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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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EDLUT Resource Report Resource Website 1+ mentions |
EDLUT (RRID:SCR_014261) | simulation software, software resource, software application | Simulation software which creates spiking cell models using either a time-driven strategy or an event-driven strategy based on look-up tables. EDLUT serves as a tool for studying the computational principles of neural systems to reveal how different functionalities of the brain and central nervous system are based on cell and topology properties. | spiking neural network, simulation software, | has parent organization: University of Granada; Granada; Spain | DOI:10.1162/neco.2006.18.12.2959 | Open source, Available for download | SCR_014261 | EDLUT: Event-Driven simulator based on Look-Up-Tables, Event-Driven simulator based on Look-Up-Tables | 2026-08-12 10:50:59 | 4 | ||||||||
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Integrated Digitized Biocollections Resource Report Resource Website 100+ mentions |
Integrated Digitized Biocollections (RRID:SCR_014336) | iDigBio | service resource, data repository, storage service resource | iDigBio is the National Resource for Advancing Digitization of Biodiversity Collections (ADBC) funded by the National Science Foundation. Through ADBC, data and images for millions of biological specimens are being made available in electronic format for the research community, government agencies, students, educators, and the general public. | biospecimen | NSF Cooperative Agreement EF-1115210 | Open | r3d100011126 | https://doi.org/10.17616/R3J90V | SCR_014336 | 2026-08-12 10:50:56 | 116 | |||||||
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Gsnap2Augustus Resource Report Resource Website 1+ mentions |
Gsnap2Augustus (RRID:SCR_017555) | simulation software, software resource, software application | Software tool to generate hints for Augustus in ab initio gene prediction using 2 step mapping by Gsnap. | Generate, hint, Augustus, gene, prediction, mapping, Gsnap |
uses: GSNAP works with: Augustus |
Free, Available for download, Freely available | SCR_017555 | 2026-08-12 10:51:49 | 1 | ||||||||||
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HiCRes Resource Report Resource Website 1+ mentions |
HiCRes (RRID:SCR_022319) | simulation software, software resource, software application | Software pipeline to estimate and predict genomic resolution of Hi-C libraries. Used for estimating and predicting HiC library resolution. | Hi-C libraries, 3D chromatin interactions genome wide measurement, estimate resolution of dataset, genomic resolution | NEI ZIAEY000450; NEI ZIAEY000546 |
DOI:10.1093/nar/gkab1235 | Free, Available for download, Freely available | https://github.com/ClaireMarchal/HiCRes | SCR_022319 | 2026-08-12 10:52:52 | 1 | ||||||||
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Sustainable Grazing System Pasture Model Resource Report Resource Website |
Sustainable Grazing System Pasture Model (RRID:SCR_021854) | simulation software, software resource, software application | Software tool as biophysical simulation model for livestock systems. It has flexible interface for setting up and running simulations with extensive graphical and data output. | simulation model, livestock systems | Free, Available for download, Freely available | SCR_021854 | SGS Pasture Model | 2026-08-12 10:52:24 | 0 | ||||||||||
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PlaForNEA Resource Report Resource Website |
PlaForNEA (RRID:SCR_022027) | simulation software, software resource, software application | Software allows estimating growth and production at stand level of main forest species implanted in Argentine Mesopotamia such as Pino taeda, Eucalyptus grandis, Pino elliottii and Araucaria angustifolia. Areas for which models were adjusted correspond to province of Misiones, northeast of Corrientes and Concordia in province of Entre Ríos. | estimating growth and production, forest species, Argentine Mesopotamia | Free, Available for download, Freely available | https://plafornea.software.informer.com/ | SCR_022027 | PLAFORNEA | 2026-08-12 10:52:26 | 0 | |||||||||
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SimulaBeta Resource Report Resource Website 1+ mentions |
SimulaBeta (RRID:SCR_021900) | simulation software, software resource, software application | Software tool as simulation program for insulin glucose feedback control. Based on nonlinear MiMe-NoCoDI model. | Open source, insulin, glucose, simulation, modelling, model, beta cell, homeostasis |
uses: CyberUnits is related to: SPINA Carb is related to: SimThyr has parent organization: Ruhr University Bochum; North Rhine-Westphalia; Germany has parent organization: Ulm University; Baden-Wurttemberg; Germany |
Deutsche Forschungsgemeinschaft (DFG) GRK 1041; Open Access Publication Funds of the Ruhr-Universität Bochum ; Germany ; Ministry of Education (MOE) Singapore |
PMID:36271244 | Free, Available for download, Freely available | DOI:10.5281/zenodo.4922800 | https://doi.org/10.5281/zenodo.4922800 | SCR_021900 | 2026-08-12 10:52:46 | 2 | ||||||
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MEGSIM Resource Report Resource Website |
MEGSIM (RRID:SCR_002420) | MEGSIM | data or information resource, simulation software, software application, data set, software resource | Realistic simulated MEG datasets ranging from basic sensory to oscillatory sets that mimic functional connectivity; as well as basic visual, auditory, and somatosensory empirical sets. The simulated sets were created for the purpose of testing analysis algorithms across the different MEG systems when the truth is known. MEG baseline recordings were obtained from 5 healthy participants, using three MEG systems: VSM/CTF Omega, Elekta Neuromag Vectorview, 4-D Magnes 3600. Simulated signals were embedded within the CTF and Neuromag 306 baseline recordings (4-D to be added). Participant MRIs are available. Averaged simulation files are available as netcdf files. Neuromag 306 averaged simulations are also available in fif format. Also available: single trials of data where the simulated signal is jittered about a mean value, continuous fif files where the simulated signal is marked by a trigger, and simulations with oscillations added to mimic functional connectivity. | eeg, meg, electrocorticography, forward - inverse, mri, meg modeling, model, simulation, os independent, test data, image collection |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Mind Research Network |
NIMH R21MH080141 | PMID:22068921 | Free, Freely available | nlx_155793 | http://www.nitrc.org/projects/megsim | SCR_002420 | 2026-08-12 10:48:35 | 0 | |||||
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OpenSim Resource Report Resource Website 500+ mentions |
OpenSim (RRID:SCR_002683) | simulation software, software resource, software application | OpenSim is an open-source software system that lets users develop models of musculoskeletal structures and create dynamic simulations of movement. The software provides a platform on which the biomechanics community can build a library of simulations that can be exchanged, tested, analyzed, and improved through multi-institutional collaboration. The underlying software is written in ANSI C++, and the graphical user interface (GUI) is written in Java. OpenSim technology makes it possible to develop customized controllers, analyses, contact models, and muscle models among other things. These plugins can be shared without the need to alter or compile source code. Users can analyze existing models and simulations and develop new models and simulations from within the GUI. | muscle-driven simulation, musculoskeletal biomechanics, neuromuscular simulation, modeling software, simulation software |
is related to: Simtk.org is related to: Neuromuscular Models Library has parent organization: Stanford University; Stanford; California |
Simbios ; NIGMS U54 GM072970; DARPA |
Public, Free, Acknowledgement requested | nif-0000-23308 | https://simtk.org/home/opensim, http://opensim.stanford.edu/support/index.html | SCR_002683 | 2026-08-12 10:48:39 | 612 | |||||||
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eNeoTutor Resource Report Resource Website |
eNeoTutor (RRID:SCR_001590) | eNeoTutor | data or information resource, narrative resource, software application, training material, software resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented August 17, 2016. ASP.NET AJAX .NET 4, Telerik controls enabled application designed to be used with the books presented, papers and web content to help with the acceleration of learning and software development for the neurosciences. All content developed at The Cromwell Workshop is intended to accelerate the implementation of biomedical knowledge, help with EEG clinical certifications and provide the opportunity for students, software developers, neuroscientists, neurologists and neurosurgeons to collaborate globally with knowledge content. e-NeoTutor relies on a subscription model to build software components in multiple languages and access book material. Tutor designed to complement free online course content in neuroscience, work with the Society of Neuroscience, The Human Connectome Project and assist researchers with CNIM certification, biomedical informatics, neuroinformatics and neuroscience training programs. | neuroscience, curriculum, brain computer interface, eeg, tutorial, software development |
is related to: iBIOFind has parent organization: The Cromwell Workshop |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_153831 | http://neuronalarchitects.com/eneotutor.html | SCR_001590 | e-NeoTutor | 2026-08-12 10:48:26 | 0 | ||||||
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Monte Carlo Simulation Software: tMCimg Resource Report Resource Website 1+ mentions |
Monte Carlo Simulation Software: tMCimg (RRID:SCR_002588) | tMCimg | simulation software, software resource, software application | Software application that uses a Monte Carlo algorithm to model the transport of photons through 3D volumes with spatially varying optical properties. Both highly-scattering tissues (e.g. white matter) and weakly scattering tissues (e.g. cerebral spinal fluid) are supported. Using the anatomical information provided by MRI, X-ray CT, or ultrasound, accurate solutions to the photon migration forward problems are computed in times ranging from minutes to hours, depending on the optical properties and the computing resources available. | c, computed tomography, macos, microsoft, modeling, monte carlo, magnetic resonance, optical imaging, posix/unix-like, windows, mri, x-ray ct, ultrasound, photon | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | PMID:19424345 | Free, Available for download, Freely available | nlx_155993 | http://www.nitrc.org/projects/tmcimg | SCR_002588 | Monte Carlo Photon Transport | 2026-08-12 10:48:37 | 1 | |||||
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TumorSim Resource Report Resource Website 1+ mentions |
TumorSim (RRID:SCR_002604) | simulation software, software resource, software application | Simulation software that generates pathological ground truth from a healthy ground truth. The software requires an input directory that describes a healthy anatomy (anatomical probabilities, mesh, diffusion tensor image, etc) and then outputs simulation images. | clinical neuroinformatics, magnetic resonance, mri, brain, segmentation, simulation, tumor, ground truth |
uses: BrainWeb - Simulated Brain Database is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of Utah; Utah; USA |
Cancer | NIBIB R01 EB000219 | PMID:19119055 | Free, Available for download, Freely available | nlx_156007 | SCR_002604 | 2026-08-12 10:48:38 | 1 | ||||||
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ChemChaste Resource Report Resource Website 1+ mentions |
ChemChaste (RRID:SCR_022208) | simulation software, software resource, software application | Software tool for simulating spatially inhomogenous biochemical reaction diffusion systems for modelling cell environment feedbacks. Simulation software for spatially organised biochemical systems. | spatially organised, biochemical systems, simulating biochemical systems, spatially inhomogenous biochemical reaction diffusion systems, modelling cell environment feedbacks | DOI:10.1101/2021.10.21.465304 | Free, Available for download, Freely available | SCR_022208 | 2026-08-12 10:52:28 | 1 | ||||||||||
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PBSIM Resource Report Resource Website 10+ mentions |
PBSIM (RRID:SCR_002512) | simulation software, software resource, software application | Software that simulates PacBio reads by using either a model-based or sampling-based simulation. | pacbio simulation, model-based simulation, sampling-based simulation |
is listed by: OMICtools is listed by: Debian |
PMID:23129296 DOI:10.1093/bioinformatics/bts649 |
Free, Available for download, Freely available | OMICS_00253 | https://sources.debian.org/src/pbsim/ | SCR_002512 | PacBio reads simulator | 2026-08-12 10:48:36 | 11 | ||||||
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PICRUSt2 Resource Report Resource Website 500+ mentions |
PICRUSt2 (RRID:SCR_022647) | simulation software, software resource, software application | Software for predicting functional abundances based only on marker gene sequences.Used for prediction of metagenome functions. Contains updated and larger database of gene families and reference genomes, provides interoperability with any operational taxonomic unit (OTU)-picking or denoising algorithm, and enables phenotype predictions. Allows addition of custom reference databases. | predicting functional abundances, marker gene sequences, metagenome functions prediction | is related to: PICRUSt | NSF IOS CAREER 1942647; NIDDK U54DK102557; NIDDK R24DK110499; NSERC ; GlaxoSmithKline |
PMID:32483366 | Free, Available for download, Freely available | https://github.com/picrust/picrust2 | SCR_022647 | Phylogenetic Investigation of Communities by Reconstruction of Unobserved States | 2026-08-12 10:52:46 | 583 | ||||||
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AIRR Community Resource Report Resource Website |
AIRR Community (RRID:SCR_022598) | data or information resource, narrative resource, portal, standard specification | Research driven group that is organizing and coordinating stakeholders in use of next generation sequencing technologies to study antibody/B-cell and T-cell receptor repertoires. Develops and promotes standards and recommendations for obtaining, analyzing, curating and comparing/sharing AIRR-seq datasets;using and validating tools for analyzing AIRR-seq data;relating AIRR-seq datasets to other “big data” sets, such as microarray, flow cytometric, and MiSeq and single-cell gene-expression data; legal and ethical issues involving use and sharing of AIRR-seq data sets derived from human sources. | next generation sequencing technologies use, study antibody, B-cell and T-cell receptor repertoires, standards and recommendations for AIRR-seq datasets | is related to: AIRR Data Commons | Free, Freely available | SCR_022598 | Adaptive Immune Receptor Repertoire Community, Adaptive Immune Receptor Repertoire Community of The Antibody Society | 2026-08-12 10:52:34 | 0 | |||||||||
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Enhancing Quality In Preclinical Data Quality System Resource Report Resource Website 1+ mentions |
Enhancing Quality In Preclinical Data Quality System (RRID:SCR_022729) | data or information resource, narrative resource, standard specification | Preclinical research quality system that can be applied in public and private sectors to ensure that early drug development research proceeds along structured lines. Used for ensuring generation of reliable preclinical data. Proposes guidance on expectations for quality related measures, defines criteria for adequate processes like performance standards, and provides examples of how such measures can be developed and implemented. EQIPD certification was established by EQIPD consortium and is now managed by its legacy organisation GoEQIPD. | EQIPD certification, guidance on expectations, Enhancing Quality In Preclinical Data, EQIPD consortium, GoEQIPD, reliable preclinical data generation | PMID:34028353 | Free, Freely available | SCR_022729 | EQIPD Quality System | 2026-08-12 10:52:47 | 1 | |||||||||
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4TU.ResearchData Resource Report Resource Website |
4TU.ResearchData (RRID:SCR_023125) | service resource, data repository, storage service resource | International data repository for science, engineering and design. Services include curation, sharing, long-term access and preservation of research datasets. These services are available to anyone around the world. In addition, 4TU.ResearchData also offers training and resources to researchers to support them in making research data findable, accessible, interoperable and reproducible (FAIR). | International data repository, science data, engineering data, design data, |
is listed by: DataCite is listed by: FAIRsharing is listed by: re3data.org |
Free, Freely available | DOI:10.4121, DOI:10.17616/R3VG6N, DOI:10.25504/FAIRsharing.zcveaz | https://doi.org/10.4121, https://dx.doi.org/10.4121, http://doi.org/10.17616/R3VG6N, https://fairsharing.org/10.25504/FAIRsharing.zcveaz | SCR_023125 | 4TU.ResearchData | 2026-08-12 10:52:51 | 0 | |||||||
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CytoTRACE Resource Report Resource Website 100+ mentions |
CytoTRACE (RRID:SCR_022828) | simulation software, software resource, software application | Software tool that predicts differentiation state of cells from single cell RNA sequencing data. Used for predicting differentiation states from scRNA-seq data. | differentiation state of cells, single cell RNA sequencing data, predicting differentiation states, scRNA-seq data | NCI R00CA187192; NCI R01CA100225; Stinehart Reed foundation ; Stanford Bio-X Interdisciplinary Initiatives Seed Grants Program ; Virginia and D.K. Ludwig Fund for Cancer Research ; U.S. Department of Defense ; National Science Foundation Graduate Research Fellowship ; Stanford Bio-X Bowes Graduate Student Fellowship ; Stanford Medical Science Training Program |
PMID:31974247 | Free, Freely available | SCR_022828 | Cellular (Cyto) Trajectory Reconstruction Analysis using gene Counts and Expression | 2026-08-12 10:52:56 | 170 | ||||||||
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Australian Ocean Data Network Resource Report Resource Website 10+ mentions |
Australian Ocean Data Network (RRID:SCR_023134) | service resource, data repository, storage service resource | Interoperable online network of marine and climate data resources.AODN Portal provides access to all available Australian marine and climate science data and provides the primary access to IMOS data. |
is listed by: DataCite is listed by: re3data.org is listed by: FAIRsharing |
Free, Freely available | DOI:10.26198, r3d100011749, DOI:10.17616/R3CG82, r3d100010914, DOI:10.25504/FAIRsharing.j5eden | https://doi.org/10.26198, https://dx.doi.org/10.26198, http://doi.org/10.17616/R3CG82, https://fairsharing.org/10.25504/FAIRsharing.j5eden, https://doi.org/10.17616/R3CG82, https://doi.org/10.17616/R35057 | SCR_023134 | Australian Ocean Data Network | 2026-08-12 10:52:51 | 18 |
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