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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Image Data Resource (IDR) Resource Report Resource Website 1+ mentions |
Image Data Resource (IDR) (RRID:SCR_017421) | IDR | service resource, data repository, storage service resource | Public repository of reference image datasets from published scientific studies. Platform for publishing, mining and integrating bioimaging data, following FAIR principles and Euro-BioImaging/ELIXIR imaging strategy using OMERO and Bio-Formats open source software built by Open Microscopy Environment. Deployed on OpenStack cloud running on EMBL-EBI’s Embassy resource, it includes image data linked to independent studies from genetic, RNAi, chemical, localisation and geographic high content screens, super resolution microscopy, and digital pathology. | Repository, reference, image, published, annotated, dataset, FAIR |
is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases |
Free, Available for download, Freely available | r3d100012435 | https://doi.org/10.17616/R3XR0R | SCR_017421 | Image Data Resource, IDR, Image Data Resource (IDR) | 2026-08-12 10:51:47 | 1 | ||||||
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SICAS Medical Image Repository Resource Report Resource Website 1+ mentions |
SICAS Medical Image Repository (RRID:SCR_017420) | service resource, data repository, storage service resource | Medical image repository to store medical research data. | Medical, image, repository, store, data |
is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases |
Free, Freely available | r3d100011560 | https://doi.org/10.17616/R3HP8C | SCR_017420 | Medical Image Repository, SICAS, SICAS Medical Image Repository | 2026-08-12 10:51:49 | 5 | |||||||
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GE: Biacore 3000 Real Time Biomolecular Interaction Analyzer Resource Report Resource Website 1+ mentions |
GE: Biacore 3000 Real Time Biomolecular Interaction Analyzer (RRID:SCR_018044) | instrument resource | Biacore 3000 processing unit is an established, label-free system for detailed studies of biomolecular interactions. The system delivers comprehensive characterization of the interaction, answers questions about the rate constants, affinity, specificity, and determines the active concentration of components. The ability to recover and transfer interaction partners directly to MALDI targets for identification and further characterization makes the system highly applicable to fast identification of unknown interactants. | ABRF, Real Time Biomolecular Interaction Analyzer, GE Healthcare, instrument, equipment | is listed by: USEDit | Restricted | https://raw.githubusercontent.com/SciCrunch/RRID-Instruments/main/PDF/SCR_018044.pdf | SCR_019676, SCR_018577, Model_Number_Biacore 3000 | https://www.ibps.sorbonne-universite.fr/ressources/documents/1/2276, Brochure-Biacore-3000.pdf | https://www.gelifesciences.com/en/us/shop/biacore-3000-goldseal-p-02795 | SCR_018044 | BIACORE 3000 GOLDSEAL, BiaCore 3000 Surface Plasmon Resonance | 2026-08-12 10:52:02 | 5 | |||||
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StatPackets Resource Report Resource Website |
StatPackets (RRID:SCR_017613) | data or information resource, narrative resource, standard specification | Standardized method to export statistical data, associated with KOMP project. Standard way to keep data and results of analyzing that data together. | Standardized, method, export, statistical, data, KOMP, result, analysis, together | is related to: Knockout Mouse Project | Free, Freely available | SCR_017613 | 2026-08-12 10:51:47 | 0 | ||||||||||
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sietraj Resource Report Resource Website 1+ mentions |
sietraj (RRID:SCR_018021) | simulation software, software resource, software application | Software tool for binding free energies from Amber-generated MD trajectories. Alternative to MM-PBSA software provided by AMBER distribution. Virtual alanine mutations are also possible. Solvated interaction energies are calculated using parameters that have been fitted to reproduce binding free energies of data set of 99 protein-ligand complexes. | Binding free energy, Amber, MD trajctory, MM-PBSA, virtual alanine mutation, solvated interaction energy, calculation, parameter, protein-ligand complex | Restricted | SCR_018021 | 2026-08-12 10:52:00 | 2 | |||||||||||
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NanoSim Resource Report Resource Website 10+ mentions |
NanoSim (RRID:SCR_018243) | simulation software, software resource, software application | Software tool as Nanopore sequence read simulator based on statistical characterization. Oxford Nanopore Technology sequence simulator written in Python and R. Benefits development of scalable next generation sequencing technologies for long nanopore reads, including genome assembly, mutation detection, and metagenomic analysis software. | Nanopore sequence read, sequence simulator, Oxford Nanopore Technology, next generation sequencing, long nanopore read, genome assembly, mutation detection, bio.tools, bio.tools |
is listed by: Debian is listed by: bio.tools |
NHGRI R01 HG007182; Genome Canada ; Genome British Columbia ; British Columbia Cancer Foundation ; University of British Columbia |
DOI:10.1093/gigascience/gix010 | Free, Available for download, Freely available | biotools:trans-nanosim, biotools:nanosim | https://www.bcgsc.ca/resources/software/nanosim, https://bio.tools/nanosim, https://bio.tools/Trans-NanoSim | SCR_018243 | 2026-08-12 10:52:03 | 21 | ||||||
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PRISMA Resource Report Resource Website 1000+ mentions |
PRISMA (RRID:SCR_018721) | PRISMA | data or information resource, narrative resource, portal, standard specification | Evidence based minimum set of items for reporting in systematic reviews and meta analyses. Focuses on reporting of reviews evaluating randomized trials, but can also be used as basis for reporting systematic reviews of other types of research, particularly evaluations of interventions. | MDAR, standard, report standard, reporting reviews, randomized trial, evaluating randomized trial, reporting systematic review, intervention evaluation, meta analysis | is listed by: SoftCite | Ottawa Hospital Research Institute ; University of Oxford |
Free, Freely available | SCR_018721 | Preferred Reporting Items for Systematic Reviews and Meta-Analyses | 2026-08-12 10:52:12 | 1593 | |||||||
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PhyDyn Resource Report Resource Website 10+ mentions |
PhyDyn (RRID:SCR_018544) | simulation software, software resource, software application | Sofware package for performing Bayesian phylogenetic inference under models that deal with structured populations with complex population dynamics. Enables simultaneous estimation of epidemiological parameters and pathogen phylogenies. Epidemiological modelling in BEAST. | Bayesian phylogenetic inference, epidemiological modelling, epidemiological parameter estimation, pathogen phylogeny estimation |
is related to: BEAST2 is related to: BEAST |
NIGMS U01 GM110749; MRC Centre for Global Infectious Disease Analysis |
PMID:30422979 | Free, Available for download, Freely available | SCR_018544 | 2026-08-12 10:52:10 | 10 | ||||||||
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missForest Resource Report Resource Website 100+ mentions |
missForest (RRID:SCR_018543) | simulation software, software resource, software application | Software R package to impute missing values particularly in case of mixed type data. Non parametric, mixed type imputation method for any type of data for statistical software R. Predicts missing values. | Missing value prediction, mixed type data, non parametric, missing value, mixed data, predictor | is related to: CRAN | PMID:22039212 | Free, Available for download, Freely available | http://stat.ethz.ch/CRAN/ | SCR_018543 | 2026-08-12 10:52:10 | 173 | ||||||||
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PyRx Resource Report Resource Website 500+ mentions |
PyRx (RRID:SCR_018548) | simulation software, data processing software, software resource, software application | Open source virtual screening software for computational drug discovery with intuitive user interface. Runs on operating systems Linux, Windows, and Mac OS. Used to screen libraries of compounds against potential drug targets. | Virtual screening, computational drug discovery, drug, medicinal chemistry, target compound, compound screening, compound library, library screening | Restricted | SCR_018548 | 2026-08-12 10:52:10 | 645 | |||||||||||
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OpenCOR Resource Report Resource Website 1+ mentions |
OpenCOR (RRID:SCR_019001) | simulation software, software resource, software application | Open source cross platform modeling environment for reproducible science. Used to organise, edit, simulate and analyse models described in CellML format, using SED-ML and COMBINE archives. | Modeling environment, reproducible science, CellML format model, CellML format model analysis, CellML format model simulation |
uses: Simulation Experiment Description Markup Language is used by: SPARC Portal |
Free, Available for download, Freely available | SCR_019001 | 2026-08-12 10:52:18 | 6 | ||||||||||
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PROSPERO Resource Report Resource Website 1000+ mentions |
PROSPERO (RRID:SCR_019061) | data or information resource, database, narrative resource, standard specification | International database of prospectively registered systematic reviews in health and social care, welfare, public health, education, crime, justice, and international development, where there is health related outcome. Key features from review protocol are recorded and maintained as permanent record. Aims to provide comprehensive listing of systematic reviews registered at inception to help avoid duplication and reduce opportunity for reporting bias by enabling comparison of completed review with what was planned in protocol. | Gold standard authority, registered systematic reviews, reviews in health, reviews in social care, reviews in welfare, reviews in public health, reviews in education, reviews in crime, reviews in justice, reviews in international development, health related outcome, protocol, FASEB list |
is related to: Centre for Reviews and Dissemination has parent organization: University of York, York, England |
NIHR | Free, Freely available | SCR_019061 | 2026-08-12 10:52:11 | 3301 | |||||||||
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Fgenesh plus plus Resource Report Resource Website 1+ mentions |
Fgenesh plus plus (RRID:SCR_018928) | simulation software, software resource, software application | Software tool as pipeline for automatic prediction of genes in eukaryotic genomes based on Softberry gene finding software. | Automatic gene prediction, eukaryotic genomes, Softberry software, gene finding | is related to: FGENESH Plus | PMID:16925832 | Restricted | SCR_018928 | Fgenesh Plus Plus, FGENESH plus plus, FGENESH Plus Plus | 2026-08-12 10:52:15 | 7 | ||||||||
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o²S²PARC Resource Report Resource Website 1+ mentions |
o²S²PARC (RRID:SCR_018997) | osparc | simulation software, software resource, software application | Simulation platform that enables users to create, access, tune, and run models or computational algorithms through web based interface. Web interactive simulation platform that hosts SPARC computational models and solvers. Allows collaborative development and sharing, model coupling and cloud based execution, data visualization and analysis, and ensures sustainability of computational models developed within SPARC. Enables users to create predictive, multiscale, multi-physics models spanning from modulation sources acting on peripheral nervous system (PNS) to resulting modulation of organ functional response. | SPARC, SPARC computational model, data sharing, model coupling, cloud based execution, data visualization, data analysis, peripheral nervous system, organ functional response |
is used by: SPARC Portal is organization facet of: SPARC Portal |
Free, Freely available | SCR_018997 | open online Simulation platform for Stimulating Peripheral Activity to Relieve Conditions | 2026-08-12 10:52:17 | 2 | ||||||||
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NeuroRD Resource Report Resource Website 10+ mentions |
NeuroRD (RRID:SCR_014769) | simulation software, software resource, software application | Stochastic reaction-diffusion simulator in Java which is used for simulating neuronal signaling pathways. | simulation software, simulator, java, neuronal signaling pathway, neuron | HFSP ; NIMH K21-MH01141; NSF IBN 0077509; CRCNS program R01 AA16022; CRCNS program AA18066 |
Available for download | https://github.com/neurord/stochdiff/releases | SCR_014769 | 2026-08-12 10:51:11 | 13 | |||||||||
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COMSOL Multiphysics Resource Report Resource Website 50+ mentions |
COMSOL Multiphysics (RRID:SCR_014767) | simulation software, software resource, software application | General-purpose software platform for modeling and simulating physics-based problems which accounts for coupled or multiphysics phenomena. The platform includes a set of core physics interfaces for common physics application areas such as structural analysis, laminar flow, pressure acoustics, transport of diluted species, electrostatics, electric currents, heat transfer, and Joule heating. | simulation software, software platform, physics, problem solver | is listed by: SoftCite | Commercially available | SCR_014767 | 2026-08-12 10:51:10 | 51 | ||||||||||
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PCSIM Resource Report Resource Website 1+ mentions |
PCSIM (RRID:SCR_014770) | simulation software, software resource, software application | Software tool for simulating heterogeneous networks composed of different model neurons and synapses. It is intended to simulate networks containing up to millions of neurons and on the order of billions of synapses by distributing the network over different nodes of a computing cluster by using MPI. | simulation software, simulator, heterogenous network, model, neuron, synapse | is related to: CSIM | DOI:10.3389/neuro.11.011.2009 | Available for download | SCR_014770 | Parallel neural Circuit SIMulator, Parallel Neural Circuit Simulator (PCSIM), Parallel Neural Circuit Simulator | 2026-08-12 10:51:10 | 4 | ||||||||
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Mvaspike Resource Report Resource Website |
Mvaspike (RRID:SCR_014760) | simulation software, software resource, software application | Tool for modeling and simulating large, complex biological neural networks, particularly pulse-coupled, spiking neural networks. Its main features include modular or hierarchical modeling strategy of networks, phase-coded neurons, event-driven simulation, and integration of standard file formats. | simulation software, neural network, biological neural network, spiking neural network, event based modeling, event based simulation | SCR_014760 | 2026-08-12 10:51:11 | 0 | ||||||||||||
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IonChannelLab Resource Report Resource Website 1+ mentions |
IonChannelLab (RRID:SCR_014762) | simulation software, software resource, software application | 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 | 2026-08-12 10:50:59 | 5 | ||||||||||
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libRoadRunner Resource Report Resource Website 10+ mentions |
libRoadRunner (RRID:SCR_014763) | simulation software, software resource, software application | 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 | 2026-08-12 10:51:11 | 11 |
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