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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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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 | 2026-08-08 12:00:47 | 0 | |||||||||
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MicrobeTracker Resource Report Resource Website 100+ mentions |
MicrobeTracker (RRID:SCR_015939) | software toolkit, image analysis software, software resource, software application, data processing software | THIS RESOURCE IS NO LONGER IN SERVICE, documented May 10, 2017. A pilot effort that has developed a centralized, web-based biospecimen locator that presents biospecimens collected and stored at participating Arizona hospitals and biospecimen banks, which are available for acquisition and use by researchers. Researchers may use this site to browse, search and request biospecimens to use in qualified studies. The development of the ABL was guided by the Arizona Biospecimen Consortium (ABC), a consortium of hospitals and medical centers in the Phoenix area, and is now being piloted by this Consortium under the direction of ABRC. You may browse by type (cells, fluid, molecular, tissue) or disease. Common data elements decided by the ABC Standards Committee, based on data elements on the National Cancer Institute''s (NCI''s) Common Biorepository Model (CBM), are displayed. These describe the minimum set of data elements that the NCI determined were most important for a researcher to see about a biospecimen. The ABL currently does not display information on whether or not clinical data is available to accompany the biospecimens. However, a requester has the ability to solicit clinical data in the request. Once a request is approved, the biospecimen provider will contact the requester to discuss the request (and the requester''s questions) before finalizing the invoice and shipment. The ABL is available to the public to browse. In order to request biospecimens from the ABL, the researcher will be required to submit the requested required information. Upon submission of the information, shipment of the requested biospecimen(s) will be dependent on the scientific and institutional review approval. Account required. Registration is open to everyone. Software for bacterial microscopy image analysis. It is designed to detect and outline bacterial cells in microscopy images and to analyze fluorescence signal inside them. | microbe, tracking, tracker, matlab, microscopy, microbiology, bacteria, cell, cell imaging, imaging, image, analysis |
uses: MATLAB requires: MATLAB |
SCR_015939 | 2026-08-08 12:00:46 | 119 | |||||||||||
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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 | 2026-08-08 12:00:28 | 0 | |||||||||
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Piggy Resource Report Resource Website 10+ mentions |
Piggy (RRID:SCR_015941) | software resource, software application, data analysis software, data processing software | Pipeline for analyzing intergenic regions in bacteria. It is designed to be used in conjunction with Roary (https://github.com/sanger-pathogens/Roary). | intergenic, region, bacterial, analysis, gene, genome, assembly | Medical Research Council | Free, Available for download | SCR_015941 | 2026-08-08 12:00:27 | 32 | ||||||||||
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Feeding Experimentation Device project Resource Report Resource Website 1+ mentions |
Feeding Experimentation Device project (RRID:SCR_015942) | FED | data or information resource, portal, topical portal | Flexible open-source device for measuring feeding behavior. FED measures food intake in mice. It is battery powered and designed to be used in rodent colony caging.Home cage-compatible feeding system that measures food intake with high accuracy and temporal resolution. FED offers alternative to commercial feeders, with convenience of use in tradition colony rack caging. | Feeding, food intake, optogenetic, behavioral data analysis, data analysis software, behavior apparatus, behavior rig, reward delivery, behavior measurement, homecage, Instrument, OpenBehavior |
is listed by: OpenBehavior has parent organization: Washington University in St. Louis; Missouri; USA |
NIH | PMID:27060385 | Commercially available | https://github.com/KravitzLab/FED1, https://edspace.american.edu/openbehavior/project/feeding-experimentation-device/, https://hackaday.io/project/72964-feeding-experimentation-device-fed-20 | SCR_015942 | , FED1, FED2, Feeding Experimentation Device system, Feeding Experimentation Device | 2026-08-08 12:00:44 | 1 | |||||
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DISULFIND Resource Report Resource Website 50+ mentions |
DISULFIND (RRID:SCR_016072) | Disulfinder | sequence analysis software, software resource, software application, data analysis software, data processing software | 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 |
EU STREP APrIL II contract no. FP6-508861; EU NoE BIOPATTERN contract no. FP6-508803; Embark Fellowship from the Irish Research Council for Science ; Engineering and Technology |
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 | Cysteines Disulfide Bonding State and Connectivity Predictor | 2026-08-08 12:00:28 | 71 | ||||
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Boutiques Resource Report Resource Website 1+ mentions |
Boutiques (RRID:SCR_016073) | software toolkit, software resource, software application, software development tool, 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 | Boutiques Tool, Boutiques Python Tool | 2026-08-08 12:00:47 | 3 | ||||||||||
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DeepNano Resource Report Resource Website 1+ mentions |
DeepNano (RRID:SCR_016070) | sequence analysis software, software resource, software application, data analysis software, data processing software | 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 |
VEGA 1/0684/16 (BB); VEGA 1/0719/14 (TV); Slovak Research and Development Agency APVV-14-0253; NVIDIA Corporation |
PMID:28582401 | Free, Available for download | OMICS_14561 | http://compbio.fmph.uniba.sk/deepnano/, https://sources.debian.org/src/deepnano/ | SCR_016070 | DeepNano: Deep recurrent neural networks for base calling in MinION nanopore reads, DeepNano: alternative basecaller for MinION reads | 2026-08-08 12:00:47 | 5 | |||||
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statsmodel Resource Report Resource Website 100+ mentions |
statsmodel (RRID:SCR_016074) | software resource, software application, data analysis software, data processing software | Statistical software that provides classes and functions for the estimation of many different models, as well as for conducting statistical tests, and statistical data exploration. The results are tested against existing statistical packages to ensure that they are correct. http://conference.scipy.org/proceedings/scipy2010/seabold.html | python, statistic, estimate, econometric, model, library, class, function, r | Open source, Available for download | SCR_016074 | Statsmodels: Econometric and Statistical Modeling with Python | 2026-08-08 12:00:48 | 253 | ||||||||||
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Gblocks Resource Report Resource Website 1000+ mentions |
Gblocks (RRID:SCR_015945) | web application, standalone software, software resource, software application | Software that eliminates poorly aligned positions and divergent regions of a DNA or protein alignment so that it becomes more suitable for phylogenetic analysis., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | position, dna, protein, align, alignment, phylogenetic, analysis, block, ansi c, deletion, removal | is listed by: SoftCite | Fundación BBVA ; Plan Nacional de Investigación Científica BIO2002-04426-C02-02; Desarrollo e Innovación Tecnológica |
PMID:10742046 PMID:17654362 |
THIS RESOURCE IS NO LONGER IN SERVICE | SCR_015945 | 2026-08-08 12:00:44 | 2043 | ||||||||
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TreeDyn Resource Report Resource Website 100+ mentions |
TreeDyn (RRID:SCR_015946) | software resource, software application, data visualization software, data processing software | Visualization software that links unique leaf labels to lists of variables/values pairs of annotations (meta-information), independently of the tree topologies, remaining fully compatible with the basic newick format. These relationships are used by dynamic graphics operators, information visualization methods like Projection, Localization, Labelization, Reflection allowing an interaction from annotations to trees, from trees to annotations and from trees to trees through annotations., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | tree, variable, annotation, metainfo, newick, topology, graphic, operator, projection, localization, reflection, leaf, label, bio.tools |
is listed by: bio.tools is listed by: Debian |
THIS RESOURCE IS NO LONGER IN SERVICE | biotools:treedyn | https://bio.tools/treedyn | SCR_015946 | 2026-08-08 12:00:46 | 357 | ||||||||
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Bpod Resource Report Resource Website 10+ mentions |
Bpod (RRID:SCR_015943) | software resource | Software for a measurement and control system for behavior research, most often used to implement operant (Go/NoGo, 2AFC) tasks. This software controls a hierarchy of hardware modules, each powered by an Arduino-programmable microcontroller. | sanworks, rodent, behavior, experiment, control, software, hardware, arduino, measurement | is listed by: OpenBehavior | Open source, Free, Available for download | https://github.com/sanworks/Bpod | SCR_015943 | 2026-08-08 12:00:46 | 42 | |||||||||
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National Gene Vector Laboratories Resource Report Resource Website 1+ mentions |
National Gene Vector Laboratories (RRID:SCR_015944) | NGVL | data or information resource, portal, topical portal | The National Gene Vector Laboratories (NGVL) was established as a cooperative national effort to produce and distribute vectors for human gene transfer studies. | gene, therapy, manufacturing, toxicology, human, research, vector, transfer, study | is used by: Adobe Illustrator | NIH | SCR_015944 | 2026-08-08 12:00:27 | 2 | |||||||||
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geocoding Resource Report Resource Website 10+ mentions |
geocoding (RRID:SCR_016007) | software resource, software application, data analysis software, data analytics software, data processing software | 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 | 2026-08-08 12:00:47 | 23 | ||||||||
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SC3 Resource Report Resource Website 10+ mentions |
SC3 (RRID:SCR_015953) | sequence analysis software, software resource, software application, data analysis software, data processing software | Software tool for the unsupervised clustering of cells from single cell RNA-Seq experiments. SC3 is capable of identifying subclones from the transcriptomes of neoplastic cells collected from patients. | scRNA-seq, interactive, cluster, clustering, cell, single, rna, rnaseq, bio.tools |
is listed by: Debian is listed by: bio.tools |
Wellcome Trust 104710/Z/14/Z; Belgian Network DYSCO ; FRS-FNRS ; Belgian State Science Policy Office ; ARC (Action de Recherche Concerte) ; Wallonia-Brussels Federation ; EPSRC EP/N014529/1; Sanger Institute ; University of Edinburgh ; Bloodwise 13003; MRC ; Kay Kendall Leukaemia Fund ; Cambridge NIHR Biomedical Research Center ; Cambridge Experimental Cancer Medicine Centre ; Leukemia and Lymphoma Society of America 07037 |
PMID:28346451 | Free, Available for download | biotools:sc3 | https://bio.tools/sc3 | SCR_015953 | SC3 package, Single-Cell Consensus Clustering | 2026-08-08 12:00:46 | 23 | |||||
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Chiron Resource Report Resource Website 10+ mentions |
Chiron (RRID:SCR_015950) | software resource, software application, data analysis software, time-series analysis software, 1d time-series analysis software, data processing software | Software basecaller for Oxford Nanopore Technologies' sequencers. | oxford, nanopore, deep, learning, basecaller, basecalling | Institute for Molecular Bioscience Centre 610246; ARC Future Fellowship FT110100972; Westpac Bicentennial Foundation |
DOI:10.1101/179531 | Free, Available for download | SCR_015950 | 2026-08-08 12:00:44 | 25 | |||||||||
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HermiT OWL Reasoner Resource Report Resource Website 10+ mentions |
HermiT OWL Reasoner (RRID:SCR_016006) | software resource, software application, algorithm resource, data analysis software, data processing software | Algorithm for a reasoner for ontologies written using the Web Ontology Language (OWL). Given an OWL file, HermiT can determine whether or not the ontology is consistent, identify subsumption relationships between classes, and much more. | web, ontology, language, reasoner, class, algorithm, terminology, term, semantic, hypertableau | Open source, Free, Available for download | SCR_016006 | 2026-08-08 12:00:46 | 13 | |||||||||||
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Cassiopee Resource Report Resource Website |
Cassiopee (RRID:SCR_016056) | sequence analysis software, software resource, software application, data analysis software, data processing software | Software to scan an input genomic sequence (dna/rna/protein). It searchs for a subsequence that has an exact match, substitutions (Hamming distance), and/or insertion/deletions with supporting alphabet ambiguity. | genomic, sequence, DNA, RNA, protein, scan, subsequence, search, match, substitution, distance, Hamming, insertion, deletion |
is listed by: Debian is listed by: OMICtools has parent organization: Durham University; Durham; England |
Free, Available for download | OMICS_19794 | https://sources.debian.org/src/cassiopee/ | SCR_016056 | cassiopee-c | 2026-08-08 12:00:47 | 0 | |||||||
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Cdbfasta Resource Report Resource Website |
Cdbfasta (RRID:SCR_016057) | CDB | data compression software, software toolkit, software resource, software application, data transfer software, data processing software | Software tool for indexing and retrieval of nucleotide sequences from FASTA (DNA and protein sequence alignment software) record databases. It has the option to compress data records. | index, retrieval, nucleotide, sequence, fasta, database, multi file, compress, record |
is listed by: Debian is listed by: OMICtools has parent organization: Carnegie Mellon University; Pennsylvania; USA has parent organization: University of Pittsburgh; Pennsylvania; USA |
The Free Software Foundation (FSF) | Free, Available for download | OMICS_19793 | https://github.com/gpertea/cdbfasta, https://sources.debian.org/src/cdbfasta/ | SCR_016057 | Constant DataBase | 2026-08-08 12:00:48 | 0 | |||||
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Stimfit Resource Report Resource Website 10+ mentions |
Stimfit (RRID:SCR_016050) | software resource, software application, data analysis software, data processing software | Software for viewing and analyzing electrophysiological data. It features an embedded Python shell that allows you to extend the program functionality by using numerical libraries such as NumPy and SciPy. | electrophysiology, python, numpy, scipy, numerical, library, stimulus, analysis |
uses: NumPy uses: SciPy |
European Research Council ; Wellcome Trust ; Gatsby Charitable Foundation |
PMID:24600389 | Free, Available for download | SCR_016050 | 2026-08-08 12:00:28 | 41 |
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