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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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ABCDreport Resource Report Resource Website |
ABCDreport (RRID:SCR_016030) | data analysis software, data processing software, software application, software resource | Software application as a simple system to review study progress. Used in ABCD study. | system, simple, review, study, progress, development, adolescence, brain, cognitive, report | is related to: University of California at San Diego; California; USA | NIDA U24 DA041123 | Free, Available for download | SCR_016030 | 2026-09-12 12:58:34 | 0 | |||||||||
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Belvu Resource Report Resource Website 10+ mentions |
Belvu (RRID:SCR_015989) | alignment software, data processing software, image analysis software, software application, software resource | Software for multiple sequence alignment viewing, editing and phylogeny. It includes a set of user-configurable modes to color residues used to create high-quality reference alignments. | editing, phylogeny, sequence, alignment, phylogenetic, viewer, multiple, editor, color, residue, reference |
is related to: SEQtools has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
NHGRI U54 HG00455; Wellcome Trust Grant 098051 |
PMID:26801397 | Free, Available for download | SCR_015989 | 2026-09-12 12:58:33 | 18 | ||||||||
|
Bio-tradis Resource Report Resource Website 50+ mentions |
Bio-tradis (RRID:SCR_015993) | TraDIS:Transposon Directed Insertion Sequencing | data analysis software, data processing software, sequence analysis software, software application, software resource, software toolkit | 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 |
Alexander von Humboldt Stiftung/Foundation ; Medical Research Council G1100100/1; Wellcome Trust WT098051 |
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 | 2026-09-12 12:58:33 | 56 | |||||
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m6ASNP: Annotation of genetic variants by m6A function Resource Report Resource Website 1+ mentions |
m6ASNP: Annotation of genetic variants by m6A function (RRID:SCR_016048) | data access protocol, data analysis software, data processing software, data visualization software, software application, software resource, web service | Web server implemented in JAVA and PHP for annotating genetic variants by m6A function. It predicts and annotates N6-methyladenosine (m6A) alterations from genetic variants data such as germline SNPs or cancer somatic mutations. It employs two accurate prediction models for human and mouse using Random Forest algorithm. It conducts a statistical analysis for all the predicted m6A alterations. Provides statistical diagrams and a genome browser to visualize the topology characteristics of predicted m6A alterations. | N6-methyladenosine (m6A), variant annotation, effect prediction, random forest, miclip, m6a, mutant | China Postdoctoral Science Foundation 2017M622864; Fundamental Research Funds for the Central Universities No. 17lgpy106; Guangdong Natural Science Foundation 2014TQ01R387; National Key Research and Development Program 2017YFA0106700; National Natural Science Foundation of China 31771462 |
PMID:29617790 DOI:10.1093/gigascience/giy035 |
Free, Available for download, Freely available | https://github.com/RenLabBioinformatics/m6ASNP | SCR_016048 | m6ASNP | 2026-09-12 12:58:34 | 3 | |||||||
|
IMAGEN Resource Report Resource Website 100+ mentions |
IMAGEN (RRID:SCR_016045) | consortium, data or information resource, organization portal, portal, project portal | Research project examining how biological, psychological, and environmental factors during adolescence may influence brain development and mental health. Using brain imaging and genetics, the project will help develop prevention strategies and improved therapies for mental health disorders in the future., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | adolescence, teen, mental, health, study, brain, development, neurological, prevention, therapy, disorder, psychology | European Commission ; German Federal Ministry of Research & Education (BMBF) ; Medical Research Council ; National Institute for Health Research UK ; National Institute for Health Research US ; National Institute on Drug Abuse ; Swedish Research Council (Vetenskapsrådet) |
PMID:21102431 | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_016045 | IMAGEN Consortium, IMAGEN Project, IMAGEN Study | 2026-09-12 12:58:34 | 158 | ||||||||
|
Barrnap Resource Report Resource Website 500+ mentions |
Barrnap (RRID:SCR_015995) | data analysis software, data processing software, sequence analysis software, software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software to predict the location of ribosomal RNA genes in genomes. It supports bacteria, archaea, mitochondria, and eukaryotes. It takes FASTA DNA sequence as input, writes GFF3 as output, and supports multithreading., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | multithreading, fasta, sequencing, software, predict, location, ribosomal, gene, genome, RNA, prediction, bacteria, archaea, mitochondria, eukaryote, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: OMICtools |
THIS RESOURCE IS NO LONGER IN SERVICE | biotools:barrnap, OMICS_13988 | https://github.com/tseemann/barrnap, https://bio.tools/barrnap, https://sources.debian.org/src/barrnap/ | SCR_015995 | Barrnap: Basic rapid ribosomal RNA predictor | 2026-09-12 12:58:33 | 722 | |||||||
|
CED: Power1401 Resource Report Resource Website 10+ mentions |
CED: Power1401 (RRID:SCR_016040) | instrument resource | Data acquisition interface from Cambridge Electronic Design Limited. Works with Spike2 to provide continuous acquisition tasks. Records waveform data, digital and marker information, and can generate waveform and digital outputs simultaneously for real-time, multi-tasking experiment control. | Cambridge Electronic Design Limited, equipment, hardware, instrument, USEDit |
is listed by: USEDit works with: Spike2 Software |
Restricted | https://drive.google.com/file/d/1fl3Sbk3t-vRgPgDNMBbZQuLSBIdJUPsO/view?usp=drivesdk | SCR_017282 | SCR_016040 | , POWER1401-3 Data Acquisition Interface, Power1401-3A, CED Power1401 3A | 2026-09-12 12:58:34 | 15 | |||||||
|
BMap Resource Report Resource Website 10+ mentions |
BMap (RRID:SCR_016044) | alignment software, data analysis software, data processing software, image analysis software, sequence analysis software, software application, software resource, source code | Software that maps whole-genome and targeted bisulfite sequence reads to reference genomes. It is especially useful for reads obtained using post-bisulfite adaptor tagging (PBAT)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | mapper, whole-genome, bisulfite, sequencing, post-bisulfite, adaptor, tagging, pbat, reads, mapping | PMID:22649061 | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_016044 | 2026-09-12 12:58:34 | 29 | ||||||||||
|
NeuroImage Field-of-View Normalization Tool Resource Report Resource Website 1+ mentions |
NeuroImage Field-of-View Normalization Tool (RRID:SCR_015957) | data or information resource, portal, topical portal | FSoftware for field-of-view normalization to minimize mismatch in different subjects' images. It aids that streamline analysis of large-scale brain MRI datasets. | normalization, fov, field, view, filed of view, brain, mri, magnetic, resonance, neuroimaging, imaging, atlas | DOI:10.1007/s12021-018-9359-z | Free, Available for download | SCR_015957 | Normalize FOV, normalizefov | 2026-09-12 12:58:32 | 4 | |||||||||
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FIONASITE Resource Report Resource Website 1+ mentions |
FIONASITE (RRID:SCR_016012) | data acquisition software, data management software, data processing software, data transfer software, software application, 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 | 2026-09-12 12:58:34 | 1 | |||||||
|
Minimally-Processed-Image-Sharing Resource Report Resource Website |
Minimally-Processed-Image-Sharing (RRID:SCR_016016) | data distribution software, data management software, data processing software, data transfer software, software application, 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 | 2026-09-12 12:58:34 | 0 | ||||||||||
|
enroll Resource Report Resource Website 10+ mentions |
enroll (RRID:SCR_016011) | data management software, data processing software, data storage software, software application, software resource | Software which provides a framework for the secure storage of Personal Identifyable Information (PII) for a multi-site longitudinal project centrally. Used in Adolescent Brain Cognitive Development (ABCD) Study. | database, secure, framework, multisite, personal, identifiable, information, adolescence, abcd |
has parent organization: University of California at San Diego; California; USA works with: ABCD Study |
NIDA U24 DA041123 | Free, Available for download | SCR_016011 | 2026-09-12 12:58:33 | 13 | |||||||||
|
Aegean Resource Report Resource Website 1+ mentions |
Aegean (RRID:SCR_015965) | data analysis software, data processing software, sequence analysis software, software application, software resource, software toolkit | Software toolkit for the analysis and evaluation of genome annotations. The toolkit includes a variety of analysis programs, e.g. for comparing distinct sets of gene structure annotations (ParsEval), computation of gene loci (LocusPocus) and more. | genome, evaluation, annotation, structure, loci |
is listed by: Debian is listed by: OMICtools |
National Science Foundation 1126267 | PMID:22852583 | Free, Available for download, Freely available, | OMICS_19721 | https://github.com/BrendelGroup/AEGeAn, https://sources.debian.org/src/aegean/ | SCR_015965 | AEGeAn: analysis and evaluation of genome annotations, Aegean Toolkit | 2026-09-12 12:58:33 | 9 | |||||
|
Aevol Resource Report Resource Website 1+ mentions |
Aevol (RRID:SCR_015966) | simulation software, software application, software resource | Simulation software for experimental evolution of microorganisms. Aevol is a digital genetics model for the study of structural variations of the genome (e.g. number of genes, synteny, proportion of coding sequences). | software, genetic, model, simulation, evolution, microorganism, coding, sequence, algorithm | Agence Nationale de la Recherche ANR-10-BLAN-1724; INSERM |
PMID:24278000 | Free, Available for download, Tutorial available | SCR_015966 | 2026-09-12 12:58:33 | 3 | |||||||||
|
andi Resource Report Resource Website 10+ mentions |
andi (RRID:SCR_015971) | algorithm resource, alignment software, data processing software, image analysis software, software application, software resource | Software tool for rapidly computing and estimating evolutionary distance between closely related genomes. Because andi does not compute full alignments it scales even up to thousands of bacterial genomes. | algorithm, computing, estimate, analysis, genome, alignment, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools |
Deutsche Forschungsgemeinschaft Pf672/3-1 | PMID:25504847 | Free, Freely available, Available for download | OMICS_09287, biotools:andi | https://bio.tools/andi, https://sources.debian.org/src/andi/ | SCR_015971 | 2026-09-12 12:58:33 | 41 | ||||||
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tick-tock Resource Report Resource Website |
tick-tock (RRID:SCR_016023) | data processing software, data visualization software, software application, software resource, web application | Software for research study observation that visualizes study related events per day. Any event generating function sends a 'tick' event to this application which will be visible on this applications web-interface. | application, research, study, visualization, event, web, interface, observation, abcd |
is related to: University of California at San Diego; California; USA works with: ABCD Study |
NIDA U24 DA041123 | Free, Available for download | SCR_016023 | 2026-09-12 12:58:34 | 0 | |||||||||
|
Anfo Resource Report Resource Website 1+ mentions |
Anfo (RRID:SCR_015972) | alignment software, data processing software, image analysis software, software application, software resource | Software for short read alignment and mapping of sequencing reads where the DNA sequence is somehow modified and/or there is more divergence between sample and reference than what fast mappers will handle. | alignment, program, mapper, software, sequence, DNA, ancient dna, bisulphite, treatment | Free Software Foundation ; Inc. |
Free, Available for download, Freely available | SCR_015973 | SCR_015972 | Anfo Short Read Aligner/Mapper | 2026-09-12 12:58:33 | 8 | ||||||||
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FIONA-protocol-compliance Resource Report Resource Website |
FIONA-protocol-compliance (RRID:SCR_016027) | data analysis software, data processing software, software application, software resource | Software that contains multiple sequential lines of MATLAB commands and function calls for numerical computing for ABCD study protocol compliance. | application, multiple, sequential, lines, commands, function, numerical, computing, protocol, compliance | is related to: University of California at San Diego; California; USA | NIDA U24 DA041123 | Free, Available for download | SCR_016027 | 2026-09-12 12:58:34 | 0 | |||||||||
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Fast-Track-Image-Sharing Resource Report Resource Website |
Fast-Track-Image-Sharing (RRID:SCR_016021) | data management software, data processing software, data transfer software, software application, 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 | 2026-09-12 12:58:34 | 0 | |||||||||
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eprime-data-clean Resource Report Resource Website |
eprime-data-clean (RRID:SCR_016020) | data management software, data processing software, software application, software resource | 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 | 2026-09-12 12:58:34 | 0 |
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The data sets included in this resource are published in Kravitz et al, 2012. Distinct roles for direct and indirect pathway striatal neurons in reinforcement (Nat. Neurosci).
