Searching the RRID Resource Information Network
Are you sure you want to leave this community? Leaving the community will revoke any permissions you have been granted in this community.
SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
Sim3C Resource Report Resource Website 1+ mentions |
Sim3C (RRID:SCR_015772) | simulation software, software application, software resource | 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 | SciCrunch Registry | 2026-10-17 01:29:01 | 5 | |||||||||
|
StreamPix Resource Report Resource Website 100+ mentions |
StreamPix (RRID:SCR_015773) | data acquisition software, data processing software, image acquisition software, software application, software resource | 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 | SciCrunch Registry | 2026-10-17 01:29:15 | 153 | |||||||||||
|
GeneSys Resource Report Resource Website 500+ mentions |
GeneSys (RRID:SCR_015770) | data acquisition software, data or information resource, data processing software, database, image acquisition software, software application, software resource | 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 | SciCrunch Registry | 2026-10-17 01:29:04 | 745 | |||||||||||
|
Genesis Resource Report Resource Website 1000+ mentions |
Genesis (RRID:SCR_015775) | data analysis software, data processing software, data visualization software, software application, software resource | 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 | SciCrunch Registry | Genesis: Cluster analysis of microarray data | 2026-10-17 01:29:04 | 1029 | ||||||
|
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 acquisition software, data distribution software, data or information resource, data processing software, portal, project portal, software application, software resource | 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 | SciCrunch Registry | Berkeley Open Infrastructure for Network Computing, Berkeley Open Infrastructure for Network Computing (BOINC) | 2026-10-17 01:28:59 | 3 | |||||||
|
Decision Decoding Toolbox Resource Report Resource Website 1+ mentions |
Decision Decoding Toolbox (RRID:SCR_015978) | DDTBOX | data analysis software, data processing software, software application, software resource, software toolkit | 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 | SciCrunch Registry | The Decision Decoding Toolbox (DDTBOX), DDTBOX: Decision Decoding Toolbox | 2026-10-17 01:29:18 | 3 | |||||||||
|
Baitfisher Resource Report Resource Website 1+ mentions |
Baitfisher (RRID:SCR_015985) | alignment software, data processing software, image analysis software, software application, software resource, software toolkit | 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 | SciCrunch Registry | 2026-10-17 01:29:06 | 5 | ||||||
|
Avogadro Resource Report Resource Website 1000+ mentions |
Avogadro (RRID:SCR_015983) | data analysis software, data processing software, data visualization software, software application, software resource, software toolkit | 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 | SciCrunch Registry | 2026-10-17 01:29:19 | 2237 | ||||||
|
redcap-importer Resource Report Resource Website |
redcap-importer (RRID:SCR_016032) | data acquisition software, data processing software, software application, software resource | 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 | SciCrunch Registry | 2026-10-17 01:29:03 | 0 | |||||||||
|
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 | SciCrunch Registry | 2026-10-17 01:29:07 | 0 | |||||||||
|
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 | SciCrunch Registry | 2026-10-17 01:29:00 | 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 | SciCrunch Registry | 2026-10-17 01:29:03 | 56 | |||||
|
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 | SciCrunch Registry | m6ASNP | 2026-10-17 01:29:20 | 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 | SciCrunch Registry | IMAGEN Consortium, IMAGEN Project, IMAGEN Study | 2026-10-17 01:29:00 | 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 | 2026-10-17 01:29:00 | 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 | 2026-10-17 01:29:03 | 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 | 2026-10-17 01:29:19 | 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 | SciCrunch Registry | Normalize FOV, normalizefov | 2026-10-17 01:29:02 | 4 | |||||||||
|
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 | 2026-10-17 01:29:00 | 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 | SciCrunch Registry | 2026-10-17 01:29:03 | 0 |
Can't find your Tool?
We recommend that you click next to the search bar to check some helpful tips on searches and refine your search firstly. Alternatively, please register your tool with the SciCrunch Registry by adding a little information to a web form, logging in will enable users to create a provisional RRID, but it not required to submit.
Welcome to the dkNET Resources search. From here you can search through a compilation of resources used by dkNET and see how data is organized within our community.
You are currently on the Community Resources tab looking through categories and sources that dkNET has compiled. You can navigate through those categories from here or change to a different tab to execute your search through. Each tab gives a different perspective on data.
If you have an account on dkNET then you can log in from here to get additional features in dkNET such as Collections, Saved Searches, and managing Resources.
Here is the search term that is being executed, you can type in anything you want to search for. Some tips to help searching:
If you are logged into dkNET you can add data records to your collections to create custom spreadsheets across multiple sources of data.
Here are the facets that you can filter the data by.
If you have any further questions please check out our FAQs Page to ask questions and see our tutorials. Click this button to view this tutorial again.
The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant U24DK097771.
Email: info_at_ dknet.org
