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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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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 | SciCrunch Registry | IMAGEN Consortium, IMAGEN Project, IMAGEN Study | 2026-11-07 11:58:09 | 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 | SciCrunch Registry | Barrnap: Basic rapid ribosomal RNA predictor | 2026-11-07 11:58:08 | 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 | SciCrunch Registry | , POWER1401-3 Data Acquisition Interface, Power1401-3A, CED Power1401 3A | 2026-11-07 11:58:31 | 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 | SciCrunch Registry | 2026-11-07 11:58:38 | 29 | ||||||||||
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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 | SciCrunch Registry | Normalize FOV, normalizefov | 2026-11-07 11:58:30 | 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 | SciCrunch Registry | 2026-11-07 11:58:09 | 1 | |||||||
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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 | SciCrunch Registry | 2026-11-07 11:58:31 | 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 | SciCrunch Registry | 2026-11-07 11:58:38 | 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 | SciCrunch Registry | AEGeAn: analysis and evaluation of genome annotations, Aegean Toolkit | 2026-11-07 11:58:18 | 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 | SciCrunch Registry | 2026-11-07 11:58:30 | 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 | SciCrunch Registry | 2026-11-07 11:58:18 | 41 | ||||||
|
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 | SciCrunch Registry | 2026-11-07 11:58:09 | 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 | SciCrunch Registry | Anfo Short Read Aligner/Mapper | 2026-11-07 11:58:30 | 8 | ||||||||
|
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 | SciCrunch Registry | 2026-11-07 11:58:38 | 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 | SciCrunch Registry | 2026-11-07 11:58:38 | 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 | SciCrunch Registry | 2026-11-07 11:58:31 | 0 | |||||||||
|
Durham University; Durham; England Resource Report Resource Website |
Durham University; Durham; England (RRID:SCR_016079) | university | University in Durham, England. | university, durham, england |
is related to: VasoTracker is parent organization of: Cassiopee |
ISNI:0000 0000 8700 0572, grid.8250.f, Wikidata:Q16848806, Crossref funder ID:501100001314 | https://ror.org/01v29qb04 | SCR_016079 | SciCrunch Registry | 2026-11-07 11:58:32 | 0 | |||||||||
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DISULFIND Resource Report Resource Website 50+ mentions |
DISULFIND (RRID:SCR_016072) | Disulfinder | 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 for predicting the disulfide bonding state of cysteines and their disulfide connectivity, starting from a protein sequence alone and may be useful in other genomic annotation tasks. | predict, disulfide, bonding, state, cysteine, protein, sequence, genomic, annotation, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools has parent organization: University of Florence; Florence; Italy |
Embark Fellowship from the Irish Research Council for Science ; Engineering and Technology ; EU NoE BIOPATTERN contract no. FP6-508803; EU STREP APrIL II contract no. FP6-508861 |
PMID:16844986 DOI:10.1093/nar/gkl266 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_04214, biotools:disulfind | https://bio.tools/disulfind, https://sources.debian.org/src/disulfinder/ | SCR_016072 | SciCrunch Registry | Cysteines Disulfide Bonding State and Connectivity Predictor | 2026-11-07 11:58:10 | 71 | ||||
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Boutiques Resource Report Resource Website 1+ mentions |
Boutiques (RRID:SCR_016073) | software application, software development tool, software resource, software toolkit, systems interoperability software | Software toolkit for a cross-platform JSON-framework for describing command-line tools and their parameters. It is accompanied by a Python tool which facilitates the creation, validation, simulation, execution, publishing, evaluation, and testing of tools described in this format. | json, standardization, interoperability, software, command, line, software containers | Free, Available for download | SCR_016073 | SciCrunch Registry | Boutiques Tool, Boutiques Python Tool | 2026-11-07 11:58:20 | 3 | ||||||||||
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DeepNano Resource Report Resource Website 1+ mentions |
DeepNano (RRID:SCR_016070) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software for an alternative basecaller for DNA base calling in the portable Oxford Nanopore MinION sequencing device, based on deep recurrent neural networks. Used to improve base calling accuracy and reduce sequencing error rate. | DNA, basecaller, Oxford Nanopore MinON read, sequencing, device, deep, recurrent, neural, network, accuracy, reduce, error |
is listed by: Debian is listed by: OMICtools has parent organization: Comenius University; Bratislava; Slovakia |
NVIDIA Corporation ; Slovak Research and Development Agency APVV-14-0253; VEGA 1/0684/16 (BB); VEGA 1/0719/14 (TV) |
PMID:28582401 | Free, Available for download | OMICS_14561 | http://compbio.fmph.uniba.sk/deepnano/, https://sources.debian.org/src/deepnano/ | SCR_016070 | SciCrunch Registry | DeepNano: Deep recurrent neural networks for base calling in MinION nanopore reads, DeepNano: alternative basecaller for MinION reads | 2026-11-07 11:58:32 | 5 |
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