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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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InnoCentive Resource Report Resource Website 1+ mentions |
InnoCentive (RRID:SCR_013851) | people resource, software resource | A global network group resource which provides crowdsourcing services for “innovation solutions.” InnoCentive utilizes an innovation framework, called Challenge Drive Innovation, which is based on leveraging open innovation and crowdsourcing. Software tools are available for idea management, innovation management, and external crowdsourcing programs and competitions. | group, crowdsourcing, Challenge Drive Innovation, software, tools, idea management |
is used by: Scientific American is listed by: Connected Researchers is related to: Connected Researchers |
Must pay for resource | SCR_013851 | 2026-08-09 09:06:20 | 9 | ||||||||||
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Vienna Drosophila Resource Center Resource Report Resource Website 100+ mentions |
Vienna Drosophila Resource Center (RRID:SCR_013805) | VDRC | material resource, biomaterial supply resource | Biomaterial supply resource which collects, maintains, and distributes independent transgenic fly lines. Most of the 38,000 fly lines are RNAi lines, but VDRC also maintains a collection of enhancer-GAL4 driver lines. Nearly all lines are in duplicate. Users can search for the stocks or DNA constructs for the gene of interest by entering CG number, synonym, or Transformant ID. | RIN, Resource Information Network, biomaterial supply resource, drosophila, fly lines, RRID Community Authority | is listed by: Resource Information Network | Free, Public, Must create an account, Acknowledgment required | https://drive.google.com/file/d/1VvsxJMXBDPlO5M_HWGOkeYXbg7zk_68E/view?usp=drivesdk | http://www.csf.ac.at/facilities/vienna-drosophila-resource-center/, http://stockcenter.vdrc.at/control/main | SCR_013805 | 2026-08-09 09:06:13 | 396 | |||||||
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L-Neuron Resource Report Resource Website 1+ mentions |
L-Neuron (RRID:SCR_014132) | simulation software, software application, software resource | A program which creates anatomically realistic virtual neurons using the formalism of the Lyndenmayer systems to implement sets of neuroanatomical rules discovered by several research groups. The program algorithms read in experimental data - in the form of statistical distributions - to generate virtual structures. L-Neuron samples the values of the parameters within these statistical distributions in a stochastic (random) fashion during dendritic growth. | simulation softare, virtual neuron, neuronal modeling |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: George Mason University; Virginia; USA |
Available to the research community | http://krasnow1.gmu.edu/cn3/L-Neuron/home.htm | SCR_014132 | L Neuron | 2026-08-09 09:06:17 | 5 | ||||||||
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CSIM Resource Report Resource Website 10+ mentions |
CSIM (RRID:SCR_014256) | simulation software, software application, software resource | Software tool for simulating heterogeneous networks composed of different model neurons and synapses. CSIM simulates networks containing up to a few thousand neurons and up to the order of 1.000.000 synapses. It is capable of supporting different levels of modeling and has an object oriented design. A user manual is available on the site. | simulation software, circuit simulator, heterogeneous network, object oriented design | is related to: PCSIM | Available for download | SCR_014256 | Circuit SIMulator, CSIM: A neural Circuit SIMulator | 2026-08-09 09:06:22 | 11 | |||||||||
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Virtual Electrode Recording Tool for EXtracellular potentials (VERTEX) Resource Report Resource Website |
Virtual Electrode Recording Tool for EXtracellular potentials (VERTEX) (RRID:SCR_014178) | VERTEX | simulation software, software application, software resource | A Matlab tool for simulating extracellular potential recordings in spiking neural network (SNN) models. VERTEX is designed to facilitate the simulation of extracellular potentials generated by activity in SNNs; in particular, spatially-organised networks containing thousands or hundreds of thousands of neurons. It has a limited scope but has a simpler user interface so that a simulation can be specified simply by setting some parameters and run using a few function calls. | simulation software, matlab, extracellular potential, spiking neural network model, snn model |
uses: MATLAB is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Newcastle University; Newcastle upon Tyne; United Kingdom |
PMID:24863422 | Available to the research community | SCR_014178 | Virtual Electrode Recording Tool for EXtracellular potentials | 2026-08-09 09:06:18 | 0 | |||||||
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BioPSE Resource Report Resource Website |
BioPSE (RRID:SCR_014044) | simulation software, software application, software resource | A simulation software package which hosts a collection of algorithms used to run bioelectric field simulations inside of SCIRun. The software provided in the package may be used for geometric modeling, simulation, and visualization for solving bioelectric field problems. | software, algorithm, simulation, modeling, visaulization, bioelectric field, tool |
is related to: SCIRun is related to: SCIRun has parent organization: University of Utah; Utah; USA |
NIH | Public | SCR_014044 | SCIRun/BioPSE | 2026-08-09 09:06:20 | 0 | ||||||||
|
NeoCortical Simulator Resource Report Resource Website |
NeoCortical Simulator (RRID:SCR_014257) | NCS | simulation software, software application, software resource | A neural simulator which models integrate-and-fire neurons with conductance-based synapses. NCS supports simulations for larger models and also supports real-time neurorobotics applications. Two versions of NCS are available: NCS 5, which is based on CPU cluster; and NCS 6, a multi-box, multi-GPU version. NCS 5 models integrate-and-fire neurons with conductance-based synapses using two clusters: four SUN 4600 machines and 208 Opteron cores. NCS 6 is a neural simulator for heterogeneous clusters of both CPUs and GPUS. | simulation software, neural simulator, conductance based synapse, neurobiotics | has parent organization: University of Nevada at Reno; Nevada; USA | Source code is available | SCR_014257 | 2026-08-09 09:06:20 | 0 | |||||||||
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SimThyr Resource Report Resource Website 10+ mentions |
SimThyr (RRID:SCR_014351) | simulation software, software application, software resource | Open source simulation software for thyroid homeostasis, based on published nonlinear model of pituitary thyroid feedback control. Simulates pituitary thyroid feedback control, which allows users to study relationship between structure and behaviour of thyroid homeostasis. | thyroid, homeostasis, simulation, software, modelling, pituitary, model |
is related to: SimulaBeta has parent organization: Ludwig-Maximilians-University; Munich; Germany has parent organization: Ruhr University Bochum; North Rhine-Westphalia; Germany |
PMID:23365787 DOI:10.1080/01969720490443354 DOI:10.1155/2012/351864 DOI:10.5281/zenodo.1303822 |
Free, Available for download, Freely available | DOI:10.5281/zenodo.1303822 | https://doi.org/10.5281/zenodo.1303822 | SCR_014351 | 2026-08-09 09:06:22 | 11 | |||||||
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Desmond Resource Report Resource Website 500+ mentions |
Desmond (RRID:SCR_014575) | simulation software, software application, software resource | Software designed to perform high-speed molecular dynamic simulations of biological systems on conventional commodity clusters, supercomputers and GPUs. This code uses novel parallel algorithms and numerical techniques to achieve high performance and accuracy on platforms with a large number of processors. It can be used with a single computer. | simulation, supercomputer, commodity cluster, gpu, parallel algorithm, biological system, parallel algorithms, computer, processor | is used by: CHARMM-GUI | Open source, Free for non-commercial use, Commercial entities must contact Schrodinger LLC | SCR_014575 | 2026-08-09 09:06:27 | 946 | ||||||||||
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Tool for Tumor Progression Resource Report Resource Website 1+ mentions |
Tool for Tumor Progression (RRID:SCR_014700) | TTP | simulation software, software application, software resource | Software used to simulate tumor progression in various stages of growth in order to study the process' dynamics. The input can be fitness landscape, mutation rate, and cell division time. The output is growth dynamics and other relevant statistics, such as expected tumor detection time and expected appearance time of surviving mutants. The tool is implemented in Java and runs on all operating systems which run a Java Virtual Machine (JVM) of version 1.7 or above. | tumor, tumor progression, cancer, simulation, simulation software, tumor dynamics, tumor growth | Cancer | Available for download, Necessary libraries are included in the file | SCR_014700 | Tool for Tumor Progression (TTP) | 2026-08-09 09:06:27 | 1 | ||||||||
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NeuroRD Resource Report Resource Website 10+ mentions |
NeuroRD (RRID:SCR_014769) | simulation software, software application, software resource | 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 | 2026-08-09 09:06:31 | 13 | |||||||||
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COMSOL Multiphysics Resource Report Resource Website 50+ mentions |
COMSOL Multiphysics (RRID:SCR_014767) | simulation software, software application, software resource | 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 | 2026-08-09 09:06:11 | 51 | ||||||||||
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PCSIM Resource Report Resource Website 1+ mentions |
PCSIM (RRID:SCR_014770) | simulation software, software application, software resource | 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 | 2026-08-09 09:06:11 | 4 | ||||||||
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Online Resource for Community Annotation of Eukaryotes Resource Report Resource Website 10+ mentions |
Online Resource for Community Annotation of Eukaryotes (RRID:SCR_014989) | OrcAE, ORCAE | data or information resource, wiki, narrative resource | Online genome annotation tool for validating and correcting gene annotations. OrcAE is community-driven and can be edited by account-holders in the research community. | genome annotation, gene validation, community driven, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Bioinformatics Gent has parent organization: Ghent University; Ghent; Belgium has parent organization: VIB; Flanders; Belgium |
PMID:23132114 | Free, Account required, The research community can contribute to this resource | biotools:orcae | https://bio.tools/orcae | SCR_014989 | Online Resource for Community Annotation of Eukaryotes (OrcAE) | 2026-08-09 09:06:14 | 17 | |||||
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Mvaspike Resource Report Resource Website |
Mvaspike (RRID:SCR_014760) | simulation software, software application, software resource | 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 | 2026-08-09 09:06:11 | 0 | ||||||||||||
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IonChannelLab Resource Report Resource Website 1+ mentions |
IonChannelLab (RRID:SCR_014762) | simulation software, software application, software resource | 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 | 2026-08-09 09:06:31 | 5 | ||||||||||
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libRoadRunner Resource Report Resource Website 10+ mentions |
libRoadRunner (RRID:SCR_014763) | simulation software, software application, software resource | 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 | 2026-08-09 09:06:11 | 11 | ||||||
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NMRbox Resource Report Resource Website 50+ mentions |
NMRbox (RRID:SCR_014827) | web application, software toolkit, software resource | Computing platform for biomolecular NMR available to not-for-profit or government users. It consists of a virtual machine (VM) provisioned with dozens of widely-used NMR software packages, and is available as a cloud-based Platform-as-a-Service (PaaS) or as a downloadable VM for local execution. | Nuclear Magnetic Resonance, nmr, spectra, computing platform, platform, virtual machine, cloud, software toolbox | NIGMS P41GM111135 | Account required | SCR_014827 | , Nuclear Magnetic Resonance box, NMRbox.org | 2026-08-09 09:06:29 | 92 | |||||||||
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BeatBox Resource Report Resource Website 10+ mentions |
BeatBox (RRID:SCR_015780) | simulation software, software application, software resource | Simulation environment that combines flexible script language user interface with computational tools in order to setup cardiac electrophysiology in-silico experiments without re-coding at low-level. It aims to include cell excitation, tissue/anatomy models, and stimulation protocols in BeatBox scripts so that simulation run either sequentially or in parallel (MPI) without re-compilation. | simulation, cardiac electrophysiology, computation, script language, c, ecg, heart, cardiology, simulation protocol | EPSRC EP/I029664; EPSRC EP/N014391/1; EPSRC EP/P008690/1 |
PMID:28467407 | Free, Available for download | https://github.com/beatbox-heart/beatbox-public/tree/v1.7.982 | SCR_015780 | BeatBox—HPC simulation environment for biophysically and anatomically realistic cardiac electrophysiology. | 2026-08-09 09:06:55 | 11 | |||||||
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o²S²PARC Resource Report Resource Website 1+ mentions |
o²S²PARC (RRID:SCR_018997) | osparc | simulation software, software application, software resource | 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 | 2026-08-09 09:07:46 | 2 |
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