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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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OpenEx Resource Report Resource Website 100+ mentions |
OpenEx (RRID:SCR_016230) | software application, data analysis software, software resource, data processing software, data visualization software, software toolkit | Software toolkit that is designed for configuration and control of TDT hardware. It can also display and analyze neurophysiology data., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | tdt, analysis, neurophysiology, hardware, companion software, control, configuration, neuroimaging, eeg, stimulation | has parent organization: Tucker-Davis Technologies | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_016230 | The OpenEx Software Suite, OpenEx suite | 2026-07-28 09:44:15 | 103 | |||||||||
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Deeptools Resource Report Resource Website 1000+ mentions |
Deeptools (RRID:SCR_016366) | software application, data analysis software, software resource, data processing software, data visualization software, software toolkit | Python based tools to process, visualize and analyse high-throughput sequencing data, such as ChIP-seq, RNA-seq or MNase-seq. Implemented within Galaxy framework. Used to perform complete bioinformatic workflows ranging from quality controls and normalizations of aligned reads to integrative analyses, including clustering and visualization approaches. | process, visualize, analysis, sequencing, data, ChIP-seq, RNA-seq, MNase-seq, quality, control, normalization, aligned, read, clustering, bioinformatic | works with: Galaxy | German Research Foundation SFB 992; German Epigenome Programme DEEP 01KU1216G |
PMID:27079975 | Free, Available for download, Freely available | http://deeptools.ie-freiburg.mpg.de/ | SCR_016366 | 2026-07-28 09:44:17 | 2418 | |||||||
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SMAGEXP Resource Report Resource Website 1+ mentions |
SMAGEXP (RRID:SCR_016360) | SMAGEXP | software application, data analysis software, software resource, data processing software, software toolkit | Software toolkit for transcriptomics data meta-analysis. It integrates metaMA and metaRNAseq packages into Galaxy, carries out meta-analysis of gene expression data, handles microarray data from Gene Expression Omnibus (GEO) database, and more. | transcriptomics, data, meta, analysis, MicroArrays, RNA-Seq, Galaxy, gene, expression, next, generation, sequencing, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: Galaxy is related to: Gene Expression Omnibus is related to: metaMA is related to: metaRNASeq |
PMID:30698691 | Free, Available for download, Freely available | biotools:SMAGEXP | https://bio.tools/SMAGEXP | SCR_016360 | Statistical Meta Analysis for Gene EXPression | 2026-07-28 09:44:17 | 2 | |||||
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nelpy Resource Report Resource Website 1+ mentions |
nelpy (RRID:SCR_016209) | software application, data analysis software, software resource, data processing software, data visualization software, software toolkit | Software toolkit for neuroelectrophysiology object modeling and data analysis in Python. Open source Python package for analysis of neuroelectrophysiology data. | model, modelling, python, neuroelectrophysiology, object, neuroimaging, analysis, neurophysiology, electrophysiology, BRAIN Initiative | is recommended by: BRAIN Initiative | NSF CBET-1351692; NSF IOS-1550994; Human Frontiers Science Program RGY0088 |
Free, Available for download, Freely available | SCR_016209 | Nelpy (Neuroelectrophysiology) | 2026-07-28 09:44:08 | 3 | ||||||||
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UTHSCSA ImageTool Resource Report Resource Website 100+ mentions |
UTHSCSA ImageTool (RRID:SCR_016208) | IT | software application, software resource, data processing software, image processing software, image analysis software | Image processing and analysis program for Windows 95 NT and has many of the same capabilities as NIH Image. ImageTool can acquire, display, edit, analyze, process, compress, save and print gray scale and color images. | image, analysis, processing, data, acquisition, compression, modification | has parent organization: University of Texas Health Science Center at San Antonio; Texas; USA | Free, Available for download, Runs on Windows | http://en.bio-soft.net/draw/ImageTool.html | SCR_016208 | UTHSCSA Image Tool, UTHSCSA ImageTool (IT) | 2026-07-28 09:44:15 | 120 | |||||||
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migec Resource Report Resource Website 1+ mentions |
migec (RRID:SCR_016337) | MIGEC | software application, data analysis software, software resource, data processing software, software toolkit | Software package for analysis of immune repertoire sequencing data. Used for recovery of T Cell Receptor ( TCR ) data from bulk population data.Used for high-throughput sequencing data analysis. Allows for error correction while preserving the natural diversity of complex immune repertoires. | high sequencing, molecular, identifier, guided, error, correction, data, analysis, immune, recovery, T cell receptor, | Molecular and Cell Biology program RAS ; Russian Foundation for Basic Research ; Russian President ; European Regional Development Fund |
PMID:24793455 | Free, Available for download, Freely available | SCR_016337 | Molecular Identifier Guided Error Correction | 2026-07-28 09:44:11 | 9 | |||||||
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FLIR tools Resource Report Resource Website 10+ mentions |
FLIR tools (RRID:SCR_016330) | software application, data analysis software, software resource, data processing software, image analysis software | Software application for thermography for FLIR Systems. It has a basic thermal image analysis function including color palette and image adjustment function. Used to analyse the thermographic measurement data. | thermography, FLIR Systems, image, data, measurement, analysis | Free, Available for download | SCR_016330 | 2026-07-28 09:44:17 | 14 | |||||||||||
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star-for-criu Resource Report Resource Website 1+ mentions |
star-for-criu (RRID:SCR_016294) | software application, software resource, data processing software, alignment software, image analysis software | Software as an Hot Start software container for STAR alignment using CRIU (Checkpoint Restore in Userspace) tool to freeze the running container. Can be deployed to align RNA sequencing data. Used in the processing of biomedical big data for better reproducibility and reliability. | hot, start, container, star, aligner, sequencing, data, processing, biomedical, cloud, reproducibility, RNA, analysis, computing, environment | is related to: Systems Transcriptional Activity Reconstruction | NHLBI U54 HL127624; AMEDD Advanced Medical Technology Initiative ; NIGMS R01 GM126019 |
Free, Freely available, Available for download | https://github.com/paizhang/Hotstarting-For-STAR-Alignment | SCR_016294 | 2026-07-28 09:44:16 | 1 | ||||||||
|
GoldWave Resource Report Resource Website 50+ mentions |
GoldWave (RRID:SCR_016189) | software application, data analysis software, software resource, data processing software | Software that enables users to digitally edit audio files. GoldWave can record, edit, and analyze audio for research-related purposes. | audio, sound, analysis, acquisition, visualization, record, edit, analysis, auditory | Commercially available, Available for purchase | SCR_016189 | 2026-07-28 09:44:07 | 86 | |||||||||||
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masked ICA (mICA) Toolbox Resource Report Resource Website 1+ mentions |
masked ICA (mICA) Toolbox (RRID:SCR_016349) | mICA | software application, data analysis software, software resource, data processing software, software toolkit | Software toolbox based on FSL command line tools that performs masked independent component analysis and related analyses in an integrated way within a spatially restricted subregion of the brain. Used for investigating functional connectivity in functional magnetic resonance imaging data in the field of neuroimaging. | masked, independent, component, analysis, neuroimaging, restricted, subregion, brain, magnetic, resonance, imaging, data, |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: FSL has parent organization: Hannover Medical School; Lower Saxony; Germany |
Horst Görtz Foundation | PMID:27168407 | Free, Freely available, Available for download | SCR_016349 | masked Independent Component Analysis | 2026-07-28 09:44:15 | 1 | ||||||
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RNA STRAND-The RNA secondary STRucture and statistical ANalysis Database Resource Report Resource Website |
RNA STRAND-The RNA secondary STRucture and statistical ANalysis Database (RRID:SCR_000086) | RNA STRAND | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. A scientific community-crowdsourced database containing the RNA secondary structures of known types and organisms. It is meant to provide a simple and powerful way to analyze, search and update a shared repository of information. | database, rna, analysis, scientific community, resource | has parent organization: University of British Columbia; British Columbia; Canada | PMID:18700982 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-03415 | SCR_000086 | RNA secondary STRucture and statistical ANalysis Database | 2026-07-28 09:39:56 | 0 | ||||||
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Sumatra Resource Report Resource Website 10+ mentions |
Sumatra (RRID:SCR_001381) | software application, electronic laboratory notebook, software resource | A software tool for managing and tracking projects based on numerical simulation or analysis to support reproducible research. It can be thought of as an automated electronic lab notebook for simulation/analysis projects. Sumatra consists of: a command-line interface, smt, for launching simulations/analyses with automatic recording of information about the context, annotating these records, linking to data files, etc.; a web interface with a built-in web-server, smtweb, for browsing and annotating simulation/analysis results; a LaTeX package and Sphinx extension for including Sumatra-tracked figures and links to provenance information in papers and other documents; and a Python API, on which smt and smtweb are based, that can be used in personalized scripts in place of using smt. | simulation, analysis, python, numerical simulation, manage, track |
uses: Python Programming Language is listed by: INCF Software Center has parent organization: NeuralEnsemble |
Free, Freely Available | nlx_152549 | SCR_001381 | Sumatra: automated tracking of scientific computations | 2026-07-28 09:40:10 | 27 | ||||||||
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Bamboo DiRT Resource Report Resource Website 1+ mentions |
Bamboo DiRT (RRID:SCR_002556) | Bamboo DiRT | data or information resource, database | Registry of digital research tools for scholarly use that makes it easy for digital humanists and others conducting digital research to find and compare resources ranging from content management systems to music OCR, statistical analysis packages to mindmapping software., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | analysis, registry | is listed by: FORCE11 | Andrew W. Mellon Foundation | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_156034 | http://www.force11.org/node/4756 | SCR_002556 | Bamboo Dirt registry of digital research tools for scholarly use, Bamboo Digital Research Tools | 2026-07-28 09:40:28 | 1 | |||||
|
VIPERdb Resource Report Resource Website 50+ mentions |
VIPERdb (RRID:SCR_002853) | data or information resource, database | Database for icosahedral virus capsid structures. The emphasis of the resource is on providing data from structural and computational analyses on these systems, as well as high quality renderings for visual exploration. In addition, all virus capsids are placed in a single icosahedral orientation convention, facilitating comparison between different structures. The web site includes powerful search utilities , links to other relevant databases, background information on virus capsid structure, and useful database interface tools. It is an information source for the analysis of high resolution virus structures. VIPERdb is a one-stop site dedicated to helping users around the world examine the many icosahedral virus structures contained within the Protein Data Bank (PDB) by providing them with an easy to use database containing current data and a variety of analytical tools. Sponsors: VIPERdb is funded by the NIH., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | exploration, analysis, capsid, computational, convention, database, icosahedral, structural, structure, system, virus, visual, bio.tools, FASEB list |
is listed by: bio.tools is listed by: Debian has parent organization: Scripps Research Institute |
PMID:33313778 PMID:30265627 |
Free, Freely available | nif-0000-25311, r3d100012362, nif-0000-03630, biotools:viperdb, SCR_007970 | https://bio.tools/viperdb, https://doi.org/10.17616/R3HT0Q | SCR_002853 | Virus Particle ExploreR | 2026-07-28 09:40:32 | 59 | ||||||
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GeneWindow Resource Report Resource Website 1+ mentions |
GeneWindow (RRID:SCR_008183) | software application, software resource, data analysis software, data processing software | Software tool for pre- and post-genetic bioinformatics and analytical work, developed and used at the Core Genotyping Facility (CGF) at the National Cancer Institute. While Genewindow is implemented for the human genome and integrated with the CGF laboratory data, it stands as a useful tool to assist investigators in the selection of variants for study in vitro, or in novel genetic association studies. The Genewindow application and source code is publicly available for use in other genomes, and can be integrated with the analysis, storage, and archiving of data generated in any laboratory setting. This can assist laboratories in the choice and tracking of information related to genetic annotations, including variations and genomic positions. Features of GeneWindow include: -Intuitive representation of genomic variation using advanced web-based graphics (SVG) -Search by HUGO gene symbol, dbSNP ID, internal CGF polymorphism ID, or chromosome coordinates -Gene-centric display (only when a gene of interest is in view) oriented 5 to 3 regardless of the reference strand and adjacent genes -Two views, a Locus Overview, which varies in size depending on the gene or genomic region being viewed and, below it, a Sequence View displaying 2000 base pairs within the overview -Navigate the genome by clicking along the gene in the Locus Overview to change the Sequence View, expand or contract the genomic interval, or shift the view in the 5 or 3 direction (relative to the current gene) -Lists of available genomic features -Search for sequence matches in the Locus Overview -Genomic features are represented by shape, color and opacity with contextual information visible when the user moves over or clicks on a feature -Administrators can insert newly-discovered polymorphisms into the Genewindow database by entering annotations directly through the GUI -Integration with a Laboratory Information Management System (LIMS) or other databases is possible | gene, genetic, analysis, annotation, archive, bioinformatic, cancer, genome, genomic, genotype, genotyping, human, human genome databases, maps, polymorphism, position, variation, data set |
is listed by: 3DVC has parent organization: National Cancer Institute |
nif-0000-21173 | SCR_008183 | GeneWindow | 2026-07-28 09:42:04 | 1 | |||||||||
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Emergent Resource Report Resource Website 1+ mentions |
Emergent (RRID:SCR_008500) | Emergent | software application, narrative resource, data or information resource, software resource, wiki, simulation software | emergent is a comprehensive, full-featured neural network simulator that allows for the creation and analysis of complex, sophisticated models of the brain in the world. With an emphasis on qualitative analysis and teaching, it also supports the workflow of professional neural network researchers. Its high level drag-and-drop programming interface, built on top of a scripting language that has full introspective access to all aspects of networks and the software itself, allows one to write programs that seamlessly weave together the training of a network and evolution of its environment without ever typing out a line of code. Networks and all of their state variables are visually inspected in 3d, allowing for a quick visual regression of network dynamics and robot behavior. This same 3d world sports a highly accurate Newtonian physics simulation, allowing you to create rich robotics simulations (for example, a car). As a direct descendant of PDP (1986) and PDP (1999), emergent has been in development for decades. In the most recent versions available strive to distill it down to its essential elements. Those that take the time to learn the best practices will be rewarded with the ability to create and understand the most complicated neural models ever published. | neural, simulator, network, analysis, software, simulation, physics, newtonian |
is related to: PDP++ Software Home Page has parent organization: University of Colorado Boulder; Colorado; USA |
NIMH R01 MH069597-01; NIMH MH47566; DARPA/ONR N00014-05-1-0880; ONR N00014-03-1-0428 |
nif-0000-30515 | SCR_008500 | Emergent Neural Network Simulation System, PDP++ | 2026-07-28 09:42:20 | 4 | |||||||
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Cambridge Neuroscience Department Resource Report Resource Website 1+ mentions |
Cambridge Neuroscience Department (RRID:SCR_008649) | data or information resource, organization portal, department portal, portal | This portal provides information about the neuroscience department at the University of Cambridge. Cambridge has a strong tradition in neuroscience having been host to the first analyses of neural signaling in the 1930s, determined the mechanisms of neuronal firing in the 1950s, and heralded some of the early theoretical approaches to the functions of neural circuitry in the 1960s. Neuroscience continues to grow at Cambridge, with an impressive record of achievement in multidisciplinary research. | education, analysis, circuitry, department, graduate, mechanism, neural, neuron, neuronal, neuroscience, research, signaling, theoretical, undergraduate | has parent organization: University of Cambridge; Cambridge; United Kingdom | nif-0000-33002 | SCR_008649 | Cambridge Neuroscience | 2026-07-28 09:42:10 | 1 | |||||||||
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Agile Protein Interactomes DataServer Resource Report Resource Website 10+ mentions |
Agile Protein Interactomes DataServer (RRID:SCR_008871) | APID | service resource, data or information resource, data analysis service, database, data access protocol, software resource, production service resource, web service, analysis service resource | APID Interactomes (Agile Protein Interactomes DataServer) provides information on the protein interactomes of numerous organisms, based on the integration of known experimentally validated protein-protein physical interactions (PPIs). The interactome data includes a report on quality levels and coverage over the proteomes for each organism included. APID integrates PPIs from primary databases of molecular interactions (BIND, BioGRID, DIP, HPRD, IntAct, MINT) and also from experimentally resolved 3D structures (PDB) where more than two distinct proteins have been identified. This collection references protein interactors, through a UniProt identifier. | protein, protein interaction, interactions, ppi, interactomes, analysis, gene, ontology, functional, environment, data, network, graphic, visualize |
is listed by: Gene Ontology Tools is related to: PSICQUIC Registry is related to: Gene Ontology is related to: BIND is related to: Biological General Repository for Interaction Datasets (BioGRID) is related to: Database of Interacting Proteins (DIP) is related to: HPRD - Human Protein Reference Database is related to: IntAct is related to: MINT has parent organization: University of Salamanca; Salamanca; Spain |
Spanish Ministerio de Sanidad y Consumo ; Junta de Castilla y Leon |
PMID:27131791 PMID:30715274 |
Free for academic use | r3d100012339, nlx_149321 | https://doi.org/10.17616/R3407P, https://doi.org/10.17616/R3407P | SCR_008871 | Agile Protein Interactomes DataServer, APID, APID Interactomes, Agile Protein Interactomes DataServer (APID), APID (Agile Protein Interactomes DataServer) | 2026-07-28 09:42:14 | 14 | ||||
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GMA Resource Report Resource Website |
GMA (RRID:SCR_009212) | GMA | software application, data analysis software, software resource, data processing software, time-series analysis software | Software package to perform Granger mediation analysis for time series. Includes single level GMA model and two-level GMA model, for time series with hierarchically nested structure. | Granger, meditation, analysis, time, series, level, GMA, model, BRAIN Initiative, bio.tools |
is recommended by: BRAIN Initiative is listed by: Genetic Analysis Software is listed by: Debian is listed by: bio.tools |
NIBIB EB022911 | PMID:31070732 | Free, Available for download, Freely available | nlx_154361, biotools:GMA | https://github.com/chaoning/GMA, https://bio.tools/GMA | http://www.montana.edu/kalinowski/GMA/GMA_Home.htm | SCR_009212 | Granger Mediation Analysis | 2026-07-28 09:42:26 | 0 | |||
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Neural Decoding Toolbox Resource Report Resource Website 10+ mentions |
Neural Decoding Toolbox (RRID:SCR_009012) | NDT | software application, data analysis software, software resource, data processing software, software toolkit | Matlab toolbox that makes it easy to apply decoding analyses to neural data. The design of the toolbox revolves around four abstract object classes which enables users to interchange particular modules in order to try different analyses while keeping the rest of the processing stream intact. The toolbox is capable of analyzing data from many different types of recording modalities, and examples are given on how it can be used to decode basic visual information from neural spiking activity and how it can be used to examine how invariant the activity of a neural population is to stimulus transformations. | population decoding, neuron, analysis, matlab, data analysis, machine learning, multivariate pattern analysis, neural decoding | has parent organization: Massachusetts Institute of Technology; Massachusetts; USA; | DARPA ; IPTO ; DSO ; AFSOR-THRL ; Adobe Systems ; Honda Research Institute USA ; King Abdullah University of Science and Technology ; NEU ; Sony ; Eugene McDermott Foundation ; NSF 0640097; NSF 0827427; NSF FA8650-05-C-7262 |
PMID:23734125 | Acknowledgement requested, Account required | nlx_152729 | SCR_009012 | 2026-07-28 09:42:25 | 18 |
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