem of spines with thin necks of an internal diameter approaching the SBFSEM resolution. * Separation (Coloring) of subcellular structures: Algorithms for the separation of spines from their root dendritic stem. * Evaluation and analysis of the imaged neuroanatomy: Calculation of the dendritic and spine membrane''s surface, spine density and variation, models of dendrites and spines | neuroanatomy, imaging, analysis, tracing, electron microscopy, neuron, image processing, image reconstruction, serial block face scanning electron microscopic imaging assay |
has parent organization: Heidelberg University; Baden-Wurttemberg; Germany has parent organization: Max Planck Institute for Biological Intelligence |
PMID:21424815 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_149368 | SCR_008861 | Neurostruct - Project: Image and object processing filters for the tracing and analysis of neuroanatomy, Neurostruct-Project, Neurostruct - Project | 2026-08-04 09:42:14 | 1 | ||||||
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InterPro Resource Report Resource Website 5000+ mentions |
InterPro (RRID:SCR_006695) | InterPro | data analysis service, analysis service resource, web service, software resource, data access protocol, production service resource, service resource, database, data or information 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 | 2026-08-04 09:41:39 | 7000 | ||||
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MITK Diffusion Resource Report Resource Website 1+ mentions |
MITK Diffusion (RRID:SCR_006846) | MITK-DI | data processing software, source code, software resource, software application, image processing software, image analysis software, data visualization software, software toolkit | 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 | 2026-08-04 09:41:43 | 3 | |||||
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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 | topical portal, portal, software resource, data or information 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. | 2026-08-04 09:41:41 | 168 | ||||||||
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g:Profiler Resource Report Resource Website 1000+ mentions |
g:Profiler (RRID:SCR_006809) | data analysis service, analysis service resource, web service, software resource, data access protocol, production service resource, 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 | 2026-08-04 09:41:42 | 2078 | ||||||
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mAdb Resource Report Resource Website 10+ mentions |
mAdb (RRID:SCR_006677) | mAdb | data analysis service, analysis service resource, storage service resource, production service resource, service resource, data repository, database, data or information 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 | 2026-08-04 09:41:39 | 38 |
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