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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Olympus IX-53 Resource Report Resource Website 1+ mentions |
Olympus IX-53 (RRID:SCR_015801) | IX-53 | resource | Equipment that is a microscope for routine inverted microscopic analysis. Its features include pre-centered phase contrast, relief contrast, and UIS2 DIC optics for visualization across all magnifications for both thin and thick specimens. | microscope, inverted microscope, routine inverted microscopic analysis, phase contrast, relief contrast, uis2 dic optic, hardware, instrument, equipment | is provided by: Olympus | Commercially available, Available for purchase | SCR_015801 | IX53, IX53 Inverted Microscope, Olympus IX53 Inverted Microscope | 2026-08-08 12:00:42 | 3 | ||||||||
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UK Brain Expression Consortium Resource Report Resource Website 1+ mentions |
UK Brain Expression Consortium (RRID:SCR_015889) | UKBEC | data or information resource, portal, organization portal, consortium | Consortium studying the regulation and alternative splicing of gene expression in multiple tissues from human brains. The UKBEC dataset comprises of brains from individuals free of neurodegenerative disorders. | neurodegenerative, brain, disorder, mrna, dna, eqtl, snp, gene, visualization, expression | is parent organization of: Braineac | SCR_015889 | 2026-08-08 12:00:45 | 3 | ||||||||||
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Sequence Detector System Resource Report Resource Website 1+ mentions |
Sequence Detector System (RRID:SCR_015806) | SDS | sequence analysis software, software resource, software application, data analysis software, data processing software | Software for high-throughput gene expression and genotyping analysis for use with the Applied Biosystems® 7900HT Fast Real Time PCR System. It features automation software tools to fully automate high-throughput applications for gene expression and SNP genotyping. | sequence detection, gene expression, genotype analysis, snp, automation | Commercially available, Available for purchase | SCR_015806 | Sequence Detection System (SDS), Sequence Detection System (SDS) Software | 2026-08-08 12:00:42 | 6 | |||||||||
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NanoDrop 3300 Fluorospectrometer Resource Report Resource Website 100+ mentions |
NanoDrop 3300 Fluorospectrometer (RRID:SCR_015804) | data or information resource, portal, topical portal | Fluorospectrometer for broad spectrum fluorescence analysis. It uses as little as 1 μL of sample volume and lowers the mass detection limit more than an order of magnitude. | spectrophotometer, fluorospectrometer, broad spectrum fluorescence analysis, mass detection, spectrometry | Commercially available, Available for purchase | SCR_015804 | NanoDrop 3300, NanoDrop™ 3300, NanoDrop™ 3300 Fluorospectrometer | 2026-08-08 12:00:44 | 481 | ||||||||||
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Thermo Fisher: StepOnePlus Real-Time PCR System Resource Report Resource Website 50+ mentions |
Thermo Fisher: StepOnePlus Real-Time PCR System (RRID:SCR_015805) | instrument resource, data acquisition software, software resource, software application, data processing software | Equipment and software system that is a real-time thermal cycler for intuitive data analysis of polymerase chain reactions. It comes with analysis software, instrument control software, and a LED-based 4-color optical recording feature. | image acquisition software, genotype, real time pcr, qPCR, thermal cycler, hardware, pcr, polymerase chain reaction, instrument, equipment | Commercially available, Available for purchase, Runs on Windows | SCR_015805 | StepOnePlus, StepOnePlus™ Real-Time PCR System | 2026-08-08 12:00:26 | 58 | ||||||||||
|
Sim3C Resource Report Resource Website 1+ mentions |
Sim3C (RRID:SCR_015772) | software resource, software application, simulation software | Software for read-pair simulation of 3C-based sequencing methodologies (HiC, Meta3C, DNase-HiC). Sim3C's potential applications include addressing questions directed at the spatial organization of DNA in samples of eukaryotic tissue, single cells, and microbial communities. | hic, simulation, dna sequencing, python, 3c, read-pair simulation, chromosome conformation capture | Australian Research Council LP150100912; Education Investment Fund (EIF) ; National Collaborative Research Infrastructure Strategy (NCRIS) |
Free, Available for download | https://zenodo.org/badge/latestdoi/85548752 | SCR_015772 | 2026-08-08 12:00:26 | 5 | |||||||||
|
StreamPix Resource Report Resource Website 100+ mentions |
StreamPix (RRID:SCR_015773) | image acquisition software, data acquisition software, software resource, software application, data processing software | Software for digital video camera recording that allows users to control and acquire dadta from multiple cameras simultaneously in a singleuser interface. StreamPix provides a complete management console for cameras, simplifying the setup, control and acquisition from any number and type of camera. | camera, digital camera, recording software, video data | Commercially available, Demo available, Tutorial available | SCR_015773 | 2026-08-08 12:00:41 | 153 | |||||||||||
|
GeneSys Resource Report Resource Website 500+ mentions |
GeneSys (RRID:SCR_015770) | image acquisition software, data or information resource, data acquisition software, software resource, software application, database, data processing software | Imaging software that works with G:BOX Chemi and PXi imaging systems to automatically or manually capture images. GeneSys also includes a database containing information about applications such as fluorescence, chemiluminescence and chemifluorescence. | image capture, imaging software, gel, blot, fluorescence, luminescence, camera, camera setting control, FASEB list | Commercially available, Tutorial available | SCR_015770 | 2026-08-08 12:00:44 | 745 | |||||||||||
|
Genesis Resource Report Resource Website 1000+ mentions |
Genesis (RRID:SCR_015775) | software resource, software application, data analysis software, data visualization software, data processing software | Software for cluster analysis of microarray data. Genesis is a platform independent Java package of tools to simultaneously visualize and analyze a whole set of gene expression experiments. | cluster analysis, microarray data, java, gene expression, visualization, analysis, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: SoftCite |
PMID:11836235 | Free for academic use, Free for non-profits, Available for download, Runs on Windows, Runs on Mac OS, Runs on Linux | biotools:genesis_microarray | https://bio.tools/genesis_microarray | SCR_015775 | Genesis: Cluster analysis of microarray data | 2026-08-08 12:00:26 | 1029 | ||||||
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BOINC - Berkeley Open Infrastructure for Network Computing Resource Report Resource Website 1+ mentions |
BOINC - Berkeley Open Infrastructure for Network Computing (RRID:SCR_015896) | BOINC | data or information resource, data acquisition software, software resource, software application, data distribution software, project portal, portal, data processing software | 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) | 2026-08-08 12:00:45 | 3 | |||||||
|
Decision Decoding Toolbox Resource Report Resource Website 1+ mentions |
Decision Decoding Toolbox (RRID:SCR_015978) | DDTBOX | software toolkit, software resource, software application, data analysis software, data processing software | Software toolkit for multivariate pattern analysis (MVPA) of event-related potentials. This software is written in MATLAB. | erp, event, related, potential, multivariate, analysis, pattern, matlab, mvpa | Free, Available for download | SCR_015978 | The Decision Decoding Toolbox (DDTBOX), DDTBOX: Decision Decoding Toolbox | 2026-08-08 12:00:47 | 3 | |||||||||
|
Baitfisher Resource Report Resource Website 1+ mentions |
Baitfisher (RRID:SCR_015985) | software toolkit, image analysis software, software resource, software application, alignment software, data processing software | Software toolkit for multispecies target DNA enrichment probe design. It consists of two programs: BaitFisher and BaitFilter, which are designed to construct hybrid enrichment baits for multiple sequence alignments or annotated features in multiple sequence alignments. | software, package, multispecies, comparative, genomics, hybrid, enrichment, DNA, probe, design, sequence, alignments |
is listed by: Debian is listed by: OMICtools |
German Research Foundation (DFG) OH81/9-1; NI 1387/1-1; Spanish Ministry of Science and Education (MEC) RYC-2014-15615 |
PMID:27009209 DOI:10.1093/molbev/msw056 |
Free, Available for download | OMICS_11740 | https://sources.debian.org/src/ballview/ | SCR_015985 | 2026-08-08 12:00:47 | 5 | ||||||
|
Avogadro Resource Report Resource Website 1000+ mentions |
Avogadro (RRID:SCR_015983) | software toolkit, software resource, software application, data analysis software, data visualization software, data processing software | Software for semantic chemical editing, visualization, and analysis. It is designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. | semantic, optimization, crystallography, chemical, editor, visualization, analysis, molecular, modeling, drug, design, biomolecule, simulation, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: OMICtools |
Engineering Research Development Center W912HZ-11-P-0019; NSF DMR-1005413 |
PMID:22889332 DOI:10.1186/1758-2946-4-17 |
Open source, Free, Free to download | OMICS_04967, biotools:avogadro | http://avogadro.openmolecules.net/, https://github.com/avogadro, https://bio.tools/avogadro, https://sources.debian.org/src/axe-demultiplexer/ | SCR_015983 | 2026-08-08 12:00:27 | 2237 | ||||||
|
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 | 2026-08-08 12:00:46 | 0 | |||||||||
|
ABCDreport Resource Report Resource Website |
ABCDreport (RRID:SCR_016030) | software resource, software application, data analysis software, data processing software | 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 | 2026-08-08 12:00:28 | 0 | |||||||||
|
Belvu Resource Report Resource Website 10+ mentions |
Belvu (RRID:SCR_015989) | image analysis software, software resource, software application, alignment software, data processing software | 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 |
Wellcome Trust Grant 098051; NHGRI U54 HG00455 |
PMID:26801397 | Free, Available for download | SCR_015989 | 2026-08-08 12:00:47 | 18 | ||||||||
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Bio-tradis Resource Report Resource Website 50+ mentions |
Bio-tradis (RRID:SCR_015993) | TraDIS:Transposon Directed Insertion Sequencing | sequence analysis software, software toolkit, software resource, software application, data analysis software, data processing software | 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 | 2026-08-08 12:00:45 | 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) | web service, software resource, data access protocol, software application, data analysis software, data visualization software, data processing software | 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 | National Key Research and Development Program 2017YFA0106700; National Natural Science Foundation of China 31771462; China Postdoctoral Science Foundation 2017M622864; Fundamental Research Funds for the Central Universities No. 17lgpy106; Guangdong Natural Science Foundation 2014TQ01R387 |
PMID:29617790 DOI:10.1093/gigascience/giy035 |
Free, Available for download, Freely available | https://github.com/RenLabBioinformatics/m6ASNP | SCR_016048 | m6ASNP | 2026-08-08 12:00:46 | 3 | |||||||
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IMAGEN Resource Report Resource Website 100+ mentions |
IMAGEN (RRID:SCR_016045) | data or information resource, consortium, project portal, portal, organization 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 ; Medical Research Council ; National Institute for Health Research UK ; Swedish Research Council (Vetenskapsrådet) ; German Federal Ministry of Research & Education (BMBF) ; National Institute for Health Research US ; National Institute on Drug Abuse |
PMID:21102431 | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_016045 | IMAGEN Consortium, IMAGEN Project, IMAGEN Study | 2026-08-08 12:00:46 | 158 | ||||||||
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Barrnap Resource Report Resource Website 500+ mentions |
Barrnap (RRID:SCR_015995) | 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 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 | 2026-08-08 12:00:27 | 722 |
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