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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Brain-CODE Resource Report Resource Website 10+ mentions |
Brain-CODE (RRID:SCR_015877) | storage service resource, data repository, service resource | Brain-CODE is a large-scale informatics platform that manages the acquisition and storage of multidimensional data collected from participants with a variety of brain disorders. | informatics, data storage, brain disorder | brain disorder, neurological disorder, informatics platform, data repository, data storage service, neuroscience | Public, Freely available, The research community can contribute to this resource | r3d100012181 | https://doi.org/10.17616/R3CK9G | SCR_015877 | 2026-08-08 12:00:43 | 49 | ||||||||
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Emory Epithelial Pathobiology Research Development Center Resource Report Resource Website |
Emory Epithelial Pathobiology Research Development Center (RRID:SCR_015916) | data or information resource, topical portal, organizational portal, portal, disease-related portal | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 5th,2023. Center for pathobiology research development. | pathobiology, research, development | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_015916 | 2026-08-08 12:00:27 | 0 | |||||||||||
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Antha Resource Report Resource Website |
Antha (RRID:SCR_015761) | software resource | Software language for methods to simplify protocols into reusable components that can be exchanged or removed to produce simple, reproducible, and scalable workflows. It allows users to develop, execute, and analyse biological experiments faster, while also introducing standardization and modularity to bioengineering. | software language, programming language, method, protocol, bioengineering, standardization, robot, robotics software | Freely available | https://github.com/antha-lang/antha | SCR_015761 | Synthace Antha | 2026-08-08 12:00:43 | 0 | |||||||||
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MetaNetX Resource Report Resource Website 50+ mentions |
MetaNetX (RRID:SCR_015882) | software resource, data access protocol, web service | Web application to perform automated model construction and genome annotation for large-scale metabolic networks. Platform for accessing, analyzing and manipulating genome-scale metabolic networks (GSM) as well as biochemical pathways. | automated model construction, genome annotation, model, construction, genome, annotation, metabolic network, repository, gsm, biochemical, pathway | Swiss National Science Foundation ; Swiss Federal Government ; SIB Swiss Institute of Bioinformatics |
PMID:26527720 PMID:23357920 PMID:23172809 |
Free, Freely available | SCR_015882 | MNXref, MetaNetX: Automated Model Construction and Genome Annotation for Large-Scale Metabolic Networks | 2026-08-08 12:00:45 | 94 | ||||||||
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Canu Resource Report Resource Website 1000+ mentions |
Canu (RRID:SCR_015880) | sequence analysis software, software resource, software application, data analysis software, data processing software | 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 ; US Department of Homeland Security (DHS) HSHQDC-07-C-00020; National Science Foundation NSF IOS-1237993 |
PMID:28298431 DOI:10.1101/071282 |
Free, Available for download | biotools:canu, OMICS_14592 | http://canu.readthedocs.io/en/latest/, https://bio.tools/canu, https://sources.debian.org/src/canu/ | SCR_015880 | 2026-08-08 12:00:26 | 2451 | ||||||
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eHistology Resource Report Resource Website 1+ mentions |
eHistology (RRID:SCR_015887) | data or information resource, atlas, service resource, storage service resource, data repository, image repository | 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 | 2026-08-08 12:00:43 | 1 | |||||||
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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 | BioIO | 2026-08-08 12:00:43 | 3 | ||||||||||
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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 | ||||||||||
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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 | |||||||||
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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 | |||||||||||
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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 | |||||||||||
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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 | |||||||
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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 | |||||||||
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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 | ||||||
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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 |
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