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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 | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Canu Resource Report Resource Website 1000+ mentions |
Canu (RRID:SCR_015880) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software for scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. Canu is a fork of the Celera Assembler and is designed for high-noise single-molecule sequencing (such as the PacBio RS II/Sequel or Oxford Nanopore MinION). | long-read, assembly, k-mer, weighting, repeat separation, adaptive, pacbio, single-molecule, sequencing, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: OMICtools is related to: Celera assembler |
National Human Genome Research Institute ; National Science Foundation NSF IOS-1237993; US Department of Homeland Security (DHS) HSHQDC-07-C-00020 |
PMID:28298431 DOI:10.1101/071282 |
Free, Available for download | OMICS_14592, biotools:canu | http://canu.readthedocs.io/en/latest/, https://bio.tools/canu, https://sources.debian.org/src/canu/ | SCR_015880 | SciCrunch Registry | 2026-11-07 11:58:07 | 2451 | ||||||
|
eHistology Resource Report Resource Website 1+ mentions |
eHistology (RRID:SCR_015887) | atlas, data or information resource, data repository, image repository, service resource, storage service resource | Image repository that allows researchers to interactively explore a collection of cellular-resolution colour histology images detailing mouse development. The original histological sections have been re-digitised at high resolution, in colour and in collaboration with Elsevier, the eHistology Atlas provides the annotations as presented in the original printed version. | histology, embryo, mouse, section, atlas, anatomy, imaging, 2d, spatial, image, repository, annotation | has parent organization: University of Edinburgh; Scotland; United Kingdom | Medical Research Council | PMID:26015534 | Free, Public | http://www.emouseatlas.org/emap/about/what_is_eHistology.html | SCR_015887 | SciCrunch Registry | 2026-11-07 11:58:07 | 1 | |||||||
|
Autoprotocol Resource Report Resource Website 1+ mentions |
Autoprotocol (RRID:SCR_015764) | software resource | Language standard for automating English language protocols. Autoprotocol specifies experimental protocols for biological research as a way to define experiments that could be run over the internet on remote robotic automation. | language, protocol, research publication, automation, translation | Freely available | SCR_015764 | SciCrunch Registry | BioIO | 2026-11-07 11:58:28 | 3 | ||||||||||
|
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 | SciCrunch Registry | IX53, IX53 Inverted Microscope, Olympus IX53 Inverted Microscope | 2026-11-07 11:58:05 | 3 | ||||||||
|
UK Brain Expression Consortium Resource Report Resource Website 1+ mentions |
UK Brain Expression Consortium (RRID:SCR_015889) | UKBEC | consortium, data or information resource, organization portal, portal | 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 | SciCrunch Registry | 2026-11-07 11:58:17 | 3 | ||||||||||
|
Sequence Detector System Resource Report Resource Website 1+ mentions |
Sequence Detector System (RRID:SCR_015806) | SDS | data analysis software, data processing software, sequence analysis software, software application, software resource | 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 | SciCrunch Registry | Sequence Detection System (SDS), Sequence Detection System (SDS) Software | 2026-11-07 11:58:33 | 6 | |||||||||
|
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 | SciCrunch Registry | NanoDrop 3300, NanoDrop™ 3300, NanoDrop™ 3300 Fluorospectrometer | 2026-11-07 11:58:16 | 481 | ||||||||||
|
Thermo Fisher: StepOnePlus Real-Time PCR System Resource Report Resource Website 50+ mentions |
Thermo Fisher: StepOnePlus Real-Time PCR System (RRID:SCR_015805) | data acquisition software, data processing software, instrument resource, software application, software resource | 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 | SciCrunch Registry | StepOnePlus, StepOnePlus™ Real-Time PCR System | 2026-11-07 11:58:29 | 58 | ||||||||||
|
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 | 2026-11-07 11:58:28 | 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 | 2026-11-07 11:58:32 | 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 | 2026-11-07 11:58:15 | 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 | 2026-11-07 11:58:15 | 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) | 2026-11-07 11:58:07 | 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 | 2026-11-07 11:58:37 | 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 | 2026-11-07 11:58:18 | 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 | 2026-11-07 11:58:37 | 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 | 2026-11-07 11:58:31 | 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 | 2026-11-07 11:58:19 | 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 | 2026-11-07 11:58:08 | 18 | ||||||||
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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 | 2026-11-07 11:58:31 | 56 |
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