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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Allen Institute for Brain Science Sleep Study Resource Report Resource Website 1+ mentions |
Allen Institute for Brain Science Sleep Study (RRID:SCR_002983) | Allen Sleep Study | data or information resource, atlas, data set | Collection of gene expression data in mouse brain for five different conditions of sleep and wakefulness to understand sleep deprivation and dynamic changes underlying sleep and wake cycles. Platform to generate cellular resolution expression data. | gene, expression, brain, data, image, mice, microarray, nissl, sleep, deprivation, wake, cycle, wakefulness, neuroanatomy |
is listed by: 3DVC has parent organization: Allen Institute for Brain Science |
Free, Public | nif-0000-00507 | SCR_002983 | Sleep Study | 2026-08-03 09:32:07 | 2 | |||||||
|
Neuroscience Gateway Resource Report Resource Website 10+ mentions |
Neuroscience Gateway (RRID:SCR_008915) | NSG | data or information resource, software resource, portal, project portal | Web portal that allows free access to supercomputing resources for large scale modeling and data processing. Portal facilitates access and use of National Science Foundation (NSF) High Performance Computing (HPC) resources by neuroscientists. | Large, scale, modeling, data, computing, neuroscience, neuron, BRAIN Initiative |
is recommended by: BRAIN Initiative lists: ModelRun is related to: XSEDE - Extreme Science and Engineering Discovery Environment is related to: NEURON is related to: GENESIS Neural Database and Modelers Workspace has parent organization: San Diego Supercomputer Center has parent organization: Neuroscience Information Framework has parent organization: Yale School of Medicine; Connecticut; USA |
NSF 1458840; NSF 1458495; BBSRC N005236; NIBIB R01 EB023297; NSF 1339856; NSF 1146949 |
Free, Freely available | nlx_151553, SCR_015767 | http://www.nitrc.org/projects/nsg/ | SCR_008915 | Neuroscience Gateway - A Portal for Computational Neuroscience, Neuroscience Gateway, Neuroscience Gateway (NSG) Portal | 2026-08-03 09:34:10 | 23 | |||||
|
Trim Galore Resource Report Resource Website 5000+ mentions Rating or validation data |
Trim Galore (RRID:SCR_011847) | Trim Galore! | software resource, software application, data processing software | Software tool to automate quality and adapter trimming as well as quality control, with some added functionality to remove biased methylation positions for RRBS sequence files for directional, non-directional or paired-end sequencing. Wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for Reduced Representation Bisulfite Sequencing data. | Automate, quality, adapter, trimming, remove, biased, methylation, position, RRBS, reduced, representation, bisulfite, data, sequence, wrapper, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Babraham Institute works with: cutadapt |
Free, Available for download, Freely available | biotools:trim_galore, OMICS_01096, SCR_016946 | https://github.com/FelixKrueger/TrimGalore, https://bio.tools/trim_galore, https://sources.debian.org/src/trim-galore/ | SCR_011847 | TrimGalore | 2026-08-03 09:35:00 | 6255 | ||||||
|
Apache Spark Resource Report Resource Website 10+ mentions |
Apache Spark (RRID:SCR_016557) | data processing software, software resource, software application, data analytics software | Software tool as a unified analytics engine for large scale data processing. An open source distributed general purpose cluster computing framework. | unified, analytics, engine, large, scale, data, processing |
is related to: VariantSpark is related to: spark-xml is related to: spark-xml-utils is related to: SparkFHE has parent organization: University of California at Berkeley; Berkeley; USA |
DOI:10.1145/2934664 | Free, Available for download, Freely available | SCR_016557 | 2026-08-03 09:36:23 | 31 | |||||||||
|
Data Biosphere Resource Report Resource Website 1+ mentions |
Data Biosphere (RRID:SCR_016154) | data or information resource, portal, project portal | Project whose goal is to provide Data Environments to the biomedical community. The Data Biosphere works to create a user experience around key modular components — each having discrete capabilities and clear rules of interaction, and each served by multiple alternative implementations. | data, environment, biomedicine, standard, module, community | Freely available | https://github.com/databiosphere/ | SCR_016154 | 2026-08-03 09:36:18 | 1 | ||||||||||
|
atacr Resource Report Resource Website 1+ mentions |
atacr (RRID:SCR_016286) | software resource, software application, data processing software | Software that analyzes count data from RNA-capture-seq and ATAC-capture-seq experiments. Using BioConductor RangedSummarizedExperiment objects, atacr implements a set of helper functions and quality control plots specific to the analysis of counts of reads in windows across genomes. | normalization, bootstrap, bayes, factor, test, reference, design, seq, count, capture, data | Gatsby Charitable Foundation ; Marie Curie 656243 |
Free, Available for download, Tutorial available | SCR_016286 | 2026-08-03 09:36:41 | 2 | ||||||||||
|
Inxight Resource Report Resource Website 10+ mentions |
Inxight (RRID:SCR_016490) | organization portal, data or information resource, database, portal | Portal of NCATS (the National Center for Advancing Translational Sciences) for drug development information including:US approved drugs, marketed drugs, investigational drugs. Provides manually curated data supplied by the FDA and private companies. Provides drugs marketing and regulatory status, drug ingredient definitions, biological activity and clinical use. | drug, development, information, approved, marketed, investigational, data, supply, FDA, company, regulatory, status, ingredient, definition, biological, activity, clinical, use | NIH | Free, Freely available | SCR_016490 | 2026-08-03 09:36:48 | 11 | ||||||||||
|
ProCon - PROteomics CONversion Resource Report Resource Website 1+ mentions |
ProCon - PROteomics CONversion (RRID:SCR_016363) | ProCon | software resource, software application, data processing software | Java based conversion tool for conversion of data from Proteomics files or a LIMS (Laboratory Information Management System) database into standard formats. Used to support wet-lab scientists in creating proteomics data files ready for upload into the public repositories. | data, proteomics, conversion, file, laboratory, information, management, system, database, standard, format, , bio.tools |
is listed by: Debian is listed by: bio.tools is related to: Ruhr University Bochum; North Rhine-Westphalia; Germany |
European Union Projects ProDac ; European Union Projects ProteomeXchange ; the German Federal Ministry of Education and Research BMBF |
PMID:26182917 | Free, Available for download, Freely available | biotools:procon | https://bio.tools/procon | SCR_016363 | PROteomics CONversion | 2026-08-03 09:36:23 | 1 | ||||
|
NanoFilt Resource Report Resource Website 100+ mentions |
NanoFilt (RRID:SCR_016966) | software resource, software application, data processing software | Software tool written in Python to perform its filtering based on mean read quality and GC content and read length. Used for filtering and trimming of long read sequencing data. | filtering, trimming, long, sequencing, data, read |
is listed by: OMICtools is listed by: Debian |
Free, Available for download, Freely available | https://sources.debian.org/src/nanofilt/ | SCR_016966 | 2026-08-03 09:36:40 | 268 | |||||||||
|
GEOMAGIC Studio Resource Report Resource Website 1+ mentions |
GEOMAGIC Studio (RRID:SCR_016978) | GEOMAGIC Studio 12 | software resource, software application, data processing software | Software tool to convert 3D scans into parametric models. Transforms 3D scan data into highly accurate surface, polygon and native CAD models. Used for reverse engineering, product design, rapid prototyping and analysis. | 3D, scan, convert, data, surface, polygon, native, CAD, model | Free, Available for download, Freely available | https://de.3dsystems.com/press-releases/geomagic/studio-12-offers-fastest-way-to-convert-3d-scans-of-phy | SCR_016978 | 2026-08-03 09:36:58 | 1 | |||||||||
|
BOINC - Berkeley Open Infrastructure for Network Computing Resource Report Resource Website 1+ mentions |
BOINC - Berkeley Open Infrastructure for Network Computing (RRID:SCR_015896) | BOINC | portal, data acquisition software, data distribution software, software application, data processing software, data or information resource, software resource, project portal | Software to orchestrate the distribution of computational work units (data and applications) to volunteers and have results collected back. It supports diverse applications, including those with large storage or communication requirements, and addresses unsolved issues in biology, medicine, physics, astronomy and computer science. | infrastructure, computing, network, volunteer, data, application, distribution, storage, communication, biology, medicine, physics, astronomy, computer science | has parent organization: University of California at Berkeley; Berkeley; USA | PMID:27547555 | Open source, Free, Available for download, The public can contribute to this resource, The research community can contribute to this resource, Available on Google Play Store, Available on Kindle Store, Available on Amazon App Store | SCR_015896 | Berkeley Open Infrastructure for Network Computing, Berkeley Open Infrastructure for Network Computing (BOINC) | 2026-08-03 09:36:29 | 3 | |||||||
|
redcap-importer Resource Report Resource Website |
redcap-importer (RRID:SCR_016032) | data acquisition software, software resource, software application, data processing software | Software that automates the process of retrieving and converting data to the format of a RedCap table and allows selection of directories and files for import. | automate, process, retrvinig, converting, data, format, research, electronic, data, capture, table, selection, directory, import | is related to: University of California at San Diego; California; USA | NIDA U24 DA041123 | Free, Available for download | SCR_016032 | 2026-08-03 09:36:16 | 0 | |||||||||
|
Bio-tradis Resource Report Resource Website 50+ mentions |
Bio-tradis (RRID:SCR_015993) | TraDIS:Transposon Directed Insertion Sequencing | sequence analysis software, software toolkit, software application, data processing software, data analysis software, software resource | Analysis software for the output from TraDIS (Transposon Directed Insertion Sequencing) analyses of dense transposon mutant libraries. The Bio-Tradis analysis pipeline is implemented as an extensible Perl library which can either be used as is, or as a basis for the development of more advanced analysis tools. | software, tool, analysis, data, sequencing, insertion, transponson, direct, mutant, library, perl, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
Wellcome Trust WT098051; Alexander von Humboldt Stiftung/Foundation ; Medical Research Council G1100100/1 |
PMID:26794317 DOI:10.1093/bioinformatics/btw022 |
Free, Available for download, Freely available | OMICS_11083, biotools:bio-tradis | https://bio.tools/bio-tradis, https://sources.debian.org/src/bio-tradis/ | SCR_015993 | 2026-08-03 09:36:16 | 51 | |||||
|
FIONASITE Resource Report Resource Website |
FIONASITE (RRID:SCR_016012) | data management software, data acquisition software, software application, data processing software, data transfer software, software resource | Software for uploading data to FIONA and capturing MR images and k-space data from medical image systems. It provides a web-interface to automate the data review (image viewer), integrate with the centralized electronic data record for assigning anonymized id's, and forward the data to the central archive. | automate, data, upload, collection, network, appliance, abcd, study | is related to: University of California at San Diego; California; USA | NIDA U24 DA041123 | Free, Available for download | SCR_016014, SCR_016013 | http://qi.ucsd.edu/news-article.php?id=2342&go=newer | SCR_016012 | 2026-08-03 09:36:13 | 0 | |||||||
|
Minimally-Processed-Image-Sharing Resource Report Resource Website |
Minimally-Processed-Image-Sharing (RRID:SCR_016016) | data management software, data distribution software, software application, data processing software, data transfer software, software resource | Software to share ABCD minimally processed data. It uploads minimally-processed MRI data to the NDA ( Non-Disclosure Agreement) ABCD (Adolescent Brain Cognitive Development) repository. | share, data, minimally processed, image, files, fast-track, non-processed, link, store, upload |
is related to: University of California at San Diego; California; USA works with: ABCD Study |
NIDA U24 DA041123 | SCR_016016 | 2026-08-03 09:36:32 | 0 | ||||||||||
|
Microsoft Excel Resource Report Resource Website 10000+ mentions |
Microsoft Excel (RRID:SCR_016137) | software application, data processing software, data analysis software, software resource, data visualization software | Software application with data analysis tools and spreadsheet templates to track and visualize data. It is used to manage and process data. | data, process, manage, analyze, spreadsheet, template, track, visualize, graph |
is related to: XLSTAT is related to: Statcel3 has plug in: OVAL has plug in: easyGV |
Microsoft | Commercially available, Trial available | SCR_016137 | , MS Excel | 2026-08-03 09:36:18 | 81724 | ||||||||
|
Fast-Track-Image-Sharing Resource Report Resource Website |
Fast-Track-Image-Sharing (RRID:SCR_016021) | data management software, software application, data processing software, data transfer software, software resource | Software for sharing the ABCD (Adolescent Brain Cognitive Development) study data on the National Data Archive (NDA). | sharing, tool, study, data, national, archive, abcd, nda, adolescent | is related to: University of California at San Diego; California; USA | NIDA U24 DA041123 | Free, Available for download | SCR_016021 | 2026-08-03 09:36:16 | 0 | |||||||||
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eprime-data-clean Resource Report Resource Website |
eprime-data-clean (RRID:SCR_016020) | data management software, software resource, software application, data processing software | Software to convert E-Prime (software tool for psychology computerized experiment design, data collection, and analysis) generated files to CSV files without errors during conversion. The ABCD project is using E-Prime to run behavioral tests. | convert, data, psychology, computerized, experiment, design, collection, analysis, generate, file, errors, conversion, abcd |
is related to: University of California at San Diego; California; USA works with: ABCD Study |
NIDA U24 DA041123 | Free, Available for download | SCR_016020 | 2026-08-03 09:36:13 | 0 | |||||||||
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geocoding Resource Report Resource Website 10+ mentions |
geocoding (RRID:SCR_016007) | software application, data processing software, data analysis software, data analytics software, software resource | Software that uses a geo-location database to determine individuals' residential environment in Adolescent Brain Cognitive Development (ABCD) study. It performs queries given individuals' residential history in longitude and latitude. | software, data, analysis, geo-location, residential, environment, abcd, study |
has parent organization: University of California at San Diego; California; USA works with: ABCD Study |
NIDA U24 DA041123 | Free, Available for download | SCR_016007 | ABCD geocoding, ABCD geocoding project, geocoding project | 2026-08-03 09:36:13 | 23 | ||||||||
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Gentle Resource Report Resource Website 1+ mentions |
Gentle (RRID:SCR_016127) | sequence analysis software, software toolkit, software application, data processing software, data analysis software, software resource | Software for DNA and amino acid editing, database management, plasmid maps, It can also be used for restriction and ligation, alignments, sequencer data import, calculators, gel image display, PCR, and more. | editing, database, management, plasmid maps, restriction, ligation, alignments, sequence, data, import, calculator, gel, image, display, PCR, cloning, genetic |
is listed by: Debian is listed by: OMICtools has parent organization: University of Cologne; Cologne; Germany |
Free Software Foundation | Free, Available for download | OMICS_18307 | https://sources.debian.org/src/gentle/ | SCR_016127 | GENtle | 2026-08-03 09:36:36 | 6 |
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