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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Schrodinger Resource Report Resource Website 500+ mentions |
Schrodinger (RRID:SCR_014879) | commercial organization | Commercial ogranization which provides molecular and drug discovery software and services to researchers. American software company that develops chemical simulation software for use in pharmaceutical, biotechnology, and materials science research. Provides products ranging from general molecular modeling programs to a full suite of chemical simulation and drug design software, including ligand- and structure-based methods. | software solution, drug discovery, small molecule, computational chemistry |
is parent organization of: Epik is parent organization of: Ligprep is parent organization of: Glide is parent organization of: Phase is parent organization of: MacroModel is parent organization of: Maestro is parent organization of: Protein preparation Wizard is parent organization of: Shape screening |
Wikidata: Q7432923, ISNI: 0000 0001 0903 5603, grid.421925.9, SCR_014879 | https://ror.org/05a3z6914 | SCR_014879 | Schrodinger Inc. | 2026-08-08 12:00:36 | 840 | ||||||||
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NeuroExperimenter Resource Report Resource Website 1+ mentions |
NeuroExperimenter (RRID:SCR_014759) | NEx | software resource, software application, data analysis software, data visualization software, data processing software | Software which provides an interface for MindWave Mobile hardware, allowing users to view and listen to brainwave output of different "mind states". Users can: view any or all brainwaves, specify a combination of brainwaves via a formula, compare a base line session to a performance session, and create a log and run it through the application to view different graphical outputs. NeuroExperimenter only runs on Windows | data visualization, data analysis, software, interface, brainwave, brain wave, mind state | Freely available, Available for download, Under active development | https://sites.google.com/site/fredm/neuroexperimenter | SCR_014759 | NeuroExperimenter (NEx) | 2026-08-08 12:00:30 | 1 | ||||||||
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FRED - Fast exhaustive docking Resource Report Resource Website 1+ mentions |
FRED - Fast exhaustive docking (RRID:SCR_014885) | FRED | software resource | Complementary OEDocking tool for virtual screening, it performs a systematic and non-stochastic examination of all possible protein-ligand poses. The software also filters for shape complementarity and chemical feature alignment before selecting and optimizing protein-ligand poses. | docking, protein ligand, protein-ligand, protein ligand interaction, protein-ligand interaction, protein ligand pose, protein-ligand pose, ultra high throughput, compliment | http://docs.eyesopen.com/oedocking/fred.html | SCR_014885 | Fast exhaustive docking (FRED), Fast exhaustive docking | 2026-08-08 12:00:31 | 1 | |||||||||
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Open National Cancer Institute Database Resource Report Resource Website 10+ mentions |
Open National Cancer Institute Database (RRID:SCR_014886) | web application, database, data or information resource, software resource | Public web server that provides structures, data, tools, programs and other useful information to the public for computer-aided drug design. It is the official database of the Computer-Aided Drug Design (CADD) Group. | drug design, drug testing, computer-aided, web, database, server, computer-aided drug design, cadd | Public, Available to the research communtiy | SCR_014886 | 2026-08-08 12:00:36 | 10 | |||||||||||
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IonChannelLab Resource Report Resource Website 1+ mentions |
IonChannelLab (RRID:SCR_014762) | software resource, software application, simulation software | Software for kinetic modeling of ion channels which operates on Windows XP or Windows Vista. | simulation software, kinetic modeling, ion channel, electrophysiology | CONACyT Mexico 79897; CONACyT Mexico 105457; NINDS R01 NS032337 |
Available for download | SCR_014762 | 2026-08-08 12:00:17 | 5 | ||||||||||
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libRoadRunner Resource Report Resource Website 10+ mentions |
libRoadRunner (RRID:SCR_014763) | software resource, software application, simulation software | Simulation engine for systems and synthetic biology to be used with other software applications. It retains the original functionality of RoadRunner but has changes in performance, back-end design, event handling, new C++ API, and stochastic simulation support. | simulation engine, simulation software, road runner, roadrunner, systems biology, synthetic biology |
is listed by: Debian is listed by: OMICtools |
NIGMS GM081070 | DOI:10.1093/bioinformatics/btv363 | Open source, Available for download | OMICS_09368 | https://sources.debian.org/src/libroadrunner-dev/ | SCR_014763 | 2026-08-08 12:00:30 | 11 | ||||||
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La Jolla Institute for Immunology Resource Report Resource Website 1+ mentions |
La Jolla Institute for Immunology (RRID:SCR_014845) | institution | Institute dedicated to research in immunology by utilizing the academic and research communities in the La Jolla area as well as technological advances in biomedical research, imaging and analysis. Specific topics include autoimmune disease, cancer, allergies, infectious diseases and inflammation. | la jolla, allergy, immunology, biomedical, research, autoimmune disease, cancer, allergy, infectious disease, inflammation |
is parent organization of: La Jolla Institute for Immunology Clinical Studies Core Facility is parent organization of: La Jolla Institute for Immunology Bioinformatics Core Facility is parent organization of: La Jolla Institute for Immunology Microscopy and Histology Core Facility is parent organization of: La Jolla Institute for Immunology Flow Cytometry Core Facility |
, Wikidata Q6463245, ISNI 0000 0004 0461 3162, GRID grid.185006.a | https://ror.org/05vkpd318 | SCR_014845 | 2026-08-08 12:00:18 | 3 | |||||||||
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University of Essex; England; United Kingdom Resource Report Resource Website 1+ mentions |
University of Essex; England; United Kingdom (RRID:SCR_014725) | university | A public research university in Colchester, Essex, England. The institution has degree programs that span the humanities, social sciences, and health. | university, public, research, humanities, social sciences, health, england, british | ISNI:0000 0001 0942 6946, Wikidata:Q1075104, grid.8356.8, Crossref funder ID:100010046 | https://ror.org/02nkf1q06 | SCR_014725 | 2026-08-08 12:00:29 | 2 | ||||||||||
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TeachingDemos Resource Report Resource Website 1+ mentions |
TeachingDemos (RRID:SCR_014689) | data or information resource, portal, training resource, online course | A portal and resource for tutorials on a variety of data analysis techniques, the use of tools such as MetaMapR, workshops on data visualization, and R code manuals. | is listed by: Metabolomics Workbench | Freely available | SCR_014689 | 2026-08-08 12:00:28 | 7 | |||||||||||
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Coherent X-Ray Imaging Data Bank (CXIDB) Resource Report Resource Website 10+ mentions |
Coherent X-Ray Imaging Data Bank (CXIDB) (RRID:SCR_014722) | CXIDB | data or information resource, database, service resource, storage service resource, data repository | Database of Coherent X-ray Imaging (CXI) experiments. This data is widely accessible to researchers worldwide. | coherent xray imaging, cxi, experiment, database, reproducibility |
uses: DataCite is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases |
Available to the research community | DOI:10.11577, r3d100011554 | https://doi.org/10.11577/, https://dx.doi.org/10.11577/ | SCR_014722 | Coherent X-ray Imaging Data Bank (CXIDB), CXIDB, Coherent X-ray Imaging Data Bank | 2026-08-08 12:00:16 | 23 | ||||||
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Johns Hopkins Research Data Repository Resource Report Resource Website 1+ mentions |
Johns Hopkins Research Data Repository (RRID:SCR_014728) | storage service resource, data repository, service resource | Open access repository for Johns Hopkins University researchers to share their research data. Data repository is administered by professional curators at JHU Data Services, who will work with depositors to enable future discovery and reuse of your data, and ensure your data is Findable, Accessible, Interoperable and Reusable (FAIR). Each dataset has citation and DOI, facilitating attribution, and connection to research publications. | FAIR, data collection, data set, public data, education, training, data archive | Free, Freely available | r3d100011836 | https://doi.org/10.17616/R3RW77 | https://archive.data.jhu.edu/dvn/, http://dms.data.jhu.edu/archiving-2/ | SCR_014728 | 2026-08-08 12:00:34 | 8 | ||||||||
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Prokka Resource Report Resource Website 1000+ mentions |
Prokka (RRID:SCR_014732) | 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 tool for the rapid annotation of prokaryotic genomes. It produces GFF3, GBK and SQN files that are ready for editing in Sequin and ultimately submitted to Genbank/DDJB/ENA. A typical 4 Mbp genome can be fully annotated in less than 10 minutes on a quad-core computer, and scales well to 32 core SMP systems., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | annotation, prokaryote, genome, prokaryotic genome, sequence analysis software, annotation software, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools |
DOI:10.1093/bioinformatics/btu153 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_04220, biotools:prokka | https://bio.tools/prokka, https://sources.debian.org/src/prokka/, https://sources.debian.org/src/prokka/ | SCR_014732 | 2026-08-08 12:00:16 | 4882 | |||||||
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CVODE Resource Report Resource Website 50+ mentions |
CVODE (RRID:SCR_014696) | software resource, software application, data analysis software, data processing software | Solver for stiff and nonstiff ordinary differential equation (ODE) systems (initial value problem), given in explicit form y' = f(t,y), based on Adams and BDF methods. It is one of the programs that makes up the Suite of Nonlinear and Differential/Algebraic Equation Solvers (SUNDIALS)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | data analysis software, solver, equation solver, ordinary differential equation, differential equation, stiff, nonstiff | is listed by: SoftCite | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_014696 | SUNDIALS CVODE | 2026-08-08 12:00:34 | 56 | |||||||||
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iBRAIN Resource Report Resource Website 1+ mentions |
iBRAIN (RRID:SCR_014691) | group | Brain research group affiliated with the Nanjing University of Aeronautics and Astronautics (NUAA) in China. The main research interests of iBRAIN include developing methods in machine learning, data mining, neural computation, and related areas for decoding brain functions or recognizing brain disease. Research related code and datasets can be found on the main site. | brain, human brain, brain disease, brain research, group, brain research group, machine learning, data mining, neural computation | Brain disease | Public | SCR_014691 | Intelligence BRain Analysis through Images and Networks (iBRAIN), Intelligence BRain Analysis through Images and Networks, Intelligence Brain Analysis Through Images and Networks | 2026-08-08 12:00:34 | 6 | |||||||||
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SparseTracer Resource Report Resource Website 1+ mentions |
SparseTracer (RRID:SCR_014736) | software resource, software application, data analysis software, data processing software | Software used to automatically trace single neurons. It supports VTK 3D visualization. | single neuron, automatic, trace, software, vtk, 3d visualization, vtk 3d visualization, bioinformatics | Free, Available for download | SCR_014736 | 2026-08-08 12:00:16 | 2 | |||||||||||
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SplitsTree Resource Report Resource Website 1000+ mentions |
SplitsTree (RRID:SCR_014734) | software resource, software application, data analysis software, data visualization software, data processing software | Application that uses molecular sequence data to compute unrooted phylogenetic networks. Given an alignment of sequences, a distance matrix, or a set of trees, the program will compute a phylogenetic tree or network using methods such as split decomposition, neighbor-net, consensus network, super networks methods or methods for computing hybridization or simple recombination networks., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | sequence data, unrooted phylogenetic network, phylogenetic network, phylogeny, data analysis software, data visualization software, software | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_014734 | SplitsTree3, SplitsTree4 | 2026-08-08 12:00:34 | 1361 | ||||||||||
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PePPER Prokaryote Promoter Prediction Resource Report Resource Website 10+ mentions |
PePPER Prokaryote Promoter Prediction (RRID:SCR_014740) | PePPER | sequence analysis software, software resource, software application, data analysis software, data processing software | A webserver for the prediction of prokaryote promoter elements and regulons. DNA in FASTA or plain format serve as input. A gene table can be included with the run. | promoter prediction objective, prokaryote, promoter, regulon, predict, sequence analysis software, web server | PMID:22747501 | Free, Web application | SCR_014740 | 2026-08-08 12:00:29 | 32 | |||||||||
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SCAM Resource Report Resource Website 10+ mentions |
SCAM (RRID:SCR_014741) | software toolkit, software resource, software application, data analysis software, data processing software | Software toolbox for deriving and solving circuit equations symbolically in MATLAB. | matlab, circuit equations, symbolic solving, derivation, circuit analysis | Open source, Available for download | SCR_014741 | Symbolic Circuit Analysis in Matlab, Symbolic Circuit Analysis in Matlab (SCAM) | 2026-08-08 12:00:35 | 43 | ||||||||||
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Adaptive Biotechnologies Resource Report Resource Website 10+ mentions |
Adaptive Biotechnologies (RRID:SCR_014709) | resource | Commercial organization which combines high-throughput sequencing and bioinformatics to profile T-cell and B-cell receptors. | high throughput, sequencing, bioinformatics, t cell, b cell, biotechnology | Commercially available | SCR_014709 | 2026-08-08 12:00:16 | 24 | |||||||||||
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Measures of Effect Size Toolbox Resource Report Resource Website 1+ mentions |
Measures of Effect Size Toolbox (RRID:SCR_014703) | MES | software resource, software application, data analysis software, data processing software | Matlab statistics toolbox allowing the computation of a wide range of measures of effect size. Four main toolbox functions cover common analysis designs, including two-sample-, oneway- and twoway- data sets as well as categorical data. Data may be repeated-measures. | matlab, statistics toolbox, measure of effect size, effect size, common analysis design, data analysis software | PMID:22082031 | Available for download | SCR_014703 | MES Toolbox | 2026-08-08 12:00:16 | 3 |
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