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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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FSL Resource Report Resource Website 1000+ mentions |
FSL (RRID:SCR_002823) | software library, software toolkit, software resource | Software library of image analysis and statistical tools for fMRI, MRI and DTI brain imaging data. Include registration, atlases, diffusion MRI tools for parameter reconstruction and probabilistic taractography, and viewer. Several brain atlases, integrated into FSLView and Featquery, allow viewing of structural and cytoarchitectonic standard space labels and probability maps for cortical and subcortical structures and white matter tracts. Includes Harvard-Oxford cortical and subcortical structural atlases, Julich histological atlas, JHU DTI-based white-matter atlases, Oxford thalamic connectivity atlas, Talairach atlas, MNI structural atlas, and Cerebellum atlas. | dti, brain, imaging, data, structural, mri, diffusion, function, preprocessing, analysis, statistical, tractography, atlas, neuroimaging, parameter, reconstruction, volumetric, segmentation, independent, component, temporal, transformation |
uses: Neuroimaging Data Model is used by: Spinal Cord Toolbox is used by: Functional Real-time Interactive Endogenous Neuromodulation and Decoding (FRIEND) is used by: XFSL: An FSL toolbox is used by: CMIND PY lists: SUSAN lists: FUGUE lists: Miscvis lists: BayCEST lists: ICA-PNM is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Debian is listed by: SoftCite is related to: Rodent Brain Extraction Tool is related to: Human Connectome Coordination Facility is related to: BASH4RfMRI is related to: DW-MRI registration in FSL is related to: FSL extensions is related to: Diffusion MRI of Traumatic Brain Injury is related to: Segmentation of Hippocampus Subfields is related to: masked ICA (mICA) Toolbox has parent organization: University of Oxford; Oxford; United Kingdom has plug in: Multivariate Exploratory Linear Optimized Decomposition into Independent Components has plug in: FMRI Expert Analysis Tool has plug in: FABBER has plug in: BASIL has plug in: VERBENA has plug in: Brain Extraction Tool has plug in: FMRIB's Automated Segmentation Tool has plug in: FMRIB’s Integrated Registration and Segmentation Tool has plug in: Harvard - Oxford Cortical Structural Atlas has plug in: FMRIB's Linear Image Registration Tool has plug in: FNIRT has plug in: FSLVBM has plug in: SIENA has plug in: SIENAX has plug in: Multimodal Image Segmentation Tool has plug in: Brain Intensity AbNormality Classification Algorithm has plug in: Multimodal Surface Matching has plug in: fsl_anat has plug in: FMRIB's Diffusion Toolbox has plug in: Tract Based Spatial Statistics has plug in: XTRACT has plug in: eddy has plug in: topup has plug in: eddyqc has plug in: randomise has plug in: PALM has plug in: fsl-cluster has plug in: FDR has plug in: DualRegression has plug in: FLOBS has plug in: FSLeyes has plug in: Fslutils has plug in: Atlasquery has plug in: MCFLIRT has plug in: POSSUM has plug in: FSL-MRS |
EPSRC ; MRC ; BBSRC ; GlaxoSmithKline ; Pfizer |
PMID:21979382 PMID:19059349 PMID:15501092 |
Free, Available for download, Freely available | nif-0000-00305, birnlex_2067, SCR_007368 | http://www.nitrc.org/projects/fsl, http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/, https://sources.debian.org/src/fsl/ | SCR_002823 | , FMRIB Software Library, fMRIB Software Library, Functional Magnetic Resonance Imaging of the Brain Software Library | 2026-08-02 09:03:35 | 4685 | |||||
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Indelible Resource Report Resource Website 10+ mentions |
Indelible (RRID:SCR_016163) | simulation software, software resource, software application | Software that generates nucleotide, amino acid and codon sequence data by simulating insertions and deletions (indels) as well as substitutions. It is used for biological sequence simulation of multi-partitioned nucleotide, amino-acid, or codon data sets through the processes of insertion, deletion, and substitution in continuous time. | indel, insertion, deletion, biological, sequence, simulation, multi-partitioned, nucleotide, amio-acid, codon, data, set, insertion, deletion, substitution, continous, time, non-homogeneous, non-stationary, phylogeny, simulator, evolution |
is listed by: Debian is listed by: OMICtools |
EPSRC/MRC Doctoral Training Centre studentship ; BBSRC |
PMID:19423664 | Free, Available for download | OMICS_15369 | https://sources.debian.org/src/indelible/ | SCR_016163 | 2026-08-02 09:07:15 | 23 | ||||||
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PICRUSt Resource Report Resource Website 10+ mentions |
PICRUSt (RRID:SCR_016855) | PICRUSt | simulation software, software resource, software application | Software package to predict metagenome functional content from marker gene (e.g., 16S rRNA) surveys and full genomes. Used to predict which gene families are present and then combines gene families to estimate the composite metagenome. | predict, metagenome, functional, content, DNA, sample, marker, gene, sequence, data, microbiome, 16S, RNA | is related to: PICRUSt2 | Canadian Institutes of Health Research ; Canada Research Chairs program ; Howard Hughes Medical Institute ; NIDDK P01 DK078669; NHGRI U01 HG004866; NHGRI R01 HG004872; Crohn’s and Colitis Foundation of America ; Sloan Foundation ; NHGRI R01 HG005969; NSF CAREER DBI1053486; ARO W911NF1110473 |
PMID:23975157 | Free, Available for download, Freely available | SCR_016856 | SCR_016855 | Phylogenetic Investigation of Communities by Reconstruction of Unobserved States, PICRUSt | 2026-08-02 09:07:32 | 36 | |||||
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OAI Knowledge base Resource Report Resource Website |
OAI Knowledge base (RRID:SCR_028107) | data or information resource, knowledge base | Centralized, annotated repository for the Osteoarthritis Initiative (OAI) study, designed to accelerate research by organizing and linking extensive clinical, imaging (MRI/X-ray), and biomarker data. It aims to help researchers analyze knee osteoarthritis prevention, treatment, and progression. | DRKB, clinical, imaging, MRI, X-ray, biomarker, data, osteoarthritis | Free, Freely available, | SCR_028107 | Osteoarthritis Initiative Knowledge base | 2026-08-01 12:14:41 | 0 | ||||||||||
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National Center for Integrative Biomedical Informatics Resource Report Resource Website 1+ mentions |
National Center for Integrative Biomedical Informatics (RRID:SCR_001538) | organization portal, data or information resource, portal | The Center develops conceptual models, computational infrastructure, an integrated knowledge repository, and query and analysis tools that enable scientists to effectively access and integrate the wealth of biological data. The National Center for Integrative Biomedical Informatics (NCIBI) was founded in October 2005 and is one of seven National Centers for Biomedical Computing (NCBC) in the NIH Roadmap. NCIBI is based at the University of Michigan as a part of the Center for Computational Medicine and Biology (CCMB). NCIBI is composed of biomedical researchers, computational biologists, computer scientists, developers and human-computer interaction specialists organized into seven major core functions. They work in interdisciplinary teams to collectively develop tools that are not only computationally powerful but also biologically relevant and meaningful. The four initial Driving Biological Projects (prostate cancer progression, Type 1 and type 2 diabetes and bipolar disorder) provide the nucleation point from which tool development is informed, launched, and tested. In addition to testing tools for function, a separate team is dedicated to testing usability and user interaction that is a unique feature of this Center. Once tools are developed and validated the goal of the Center is to share and disseminate data and software throughout the research community both internally and externally. This is achieved through various mechanisms such as training videos, tutorials, and demonstrations and presentations at national and international scientific conferences. NCIBI is supported by NIH Grant # U54-DA021519. | analysis tools, bipolar disorder, code, computational infrastructure, conceptual models, data, diabetes, knowledge repository, presentations, prostate cancer, query tools, seminar material, tool development, tutorials, videos, model |
is listed by: 3DVC is related to: Biological Concept Diagram Editor is related to: Gene Interaction Extraction from the Literature is related to: National Centers for Biomedical Computing has parent organization: University of Michigan; Ann Arbor; USA is parent organization of: Substructure Index-based Approximate Graph Alignment is parent organization of: miniTUBA is parent organization of: Michigan Molecular Interactions is parent organization of: Cell Line Knowledge Base is parent organization of: HubMed is parent organization of: MiMI Plugin for Cytoscape |
Type 1 diabetes, Type 2 diabetes, Diabetes, Cancer, Bipolar disorder | PMID:22101971 | Free, Freely available | nif-0000-09660 | http://portal.ncibi.org/gateway/ | SCR_001538 | NCIBI | 2026-08-02 09:03:04 | 1 | |||||
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BRAIN Initiative Resource Report Resource Website 10+ mentions |
BRAIN Initiative (RRID:SCR_006770) | NIH BRAIN Initiative | organization portal, data or information resource, portal | Project aimed at revolutionizing understanding of human brain, to show how individual cells and complex neural circuits interact, enable rapid progress in development of new technologies and data analysis tools to treat and prevent brain disorders. BRAIN Initiative encourages collaborations between neurobiologists and scientists from disciplines such as statistics, physics, mathematics, engineering, and computer and information sciences. Institutes and centers contributing to NIH BRAIN Initiative support those research efforts. | brain, connectomics, disorder, cell, neural, circuit, neurotechnology, data, repository, analysis |
uses: Single Cell Portal recommends: Human Neocortical Neurosolver recommends: Brain Gene Expression Analysis toolbox recommends: clusterExperiment recommends: BioWheel recommends: iELVis recommends: Mediation Analysis of Causality under Confounding recommends: MCell recommends: microMS recommends: MIIVsem recommends: MountainSort recommends: Myriads recommends: nelpy recommends: NetPyNE recommends: Neural Ideal recommends: NEURON recommends: Neuron Tools recommends: Neuroscience Gateway recommends: NUTMEG recommends: PetaVision recommends: PyNWB recommends: pyRayleighCuda recommends: ScanImage recommends: Scope recommends: Seizure-Waves recommends: Silver Lab Microscopy Software recommends: StimVision recommends: TReNA recommends: ALICE recommends: BioImage Suite recommends: EyeWire recommends: GIMME recommends: GMA recommends: Homer2 recommends: Brain Image Library recommends: Data Archive BRAIN Initiative recommends: OpenNeuro recommends: Brain Observatory Storage Service and Database (BossDB) recommends: 1000 Functional Connectomes Project recommends: FastProject recommends: Autopatcher recommends: cytoNet recommends: DiffuserCam recommends: gene Expression Analysis Resource recommends: NeMOarchive recommends: Distributed Archives for Neurophysiology Data Integration recommends: NIDA Data Share recommends: HED Tags lists: University of North Carolina Neuroscience Center and the BRAIN Initiative Viral Vector Core Facility is related to: Brain Image Library is related to: OpenNeuro is related to: Distributed Archives for Neurophysiology Data Integration is related to: NeMO Analytics is related to: Brainome portal is related to: CEMBA MethylC Seq Pipeline is related to: Seattle Alzheimer Disease Brain Cell Atlas is related to: EBRAINS is related to: Human Brain Variation Project has parent organization: National Institutes of Health is parent organization of: Data Archive BRAIN Initiative is parent organization of: OpenNeuro is parent organization of: Brain Observatory Storage Service and Database (BossDB) is parent organization of: Ecosystem for Multi-modal Brain-behavior Experimentation and Research has organization facet: 3D Developmental Mouse Brain Common Coordinate Framework |
Alzheimer's disease, Schizophrenia, Autism, Epilepsy, Traumatic brain injury | BRAIN Initiative | nlx_155554 | http://braininitiative.nih.gov/, http://www.whitehouse.gov/share/brain-initiative, http://en.wikipedia.org/wiki/BRAIN_Initiative | SCR_006770 | , Brain Research through Advancing Innovative Neurotechnologies Initiative, NIH Brain Research through Advancing Innovative Neurotechnologies Initiative | 2026-08-02 09:04:58 | 18 | |||||
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XSEDE - Extreme Science and Engineering Discovery Environment Resource Report Resource Website 10+ mentions |
XSEDE - Extreme Science and Engineering Discovery Environment (RRID:SCR_006091) | XSEDE | data or information resource, portal | XSEDE is a single virtual system that scientists can use to interactively share computing resources, data and expertise. People around the world use these resources and services things like supercomputers, collections of data and new tools to improve our planet. XSEDE resources may be broadly categorized as follows: High Performance Computing, High Throughput Computing, Visualization, Storage, and Data Services. Many resources provide overlapping functionality across categories. Scientists, engineers, social scientists, and humanists around the world - many of them at colleges and universities - use advanced digital resources and services every day. Things like supercomputers, collections of data, and new tools are critical to the success of those researchers, who use them to make our lives healthier, safer, and better. XSEDE integrates these resources and services, makes them easier to use, and helps more people use them. XSEDE supports 16 supercomputers and high-end visualization and data analysis resources across the country. Digital services, meanwhile, provide users with seamless integration to NSF''s high-performance computing and data resources. XSEDE''s integrated, comprehensive suite of advanced digital services will federate with other high-end facilities and with campus-based resources, serving as the foundation for a national cyberinfrastructure ecosystem. Common authentication and trust mechanisms, global namespace and filesystems, remote job submission and monitoring, and file transfer services are examples of XSEDE''s advanced digital services. XSEDE''s standards-based architecture allows open development for future digital services and enhancements. XSEDE also provides the expertise to ensure that researchers can make the most of the supercomputers and tools. | data sharing, computing, supercomputer, data, tool, visualization, data analysis, cyberinfrastructure, digital service, high performance computing, high throughput computing, visualization, storage, data service |
is related to: Neuroscience Gateway has parent organization: San Diego Supercomputer Center |
NSF OCI-1053575 | nlx_151554, grid.501421.3 | https://ror.org/05524hb64 | SCR_006091 | XSEDE - Extreme Science Engineering Discovery Environment, Extreme Science and Engineering Discovery Environment | 2026-08-02 09:04:29 | 27 | ||||||
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Stanford Center for Reproducible Neuroscience Resource Report Resource Website |
Stanford Center for Reproducible Neuroscience (RRID:SCR_016684) | organization portal, data or information resource, portal | Center with the goal of harnessing high-performance computing to make neuroscience research more reliable.Provide researchers with tools to analyze their data in ways that focus on the reproducibility of the results through the OpenfMRI ( OpenNeuro ) and Neurovault projects. | computing, tools, neuroscience, data, analyze, reproducibility, fMRI, OpenfMRI, OpenNeuro, Neurovault |
has parent organization: Stanford University; Stanford; California is parent organization of: OpenNeuro is parent organization of: OpenNeuro is parent organization of: NeuroVault |
SCR_016684 | 2026-08-02 09:07:27 | 0 | |||||||||||
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NeLS Resource Report Resource Website 1+ mentions |
NeLS (RRID:SCR_016301) | NeLS | organization portal, data or information resource, portal | Web portal for the administration of Norwegian e-Infrastructure for Life Sciences. Enables Norwegian life scientists and their international collaborators to store, share, archive, and analyse their genomics scale data. NeLS is one of the packages of the ELIXIR.NO project. | genomic, data, analyze, store, share, archive, electronic, infrastructure, administration, Norway, bio.tools |
is listed by: bio.tools is listed by: Debian |
Research Council of Norway | Free, Freely available | biotools:nels | https://bio.tools/nels, https://github.com/elixir-no-nels/nels-core, https://bio.tools/nels | SCR_016301 | Norwegian e-Infrastructure for Life Sciences | 2026-08-02 09:07:17 | 3 | |||||
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Twins Research Australia Resource Report Resource Website 1+ mentions |
Twins Research Australia (RRID:SCR_017485) | data or information resource, portal | Portal for Twins Research Australia. Brings twins and researchers together for vital health research in twins. | Twin, research, Australia, data | has parent organization: University of Melbourne; Victoria; Australia | National Health and Medical Research Council | Free, Freely available | SCR_017485 | Australian Twin Registry | 2026-08-02 09:07:50 | 3 | ||||||||
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Australian Government Data Portal Resource Report Resource Website 1+ mentions |
Australian Government Data Portal (RRID:SCR_019159) | data or information resource, portal | Portal as central source of Australian open government data. Used to find, explore and reuse Australia public data. Anyone can access the anonymised public data published by federal, state and local government agencies, publicly funded research data and datasets from private institutions that are in public interest. | Australian government data, public data, Australia public data, data, unpublised data | Free, Freely available | SCR_019159 | 2026-08-02 09:07:58 | 3 | |||||||||||
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SPAdes Resource Report Resource Website 100+ mentions |
SPAdes (RRID:SCR_000131) | SPAdes | software toolkit, software resource | Software package for assembling single cell genomes and mini metagenomes. Uses short read sets as input. Used for genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. Works with Illumina or IonTorrent reads and can provide hybrid assemblies using PacBio, Oxford Nanopore and Sanger reads. Intended for small genomes like bacterial or fungal., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | assembler, single, cell, small, genome, short, read, data |
is used by: shovill is listed by: OMICtools is listed by: Debian is listed by: SoftCite is related to: rnaSPAdes is related to: rnaQUAST has parent organization: Saint Petersburg Academic University; Saint Petersburg; Russia works with: Illumina: iSeq 100 Sequencing System |
Government of the Russian Federation ; NCRR P41 RR024851 |
PMID:24093227 PMID:22506599 DOI:10.1089/cmb.2012.0021 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01502 | https://sources.debian.org/src/spades/ | http://bioinf.spbau.ru/spades/ | SCR_000131 | SPAdes Genome Assembler | 2026-08-02 09:02:48 | 101 | |||
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FluView: A Weekly Influenza Surveillance Report Resource Report Resource Website 1+ mentions |
FluView: A Weekly Influenza Surveillance Report (RRID:SCR_001118) | data or information resource, portal | This page contains the Influenza Surveillance Report during 2008-2009 Influenza Season Week 15, ending April 18, 2009. | influenza, disease, prevention, seasonal, data, portal | has parent organization: Centers for Disease Control and Prevention | CDC | nif-0000-30241 | SCR_001118 | FluView | 2026-08-02 09:03:00 | 2 | ||||||||
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NCBI Resource List Resource Report Resource Website |
NCBI Resource List (RRID:SCR_005628) | NCBI Resources | organization portal, data or information resource, portal | The National Center for Biotechnology Information''s listing of resources. Sort by alphabetical character, Databases, Downloads, Submissions, Tools and How-To; or by Topic: Chemicals & Bioassays; Data & Software; DNA & RNA; Domains & Structures; Genes & Expression; Genetics & Medicine; Genomes & Maps; Homology; Literature; Proteins; Sequence Analysis; Taxonomy; Training & Tutorials; Variation. | database, download, submission, tool, chemical, bioassay, data, software, dna, rna, domain, structure, gene, expression, genetics, medicine, genomes, map, homology, literature, protein, sequence analysis, taxonomy, training, tutorial, variation, gold standard | has parent organization: NCBI | NLM | nlx_146242 | SCR_005628 | NCBI Resource Guide, NCBI Resource List (A-Z) | 2026-08-02 09:04:29 | 0 | |||||||
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Brain Architecture Management System Resource Report Resource Website 1+ mentions |
Brain Architecture Management System (RRID:SCR_007251) | BAMS | data repository, ontology, service resource, database, storage service resource, controlled vocabulary, data or information resource | Knowledge management system designed to handle neurobiological information at different levels of organization of vertebrate nervous system. Database and repository for information about neural circuitry, storing and analyzing data concerned with nomenclature, taxonomy, axonal connections, and neuronal cell types. Handles data and metadata collated from original literature, or inserted by scientists that is associated to four levels of organization of vertebrate nervous system. Data about expressed molecules, neuron types and classes, brain regions, and networks of brain regions. | neurobiology, vertebrate, nervous, system, database, repository, neural, circuitry, analysis, data, nomenclature, taxonomy, axonal, connection, cell, |
is used by: NIF Data Federation is used by: Integrated Nervous System Connectivity is related to: Integrated Manually Extracted Annotation has parent organization: University of Southern California; Los Angeles; USA is parent organization of: BAMS Nested Regions is parent organization of: BAMS Connectivity is parent organization of: BAMS Cells is parent organization of: BAMS Neuroanatomical Ontology |
NIBIB ; Human Brain Project ; NIMH MH61223; NINDS NS16686; NINDS NS50792 |
Restricted | nif-0000-00018 | http://brancusi.usc.edu/bkms/ | SCR_007251 | Brain Architecture Management System, The Brain Architecture Management System | 2026-08-03 09:33:19 | 6 | |||||
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CardioGenomics Resource Report Resource Website 1+ mentions |
CardioGenomics (RRID:SCR_007248) | CardioGenomics | topical portal, data or information resource, portal | The primary goal of the CardioGenomics PGA is to begin to link genes to structure, function, dysfunction and structural abnormalities of the cardiovascular system caused by clinically relevant genetic and environmental stimuli. The principal biological theme to be pursued is how the transcriptional network of the cardiovascular system responds to genetic and environmental stresses to maintain normal function and structure, and how this network is altered in disease. This PGA will generate a high quality, comprehensive data set for the functional genomics of structural and functional adaptation of the cardiovascular system by integrating expression data from animal models and human tissue samples, mutation screening of candidate genes in patients, and DNA polymorphisms in a well characterized general population. Such a data set will serve as a benchmark for future basic, clinical, and pharmacogenomic studies. Training and education are also a key focus of the CardioGenomics PGA. In addition to ongoing journal clubs and seminars, the PGA will be sponsoring symposia at major conferences, and developing workshops related to the areas of focus of this PGA. Information regarding upcoming events can be found in the Events section of this site, and information about training and education opportunities sponsored by CardioGenomics can be found on the Teaching and Education page. The CardioGenomics project came to a close in 2005. This server, cardiogenomics.med.harvard.edu, remains online in order to continue to distribute data that was generated by investigators under the auspices of the CardioGenomics Program for Genomic Applications (PGA). :Sponsors: This resource is supported by The National Heart, Lung and Blood Institute (NHLBI) of the NIH., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | genomics, clinical, genetic, environmental, stimulus, cardiovascular, disease, data, expression, gene, dna, polymorphism, population, pharmacogenomic, training, education | has parent organization: Harvard University; Cambridge; United States | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-30296 | http://www.cardiogenomics.org | SCR_007248 | The CardioGenomics Project | 2026-08-03 09:33:19 | 6 | ||||||
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Allen Human Brain Atlas Resource Report Resource Website 100+ mentions |
Allen Human Brain Atlas (RRID:SCR_007416) | database, software application, data processing software, atlas, data or information resource, software resource, data visualization software | Multi modal atlas of human brain that integrates anatomic and genomic information, coupled with suite of visualization and mining tools to create open public resource for brain researchers and other scientists. Data include magnetic resonance imaging (MRI), diffusion tensor imaging (DTI), histology and gene expression data derived from both microarray and in situ hybridization (ISH) approaches. Brain Explorer 2 is desktop software application for viewing human brain anatomy and gene expression data in 3D. | atlas, human, brain, anatomic, genomic, data, visualization, mining, tool, MRI, DTI, histology, gene, expression |
is related to: Speech Language Disorders Database has parent organization: Allen Institute for Brain Science has parent organization: Allen Brain Atlas |
Individual private donors ; U.S. Department of Health and Human Services 1C76HF15069; U.S. Department of Health and Human Services 1C76HF19619 |
PMID:23041053 | Free, Available for download, Freely available | nif-0000-00506 | http://humancortex.alleninstitute.org, http://human.brain-map.org/ | SCR_007416 | Human Cortex Study, Allen Institute for Brain Science Human Cortex Study, Allen Brain Atlas - Human Brain | 2026-08-03 09:33:30 | 135 | |||||
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GeneNetWorks Resource Report Resource Website 1+ mentions |
GeneNetWorks (RRID:SCR_008034) | data acquisition software, software application, database, data processing software, data analysis software, data or information resource, software resource, data visualization software | GeneNetWorks is designed for accumulation of experimental data, data navigation, data analysis, and analysis of dependencies in the field of gene expression regulation. It integrates the databases and programs for processing the data about structure and function of DNA, RNA, and proteins, together with the other information resources important for gene expression description. The unique property of above described system is that all the resources within the system GeneNetWorks are divided according to the natural hierarchy of molecular genetic systems and has the following levels: (1) DNA; (2) RNA; (3) proteins; and (4) gene networks. Each module contains: 1) experimental data represented as a database or some sample; 2) program for data analysis; 3) results of an automated data processing; 4) tools for the graphical representation of these data and the results of the data analyses. | experimental, expression, gene, gene regulation, genetic, analysis, data, dna, graphical, molecular, navigation, network, program, protein, rna, software, system | nif-0000-10232 | SCR_008034 | GNW | 2026-08-03 09:33:51 | 1 | ||||||||||
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Genomatix Software: Understanding Gene Regulation Resource Report Resource Website 500+ mentions |
Genomatix Software: Understanding Gene Regulation (RRID:SCR_008036) | portal, software application, database, data processing software, short course material, narrative resource, topical portal, data analysis software, data or information resource, software resource, training material | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 13,2026. Genomatix is a privately held company that offers software, databases, and services aimed at understanding gene regulation at the molecular level representing a central part of systems biology. Its multilayer integrative approach is a working implementation of systems biology principles. Genomatix combines sequence analysis, functional promoter analysis, proprietary genome annotation, promoter sequence databases, comparative genomics, scientific literature data mining, pathway databases, biological network databases, pathway analysis, network analysis, and expression profiling into working solutions and pipelines. It also enables better understanding of biological mechanisms under different conditions and stimuli in the biological context of your data. Some of Genomatix'' most valuable assets are the strong scientific background and the years of experience in research & discovery as well as in development & application of scientific software. Their firsthand knowledge of all the complexities involved in the in-silico analysis of biological data makes them a first-rate partner for all scientific projects involving the evaluation of gene regulatory mechanisms. The Genomatix team has more than a decade of scientific expertise in the successful application of computer aided analysis of gene regulatory networks, which is reflected by more than 150 peer reviewed scientific publications from Genomatix'' scientists More than 35,000 researchers in industry and academia around the world use this technology. The software available in Genomatix are: - GenomatixSuite: GenomatixSuite is our comprehensive software bundle including ElDorado, Gene2Promoter, GEMS Launcher, MatInspector and MatBase. GenomatixSuite PE also includes BiblioSphere Pathway Edition. Chromatin IP Software - RegionMiner: Fast, extensive analysis of genomic regions. - ChipInspector: Discover the real power of your microarray data. Genome Annotation Software - ElDorado: Extended Genome Annotation. - Gene2Promoter: Retrieve & analyze promoters - GPD: The Genomatix Promoter Database, which is now included with Gene2Promoter. Knowledge Mining Software - BiblioSpere : The next level of pathway/genomics analysis. - LitInspector: Literature and pathway analysis for free. Sequence Analysis Software - GEMS Launcher: Our integrated collection of sequence analysis tools. - MalInspector: Search transcription factor binding sites - MatBase: The transcription factor knowledge base. Other (no registration required) Software - DiAlign: Multiple alignment of DNA/protein sequence. - Genomatix tools: Various small tools for sequence statistics, extraction, formatting, etc. | effect, expression, functional, gene, genome, alignment, analysis, annotation, biological, cascade, cell, data, dna, in-silico analysis, mechanism, metabolic pathway, microarray, mining, molecular, network, pathway, promoter, protein, region, regulation, scientific, sequence, signaling, software, stimulus, systems biology, technology, text mining, transcription, FASEB list | has parent organization: Genomatix Solutions | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-10236 | http://www.genomatix.de/products/index.html | SCR_008036 | Genomatix | 2026-08-03 09:33:38 | 868 | |||||||
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dbEST Resource Report Resource Website 100+ mentions |
dbEST (RRID:SCR_008132) | data repository, data or information resource, database, storage service resource, service resource | Database as a division of GenBank that contains sequence data and other information on single-pass cDNA sequences, or Expressed Sequence Tags, from a number of organisms. | data, sequence, single, pass, cDNA, express, tag, bio.tools, gold standard |
is listed by: Debian is listed by: bio.tools has parent organization: NCBI |
PMID:8401577 | biotools:dbest, nif-0000-20937, r3d100010648 | http://www.ncbi.nlm.nih.gov/dbEST/, https://bio.tools/dbest, https://doi.org/10.17616/R3FG8P | SCR_008132 | database Expressed Sequence Tag (EST), database Expressed Sequence Tag | 2026-08-03 09:33:40 | 179 |
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