765 biological simulators, and the 57 you can run in a browser
Every dot is a simulator, grouped by field and coloured by how it can run. Pick a field to narrow the list, or a dot to see the tool. Ready to run here: Artistoo, COPASI, LAMMPS, msprime, NetLogo Web, SimProt, R simulators (webR). 51 guides walk through installing and running a simulator, each with an example that has been run and checked.
- Runs in the browser
- Could be ported
- Web service
- Desktop or server only
- Not assessed
Showing 765 of 765
| What it simulates | License | |||||
|---|---|---|---|---|---|---|
| R/C++ | Adaptive tau-leaping stochastic simulation of continuous-time Markov chain models (population dynamics, epidemics, biochemical networks). | Epidemiology | Run | GPL-3.0 | 2024-10 | 1 |
| R | Stochastic simulation of plant and animal breeding programs with genomes, QTL and selection. | Population genetics | Runs in the browser | MIT | 2026-10 | 75 |
| R | R package for phylogenetics whose simulation functions generate random trees (rtree, rcoal, rlineage, rbdtree) and continuous traits (rTraitCont); mostly an analysis package. | Phylogenetics and sequence evolution | Run | GPL-2 | GPL-3 | 2026-09 | 74 |
| JavaScript | Cellular Potts model simulations of cells and tissues, running in the browser or Node. | Cells and tissues | Run | MIT | 2026-07 | 41 |
| Python | Species trees and gene trees with asymmetric evolution rates, including horizontal gene transfer, plus sequence evolution on those trees. | Phylogenetics and sequence evolution | Runs in the browser | MIT | 2026-10 | 7 |
| Perl/C++ | Rule-based molecular interaction models: network generation then ODE/SSA simulation, plus network-free simulation with NFsim. | Systems biology | Runs in the browser | MIT | 2026-10 | 70 |
| JavaScript | Interactive in-browser Boolean network simulator for gene regulatory and signal transduction networks. | Gene networks and synthetic biology | Runs in the browser | — | 2021-02 | 13 |
| HTML | Engine that grows leaf arrangement, venation, silhouettes, petals and fruit from auxin transport (canalisation) rules. | Cells and tissues | Runs in the browser | MIT | 2026-09 | 38 |
| Python | Microbial community dynamics: consumer-resource models, community assembly and metacommunity migration. | Ecology and agent-based models | Runs in the browser | MIT | 2024-10 | 43 |
| C++ | Deterministic (ODE), stochastic (Gillespie, tau-leap, hybrid) and steady-state analysis of biochemical networks in SBML | Systems biology | Run | Artistic-2.0 | 2026-10 | 130 |
| JavaScript | Cellular Potts model in pure JavaScript for in-browser visualisation. | Cells and tissues | Runs in the browser | GPL-3.0 | 2019-03 | 11 |
| Python | Spatially explicit trait- and individual-based soil microbial model of litter decomposition (enzymes, taxa, substrates on a grid). | Ecology and agent-based models | Runs in the browser | MIT | 2026-08 | 16 |
| Python | Python library for phylogenetic computing, with simulation routines for birth-death and coalescent trees and for character/sequence evolution. Most of it is data handling. | Phylogenetics and sequence evolution | Runs in the browser | BSD-3-Clause | 2026-10 | 237 |
| Python | Age-structured stochastic compartmental epidemic models on contact matrices with approximate Bayesian calibration. | Epidemiology | Guide | GPL-3.0 | 2026-10 | 71 |
| JavaScript | Dependency-free JavaScript whole-body neonatal and adult cardiorespiratory physiology simulation engine that runs in a Web Worker. | Physiology and organs | Runs in the browser | MIT | 2026-10 | — |
| Python | Fast stochastic (Gillespie-type) simulation of general epidemic models on multilayer networks. | Epidemiology | Runs in the browser | MIT | 2025-12 | 3 |
| JavaScript | Whole-CNS Drosophila connectome (165k-neuron leaky integrate-and-fire spiking brain) driving a MuJoCo physics body in the browser. | Neuroscience | Runs in the browser | MIT | 2026-10 | 33 |
| R | Spatially explicit eco-evolutionary engine: dispersal, speciation, trait evolution and ecological interactions on dynamic landscapes, producing biodiversity patterns. | Ecology and agent-based models | Runs in the browser | GPL-3.0 | 2025-09 | 37 |
| R | Individual-based simulation of wildlife resource populations interacting with stakeholders and managers under management strategy evaluation. | Ecology and agent-based models | Runs in the browser | GPL (>=2) | 2026-06 | 11 |
| R | Simulates correlated gene expression data from igraph pathway/regulatory network structures via multivariate normal sampling (a data simulator, not a dynamical model). | Gene networks and synthetic biology | Runs in the browser | GPL-3.0 | 2025-05 | 25 |
| Python | Illumina metagenomic and amplicon reads with realistic error models and abundance distributions. | Sequencing and omics data | Guide | MIT | 2026-10 | 228 |
| OCaml | Stochastic network-free simulation of Kappa rule-based protein interaction models, plus static analysis and story extraction. | Systems biology | Runs in the browser | LGPL-3.0 | 2026-05 | 129 |
| C++ | General classical MD of atoms, polymers, biomolecules and coarse-grained systems. | Molecular simulation | Run | GPL-2.0 | 2026-10 | 3,090 |
| Python | SIR/SIS epidemic simulation (Gillespie and event-based) and ODE approximations on networks. | Epidemiology | Runs in the browser | MIT | 2026-09 | 165 |
| R | Simulation of landscape dynamics (habitat patch change), metapopulation persistence and range expansion under environmental change. | Ecology and agent-based models | Runs in the browser | GPL (>=2) | 2026-08 | 5 |
| R | Modular stochastic simulation of gene-drive spread through spatially explicit mosquito populations (MGDrivE 1 and 2). | Population genetics | Runs in the browser | GPL-3.0 | 2025-09 | 8 |
| R | Modular simulation of breeding programs (selection, mating, genomic/BLUP evaluation, economics) in R; MoBPSweb is a web front end. | Population genetics | Runs in the browser | GPL-3.0 | 2026-10 | 46 |
| Python/C | Exact and approximate coalescent with recombination, demography, gene conversion and mutation models; outputs tskit tree sequences. | Population genetics | Run | GPL-3.0 | 2026-09 | 218 |
| Python | Epidemic (SIR, SEIR and others) and opinion/diffusion process simulation on NetworkX and iGraph networks. | Epidemiology | Runs in the browser | BSD-2-Clause | 2026-07 | 302 |
| Python | Neural Engineering Framework models: large-scale spiking or rate neural networks (e.g. Spaun) built and simulated in Python. | Neuroscience | Runs in the browser | GPL-2.0 | 2026-08 | 950 |
| Python | Nengo backend that runs models on Intel Loihi hardware or a CPU emulator of Loihi. | Neuroscience | Runs in the browser | Apache-2.0 | 2026-08 | 42 |
| Scala | General agent-based modeling environment; its model library includes many ecology and evolution models (wolf-sheep predation etc.). | Ecology and agent-based models | Run | GPL-2.0 | 2026-10 | 1,186 |
| CoffeeScript (Scala compiler, JS runtime) | Compiler/runtime that runs NetLogo agent-based models (including ecology/evolution models) entirely in the browser. | Ecology and agent-based models | Run | GPL-2.0-or-later (commercial licenses also available) | 2026-09 | 57 |
| QML | Educational integrate-and-fire neural circuit simulator with sensors, synapses and a drag-and-drop GUI. | Neuroscience | Runs in the browser | GPL-3.0 | 2023-12 | 56 |
| R | Stochastic agent-based simulation of transmission chains for single- and dual-host (host-vector) epidemics, producing transmission trees. | Epidemiology | Runs in the browser | LGPL-3.0 | 2025-08 | 8 |
| R | Simulation of PK-PD models defined as ODE systems, with dosing regimens and population variability | Physiology and organs | Runs in the browser | MIT | 2026-09 | 51 |
| Python | Interpreter and simulator for LEMS/NeuroML2 models of neurons, channels, synapses and networks | Neuroscience | Guide | LGPL-3.0 | 2026-07 | 12 |
| Python | Simulates nucleotide, amino-acid and codon sequences along phylogenies using continuous-time Markov models of sequence evolution. | Population genetics | Guide | BSD-2-Clause | 2021-12 | 80 |
| Python | Rodent locomotion in continuous environments and synthetic activity of place, grid, boundary-vector and head-direction cells | Neuroscience | Runs in the browser | MIT | 2026-07 | 272 |
| HTML | Single-file offline browser simulator of random Boolean networks (Kauffman-type gene regulation models) under five update-scheme classifications (CRBN, ARBN, DARBN, GARBN, DGARBN). | Gene networks and synthetic biology | Runs in the browser | MIT | 2026-08 | 1 |
| Python | SEIRS compartmental and network-structured epidemic models with testing, contact tracing and social distancing extensions. | Epidemiology | Runs in the browser | MIT | 2023-03 | 681 |
| Python | Single-cell expression with stochastic transcription driven by a user-provided gene regulatory network, including differentiation trajectories. | Sequencing and omics data | Runs in the browser | GPL-3.0 | 2024-05 | 85 |
| R | Simulates genetic variants for unrelated individuals and multi-generation family pedigrees from a phased VCF, preserving LD structure and modelling recombination in pedigrees. | Population genetics | Runs in the browser | GPL-2.0-or-later | 2021-09 | 19 |
| R/C | Data-driven stochastic continuous-time Markov chain disease spread across nodes/herds with movement data (livestock). | Epidemiology | Run | GPL-3.0 | 2026-09 | 39 |
| JavaScript | Browser JavaScript ODE solver for SBML models (README: 'sim.js, an ODE solver for your browser') | Systems biology | Runs in the browser | — | 2013-08 | — |
| C++ | Protein sequence evolution along a phylogenetic tree with empirical substitution matrices (PAM/JTT/PMB), gamma rate heterogeneity and an empirical indel distribution (Qian-Goldstein), outputting true alignments for benchmarking | Phylogenetics and sequence evolution | Run | GPL-3.0-or-later (developer's rights; original UHN notice kept) | 2026-10 | — |
| R | Mechanistic simulation of individual, spatially explicit multistate animal movement in heterogeneous landscapes and river networks. | Ecology and agent-based models | Runs in the browser | GPL-3.0 | 2024-09 | 16 |
| JavaScript | Web app simulating target-controlled infusion / TIVA anaesthesia pharmacokinetics and effect-site concentrations | Physiology and organs | Runs in the browser | GPL-3.0 | 2026-09 | 20 |
| R | Simulates outbreak line lists and contact tracing data from an epidemic/transmission model. | Epidemiology | Runs in the browser | MIT | 2026-09 | 11 |
| R, Python, Julia, Scala (GitHub detects AMPL) | Models and code (R, Python, Julia, Scala) for stochastic simulation of biochemical networks (Gillespie, tau-leap, spatial) from the textbook Stochastic Modelling for Systems Biology | Systems biology | Runs in the browser | GPL-3.0 | 2025-10 | 34 |
| R | R metapackage and framework for spatial discrete-event simulation of ecological and landscape models. | Ecology and agent-based models | Runs in the browser | GPL-3.0 | 2026-09 | 55 |
| Python | Standard library of community-curated species demographic models, genetic maps and DFEs that drives msprime or SLiM population genetic simulations. | Population genetics | Guide | GPL-3.0 | 2026-10 | 145 |
| Python | Stochastic simulation of biochemical systems (Gillespie SSA variants, tau-leap, SBML import) | Systems biology | Runs in the browser | BSD-3-Clause | 2025-06 | 44 |
| R/C++ | Bayesian inference of transmission trees from genomic data; also simulateOutbreak to generate outbreaks and phylogenies. | Epidemiology | Runs in the browser | GPL-2.0 | 2026-07 | 72 |
| Python | Numerical solvers (Fisher-Kolmogorov reaction-diffusion type) for glioma/tumor growth on brain atlases and DTI. | Cells and tissues | Runs in the browser | MIT | 2025-10 | 17 |
| Python | All-sites VCFs with configurable missing data generated from msprime coalescent simulations. | Population genetics | Guide | MIT | 2026-07 | 5 |
| JavaScript | Browser-based simulation of the C. elegans connectome with an interactive 3D/SVG worm | Neuroscience | Runs in the browser | MIT | 2026-06 | 425 |
| C++ | Forward-time simulation of admixed populations with local ancestry tracts. | Population genetics | Could be ported | GPL-3.0 | 2025-12 | 7 |
| C++ | In silico experimental evolution of digital organisms with explicit genome, genes, transcription/translation and genotype-to-phenotype map. | Ecology and agent-based models | Could be ported | — | 2026-06 | 1 |
| C++ | Alignments with indels and complex substitution models (mixture, codon, heterotachy) along trees, built into IQ-TREE 2. | Phylogenetics and sequence evolution | Could be ported | GPL-2.0 | 2026-07 | 336 |
| C++ | In-silico amplicon sequencing assay reads generated from a reference and primer scheme | Sequencing and omics data | Could be ported | Apache-2.0 | 2024-03 | 2 |
| Fortran | FAO AquaCrop water-driven crop yield model (Fortran source, v7.3). | Physiology and organs | Could be ported | BSD-3-Clause | 2026-10 | 83 |
| C++ | Morphologically detailed multi-compartment neuron networks, targeting HPC (MPI) and GPU architectures. | Neuroscience | Could be ported | BSD-3-Clause | 2026-10 | 136 |
| C++ | Illumina, 454 and SOLiD next-generation sequencing reads with empirical error models and quality profiles | Sequencing and omics data | Could be ported | — | — | |
| C | Protein-peptide docking that folds a flexible peptide in the receptor potential field using Monte Carlo search (up to ~20 residues, also cyclic peptides). | Molecular simulation | Could be ported | LGPL-2.0 | 2025-10 | 64 |
| C++ | Stochastic ligand-protein molecular docking with an empirical scoring function and gradient-assisted local optimisation. | Molecular simulation | Guide | Apache-2.0 | 2026-08 | 1,081 |
| C++ | Digital evolution: self-replicating computer programs that mutate, compete and evolve under selection in a virtual world. | Ecology and agent-based models | Could be ported | LGPL-3.0-or-later | 2025-01 | 669 |
| C++ | Neutral genomic evolution in interconnected bacterial populations under a Wright-Fisher model, with mutation, recombination, indels, migration and micro-epidemics, on explicit sequences. | Phylogenetics and sequence evolution | Could be ported | BSD-3-Clause | 2018-02 | — |
| Go | Re-implementation of the BEEHAVE honeybee colony and foraging model in Go with an entity component system (basic colony and foraging models). | Ecology and agent-based models | Could be ported | GPL-3.0 | 2026-04 | 6 |
| C++ | bppseqgen generates sequence alignments under Bio++ substitution models (nucleotide, codon, protein, with rate heterogeneity) along a given tree. | Phylogenetics and sequence evolution | Guide | CECILL-2.1 | 2026-10 | 18 |
| C++ | Finite-volume solver for diffusing substrates with cell secretion and uptake in 3D tissue. | Cells and tissues | Could be ported | Apache-2.0 | 2020-10 | 3 |
| C++ | Whole-body human physiology engine for medical training and research simulation. | Physiology and organs | Could be ported | Apache-2.0 | 2026-01 | 69 |
| C++ | Rigid-body dynamics library for musculoskeletal models (forward/inverse dynamics, muscle forces). | Physiology and organs | Could be ported | MIT | 2026-09 | 85 |
| C++ | Evolution of simple neural-network-controlled virtual creatures under selection in a 2D arena (artificial life; a toy model, not a quantitative biological model). | Ecology and agent-based models | Could be ported | MIT | 2026-06 | 3,366 |
| R | R package for synchronous, asynchronous and probabilistic Boolean networks: random network generation, Markov chain simulation, perturbation robustness, attractor identification, reconstruction from time series. | Gene networks and synthetic biology | Could be ported | Artistic-2.0 | — | |
| Rust | NGS reads that mimic the nucleotide (k-mer) profile of real reads, to generate control sets that correct nucleotide-content bias. | Sequencing and omics data | Guide | MIT | 2023-03 | 6 |
| C | Multispecies coalescent software. Its --simulate mode (the former MCcoal) simulates gene trees and sequences; the main use is Bayesian inference. | Phylogenetics and sequence evolution | Could be ported | AGPL-3.0 | 2026-10 | 115 |
| R | Generic PK/PD simulation platform (model definition and trial simulation) on rxode2 and mrgsolve engines. | Physiology and organs | Could be ported | GPL-3.0 | 2026-10 | 11 |
| R/C++ | Fast phylogenetics on large trees: random tree generation, discrete and continuous trait evolution simulation, and ancestral state reconstruction. Much of it is analysis. | Phylogenetics and sequence evolution | Could be ported | GPL (>= 2) | 2026-08 | 2 |
| C | Coalescent simulation of single-cell NGS genotypes with sequencing errors, allelic dropout and doublets. | Population genetics | Could be ported | none-found | 2025-02 | 15 |
| C++ | Collective-variable library for enhanced sampling and biasing (metadynamics, ABF, etc.) inside NAMD, LAMMPS, GROMACS and others; not standalone. | Molecular simulation | Could be ported | LGPL-3.0 | 2026-10 | 243 |
| C++ | Coalescent simulation with recombination maps, demography and selection. | Population genetics | Could be ported | GPL-3.0 | 2026-05 | 5 |
| C++ | Imperial College individual-based microsimulation of COVID-19 transmission over a spatially structured population with non-pharmaceutical and pharmaceutical interventions. | Epidemiology | Could be ported | GPL-3.0 | 2023-02 | 1,234 |
| C++/Python | Structural-functional root system model for architecture growth and water/solute transport. | Physiology and organs | Could be ported | GPL-3.0-or-later | 2019-11 | 20 |
| C++ | Brownian-dynamics simulation of flexible cytoskeletal filaments with molecular motors and crosslinkers. | Cells and tissues | Guide | GPL-3.0 | 2026-10 | 8 |
| C++ | DNA sequence evolution in continuous time under a GTR model with gamma and invariant-site rate variation and a power-law indel model. It also outputs the true alignment. | Phylogenetics and sequence evolution | Could be ported | GPL-2.0 | 2022-03 | — |
| Fortran | Semiempirical density-functional tight-binding calculations, MD and QM/MM. | Molecular simulation | Guide | LGPL-3.0-or-later | 2026-10 | 437 |
| C | Coalescent samples with hard/soft sweeps, recombination, gene conversion and non-equilibrium demography. | Population genetics | Could be ported | GPL-3.0 | 2026-05 | 50 |
| R | State-dependent diversification (BiSSE, MuSSE, QuaSSE and others): simulates trees under these models, but mostly does likelihood inference. | Phylogenetics and sequence evolution | Could be ported | GPL (>= 2) | 2024-10 | 33 |
| Fortran | Process-based crop growth, soil water and nutrient simulation across many crops (Decision Support System for Agrotechnology Transfer Cropping System Model). | Physiology and organs | Could be ported | BSD-3-Clause | 2026-10 | 235 |
| C++/R | Engine for running many parallel realisations of discrete-time stochastic models (e.g. epidemic and compartmental models) with particle filtering. | Epidemiology | Could be ported | MIT | 2025-08 | 20 |
| C | Whole-genome and amplicon reads with SNPs, indels and structural variants for Illumina, SOLiD and Ion Torrent. | Sequencing and omics data | Guide | GPL-2.0 | 2025-12 | 105 |
| R | Single-cell multi-omics data (including reads-level counts) from simulated gene regulatory network dynamics along cell trajectories. | Sequencing and omics data | Could be ported | MIT | 2026-04 | 83 |
| Go | Biologically based neural network models of cognition (Leabra algorithm), in Go with a Cogent Core GUI. | Neuroscience | Could be ported | BSD-3-Clause | 2026-06 | 233 |
| R (with C++ solvers) | R library of published compartmental epidemic models (e.g. age-structured SEIR, Ebola, vaccine-leaky) with demographic structure, interventions and vaccination regimes. | Epidemiology | Could be ported | MIT | 2026-09 | 19 |
| R | Deterministic compartmental, stochastic individual-contact and network-based (ERGM/TERGM) models of infectious disease transmission. | Epidemiology | Could be ported | GPL-3.0 | 2026-10 | 281 |
| Rust | Rust agent-based epidemiology simulation framework with an engine and an orchestrator for multi-engine large-scale runs. | Epidemiology | Could be ported | AGPL-3.0 | 2024-02 | 107 |
| C++ | Metropolis Monte Carlo of coarse-grained biomolecules, electrolytes and proteins in various ensembles. | Molecular simulation | Guide | MIT | 2026-03 | 72 |
| C++ | Nonlinear implicit finite element simulation of solid biomechanics and biophysics (soft tissue, cartilage, heart mechanics, biphasic/multiphasic transport). | Physiology and organs | Could be ported | MIT | 2026-10 | 288 |
| C++ | Forward simulation of large sexual populations with many loci, recombination, selection and arbitrary epistasis, tracking genotype space (C++ with Python interface). | Population genetics | Could be ported | GPL-3.0 | 2025-10 | 14 |
| C | Spatially explicit, stochastic model of half-sarcomere myofilament-level muscle contraction. | Physiology and organs | Could be ported | — | 2026-07 | 7 |
| C++ | Stochastic agent-based influenza epidemic in synthetic US populations with pharmaceutical and social-distancing interventions. | Epidemiology | Could be ported | GPL-3.0-or-later | 2020-09 | 21 |
| Fortran | Forest successional dynamics: plant growth, reproduction, mortality, competition for light and soil resources and soil biogeochemistry (LM3-PPA based), used for evolutionarily stable strategy analysis. | Ecology and agent-based models | Could be ported | none found | 2020-05 | 13 |
| Rust | Rust library for forward-time simulation with tree-sequence recording (experimental). | Population genetics | Could be ported | MIT | 2025-02 | 5 |
| R | Fossil occurrences and taxonomy (morphospecies) simulated on phylogenies under mechanistic models of preservation and sampling. | Phylogenetics and sequence evolution | Could be ported | GPL-3.0 | 2026-10 | 12 |
| C++ | Coalescent simulation of haplotype samples under faster-than-exponential population growth. | Population genetics | Could be ported | none declared | 2017-05 | 1 |
| C++ | C++ template library for efficient forward-time population genetic simulation (Wright-Fisher, selection, recombination, tree-sequence recording). | Population genetics | Could be ported | GPL-3.0 | 2021-10 | 28 |
| C | 2D musculoskeletal dynamics model (multibody skeleton plus Hill-type muscles) for posture and gait simulation and optimal control. | Physiology and organs | Could be ported | Apache-2.0 | 2026-10 | 11 |
| R | R package for macroevolutionary model fitting that also simulates trees (sim.bdtree) and trait evolution (sim.char). Mostly analysis. | Phylogenetics and sequence evolution | Could be ported | GPL (>= 2) | 2026-08 | 26 |
| C++ | Forward-time simulator of individual-level whole-genome sequence/SNP data and phenotypes with mating systems, selection, migration and recombination. | Population genetics | Could be ported | MIT | 2019-01 | 7 |
| C++ | Rapid coalescent-based whole-genome simulation with variable recombination rates and flexible population histories. | Population genetics | Could be ported | — | — | |
| C | Fast stochastic simulation of breeding schemes (crossing, selfing, selection) with genotype tracking; C library with R and Python bindings. | Population genetics | Could be ported | MIT | 2025-11 | 10 |
| R/C++ | Gillespie stochastic simulation algorithm (exact and approximate) for arbitrary reaction systems, such as chemical kinetics, population dynamics and SIR examples. | Epidemiology | Could be ported | GPL (>= 3) | 2023-01 | 9 |
| C | Simulation and Markov chain Monte Carlo Bayesian inference for ODE models (including SBML), widely used for PBPK and toxicokinetics. | Physiology and organs | Could be ported | GPL | — | |
| C++ | Monte Carlo molecular simulation (Gibbs, NPT, grand canonical ensembles) with CPU/OpenMP and GPU builds. | Molecular simulation | Could be ported | MIT | 2026-10 | 90 |
| C++ | Classical MD of proteins, lipids and nucleic acids with GPU acceleration, free-energy and enhanced-sampling support. | Molecular simulation | Guide | LGPL-2.1 | 2026-10 | 968 |
| C++ | Biomolecular MD (md++ engine, GROMOS++ analysis) and the GROMOS force-field family. | Molecular simulation | Could be ported | GPL-2.0 | 2026-10 | 14 |
| R | Generic and chemical-specific PBTK/toxicokinetic ODE models for high-throughput prediction and IVIVE. | Physiology and organs | Could be ported | MIT + file LICENSE | 2026-04 | 32 |
| C++ | Gene genealogies under Kingman and multiple-merger (Lambda) coalescents within species trees and networks. It can also generate infinite-sites data and compute FST. | Phylogenetics and sequence evolution | Could be ported | GPL-3.0 | 2022-04 | 6 |
| C++ | Nucleotide, amino-acid and codon sequence evolution with substitutions and indels under rich substitution and indel-length models. | Population genetics | Could be ported | — | — | |
| R | R framework for specifying and simulating individual-based epidemiological models. | Epidemiology | Could be ported | MIT + file LICENSE | 2026-06 | 35 |
| Rust | CDC Rust framework for discrete-event agent-based infectious disease models. | Epidemiology | Could be ported | Apache-2.0 | 2026-10 | 36 |
| C++ | Variant haplotypes evolved from a reference genome using phylogenies, gene trees, coalescent output or VCF, plus Illumina and PacBio read simulation. | Phylogenetics and sequence evolution | Could be ported | MIT | 2025-09 | 8 |
| C | C library and reference implementation for ODE simulation of SBML models, including events, algebraic rules and delays. | Systems biology | Could be ported | LGPL-2.1 | 2021-09 | 13 |
| C++ | Markovian coalescent simulator for genome-scale haplotypes with recombination under arbitrary population histories. | Population genetics | Could be ported | Apache-2.0 | 2019-10 | 17 |
| C++ core with R interface (original C#) | Mechanistic global general ecosystem model of autotroph, herbivore, carnivore and omnivore cohorts across body sizes with stochastic ecological processes. | Ecology and agent-based models | Could be ported | GPL (>=3) | 2024-06 | 6 |
| R/C++ | Fast time-discrete compartmental simulation of malaria transmission, an R package. | Epidemiology | Could be ported | MIT + file LICENSE | 2026-07 | 1 |
| R | Imperial College individual-based P. falciparum malaria transmission model with mosquito dynamics and interventions. | Epidemiology | Could be ported | MIT + file LICENSE | 2026-10 | 23 |
| C++ | Mason2 simulates variants and Illumina/454/Sanger reads (apps/mason2 in SeqAn 2). | Sequencing and omics data | Could be ported | BSD-3-Clause | 2026-08 | 502 |
| C++ | Particle-based Monte Carlo 3D reaction-diffusion simulation of cellular microphysiology (MCell4 with BioNetGen rule-based reactions). | Systems biology | Could be ported | MIT | 2026-07 | 39 |
| C++ | Modular multi-scale epidemic simulation: ODE, graph/metapopulation and agent-based models. | Epidemiology | Could be ported | Apache-2.0 | 2026-10 | 71 |
| C++ | Mesoscopic stochastic reaction-diffusion simulation of cellular systems using the next-subvolume method. | Systems biology | Could be ported | GPL-2.0 | — | |
| C | Shotgun reads from evolving microbial populations under the sequentially Markov coalescent with substitution models. | Sequencing and omics data | Could be ported | none-found | 2019-01 | 1 |
| C | Coalescent-based (sequentially Markov coalescent) shotgun read simulation for evolving microbial populations with mutator subpopulations | Phylogenetics and sequence evolution | Could be ported | — | 2019-01 | 1 |
| R | Spatial mosquito population genetics of gene drives with seasonality, coupled to human malaria transmission via Petri-net stochastic models. | Epidemiology | Could be ported | GPL-3 | 2025-09 | 8 |
| R | Dynamic multi-species size-spectrum model of fish communities and fishing impacts. | Ecology and agent-based models | Could be ported | GPL-3 | 2026-09 | 42 |
| C++ | Multiscale simulation of compartmental neurons and chemical-kinetics signaling pathways (stochastic and deterministic). | Neuroscience | Could be ported | GPL-3.0 | 2025-03 | 19 |
| C++/R | Individual-based P. vivax malaria transmission model (R wrapper around a C++ model). | Epidemiology | Could be ported | MIT | 2023-08 | 2 |
| C | Neutral coalescent samples under a Wright-Fisher model with recombination, gene conversion, migration/subdivision and demographic changes; outputs the ms format followed by msms, scrm and discoal. | Population genetics | Could be ported | — | — | |
| Python | Musculoskeletal models (muscle-actuated limbs and bodies) and motor-control tasks simulated with the MuJoCo physics engine through a Gym API | Physiology and organs | Could be ported | Apache-2.0 | 2026-10 | 1,240 |
| C++ | Individual-based, genetically explicit stochastic forward simulation of population genetics and life-history evolution in metapopulations. | Ecology and agent-based models | Guide | GPL (version not stated; 'GNU General Public License') | — | |
| C++ | Nonequilibrium reaction-diffusion self-assembly: structure-resolved multibody assembly at the cellular scale. | Cells and tissues | Could be ported | GPL-3.0 | 2026-10 | 3 |
| C++ | Structure-resolved reaction-diffusion simulator for nonequilibrium multibody self-assembly at cellular scale. | Systems biology | Could be ported | GPL-3.0 | 2026-10 | 3 |
| C++ | Network-free stochastic simulation of rule-based (BioNetGen) models with large combinatorial state spaces. | Systems biology | Could be ported | MIT | 2026-09 | 17 |
| C++ | Continuum neural field model simulations of multi-population brain dynamics across scales (C++ core with Matlab analysis routines). | Neuroscience | Could be ported | Apache-2.0 | 2018-12 | 38 |
| C++ | Differentiable rigid-body physics engine used for biomechanics (human motion fitting, musculoskeletal dynamics) and learning | Physiology and organs | Could be ported | BSD-2-Clause | 2025-09 | 494 |
| R/C++ | Age-structured SEIR COVID-19 model with vaccination, an extension of squire, built on odin.dust. | Epidemiology | Could be ported | MIT | 2025-12 | 9 |
| R | Domain-specific language that compiles ODE and discrete-time stochastic compartmental models, widely used for epidemic models. | Epidemiology | Could be ported | MIT | 2026-01 | 106 |
| C/Python/R | Age-stratified agent-based SARS-CoV-2 epidemic on realistic social networks, with manual/digital contact tracing, NPIs and vaccination. | Epidemiology | Could be ported | GPL-3.0 | 2025-10 | 130 |
| C++ | Stochastic individual-based simulation of Plasmodium falciparum malaria epidemiology and control, including within-host dynamics, vectors and interventions. | Epidemiology | Could be ported | GPL-2.0 | 2026-10 | 90 |
| C++ | Molecular dynamics engine for molecular, soft-matter and biomolecular systems. | Molecular simulation | Could be ported | BSD-3-Clause | 2026-08 | 92 |
| C++ | Dynamic simulation of musculoskeletal models and movement (forward and inverse dynamics, muscle forces, optimal control via Moco) | Physiology and organs | Guide | Apache-2.0 | 2026-10 | 1,125 |
| C++ | Coarse-grained DNA and RNA model simulation (MD and Monte Carlo), e.g. nanostructures. | Molecular simulation | Could be ported | GPL-3.0 | 2026-10 | 76 |
| R | Simulation of fossil-record diversification and sampling processes (birth-death with preservation), plus tree time-scaling and analysis | Phylogenetics and sequence evolution | Could be ported | CC0-1.0 | 2026-07 | 23 |
| C | The evolver program of PAML simulates nucleotide, codon and amino-acid sequences along trees and generates random trees | Phylogenetics and sequence evolution | Could be ported | GPL-3.0 | 2026-01 | 206 |
| C++ | PacBio and ONT long reads with an HMM-based generative model of quality scores. | Sequencing and omics data | Guide | GPL-2.0 | 2023-07 | 76 |
| C++ | PacBio (CLR, CCS/HiFi) and ONT reads, including multi-pass and transcriptome simulation. | Sequencing and omics data | Guide | GPL-2.0 | 2025-04 | 120 |
| C++ | Haplotype data for user-defined pedigrees with sex-specific genetic maps and crossover interference, tracking IBD segments among relatives. | Population genetics | Could be ported | GPL-3.0 | 2026-08 | 34 |
| R/C++ | Coalescent simulation and likelihood under structured epidemic ODE models (phylodynamics). | Epidemiology | Could be ported | GPL-3.0 | 2025-05 | 17 |
| C++ | PhysiBoSS 2.0: PhysiCell agent-based multicellular simulation with MaBoSS stochastic Boolean intracellular networks inside each cell agent (tumour growth, drug response). | Gene networks and synthetic biology | Could be ported | BSD-3-Clause | 2026-10 | 36 |
| C++ | Open source physics-based 3-D agent-based multicellular simulator with diffusing substrates (BioFVM), cell cycle, death, volume, mechanics and motility sub-models. | Gene networks and synthetic biology | Could be ported | BSD-3-Clause | 2026-10 | 217 |
| R | Simulation of phylogenies (birth-death, coalescent) and continuous/discrete trait evolution on trees, within a broad comparative-methods package | Phylogenetics and sequence evolution | Could be ported | GPL-3.0 | 2026-09 | 234 |
| C++ | Step-wise stochastic gene expression simulator with individual polymerase and ribosome detail and codon-specific translation rates. | Systems biology | Could be ported | MIT | 2025-07 | 14 |
| C++ | Trait-based, size-structured forest/vegetation demography and ecology-evolution models of plant populations | Physiology and organs | Could be ported | AGPL-3.0 | 2026-10 | 55 |
| C++ | Enhanced-sampling and free-energy biasing library (metadynamics, umbrella sampling) plugged into MD engines. | Molecular simulation | Could be ported | LGPL-3.0 | 2026-10 | 520 |
| R/C | Simulation of and inference for partially observed Markov process models, commonly epidemic/ecological dynamics. | Epidemiology | Could be ported | GPL-3.0 | 2026-09 | 122 |
| C++ | Cellular Potts model (cell-based tissue/morphogenesis simulation) in C++ with config-file driven runs. | Cells and tissues | Could be ported | — | 2023-02 | 3 |
| C | Forward simulation under the Poisson Random Field model: demography, inbreeding, dominance, distributions of selection coefficients and allele trajectories. | Population genetics | Guide | GPL-3.0 | 2020-10 | 1 |
| C | Protein evolution along phylogenies/coalescent histories under structurally constrained (folding stability) substitution models, with recombination and birth-death forecasting | Phylogenetics and sequence evolution | Could be ported | — | 2025-09 | 6 |
| C++ | Whole-body human physiology engine (cardiovascular, respiratory, renal, drug/PK, etc.) for medical training simulation | Physiology and organs | Could be ported | — | 2026-10 | 38 |
| Python | Active finite Voronoi (AFV) model of confluent epithelial tissue, with Cython-accelerated core. | Cells and tissues | Guide | MIT | 2026-09 | 42 |
| Fortran | Python bindings to the USFS Forest Vegetation Simulator (tree growth and yield). | Ecology and agent-based models | Could be ported | — | 2026-08 | 16 |
| Cython | Particle-based reaction-diffusion simulations (Brownian particles with reactions) as a Python/Cython module. | Cells and tissues | Could be ported | MIT | 2024-06 | — |
| Python/Cython | Deterministic and stochastic compartmental epidemic models with Bayesian inference, forecasting and optimal control. | Epidemiology | Could be ported | MIT | 2024-08 | 167 |
| C++ | Individual-based (and population-based) stochastic simulation of quantitative traits and neutral markers in structured metapopulations with selection, mutation, recombination, migration and habitat heterogeneity. | Population genetics | Could be ported | GPL-3.0 | 2026-07 | 8 |
| C | Random Circuit Perturbation: generates an ensemble of ODE models with randomized kinetic parameters for a fixed gene regulatory circuit topology and analyses robust dynamical states. | Gene networks and synthetic biology | Could be ported | Apache-2.0 | 2020-06 | 16 |
| Rust | Hybridization-capture metagenomic sequencing: thermodynamic nearest-neighbour bait-target binding with Boltzmann-weighted fragment sampling, followed by platform error models. | Sequencing and omics data | Could be ported | none-found | 2026-03 | 2 |
| Rust | Minimal parallel Rust/PyO3 Gillespie SSA engine for stochastic reaction networks, with a NumPy-friendly Python API | Systems biology | Could be ported | BSD-3-Clause | 2026-02 | 3 |
| Rust | Oxford Nanopore reads with realistic quality profiles. | Sequencing and omics data | Could be ported | GPL-3.0 | 2025-12 | — |
| Rust | Fast Gillespie SSA simulator for chemical reaction networks (Rust core with Python bindings) | Systems biology | Could be ported | MIT | 2026-08 | 47 |
| C | Coalescent simulation of coding DNA sequences under codon models with recombination, migration and demography | Phylogenetics and sequence evolution | Could be ported | — | — | |
| Rust | Long reads (Nanopore/PacBio-like) following the Badread model, reimplemented in Rust. | Sequencing and omics data | Could be ported | MIT | 2022-10 | 23 |
| R | ODE-based pharmacometric (PK/PD) model simulation with inter-individual variability in R, engine of nlmixr2 | Physiology and organs | Could be ported | GPL-3.0 | 2026-10 | 67 |
| R | scRNA-seq counts with Gamma-Poisson, Beta-Gamma-Poisson and bursting kinetics modes. | Sequencing and omics data | Could be ported | GPL-3 | — | |
| C++ | Sequential coalescent with recombination (SCRM approximation) for genome-scale samples, with an ms-compatible interface. | Population genetics | Guide | GPL-3.0 | 2024-01 | 46 |
| C++ | Forward-time simulation of admixture between any number of ancestral populations with selection, epistasis, local adaptation, mate choice, and autosomes or sex chromosomes. | Population genetics | Guide | GPL-3.0 | 2023-04 | 11 |
| C | Monte Carlo simulation of nucleotide and amino-acid sequence evolution along phylogenies under common substitution models. | Population genetics | Guide | — | 2025-02 | 55 |
| Rust | Rust rewrite of SERGIO: simulates single-cell gene expression data from a gene regulatory network using stochastic differential equations/chemical Langevin dynamics. | Gene networks and synthetic biology | Could be ported | GPL-3.0 | 2026-09 | 3 |
| C | Forward population-genetic simulation of sequence data with arbitrary selection regimes, recombination, demography, indels and population structure. | Population genetics | Could be ported | GPL-2.0 | — | |
| C++ | Whole bacterial genome evolution with within- and between-species homologous recombination, coalescent-based. | Population genetics | Could be ported | GPL (version not stated) | 2024-09 | 14 |
| C++ | High-performance forward-in-time population genetic simulator with spatial structure, selection, QTLs and demography. | Ecology and agent-based models | Could be ported | MIT | 2021-09 | 6 |
| C++ | High-performance forward-in-time population genetic simulator: selection, epistasis, demography, spatial patches, mating systems, QTLs and multiple species. | Population genetics | Could be ported | MIT | 2021-09 | 6 |
| C++ | Coalescent simulation of genomic diversity over large recombining regions in subdivided populations with complex demographic histories (SIMCOAL 2.0); precursor of fastsimcoal2. | Population genetics | Could be ported | — | — | |
| C++ | Agent-based model of HIV and STI spread with relationship formation, interventions and phylogenetic output. | Epidemiology | Could be ported | GPL-3.0 | 2025-02 | 1 |
| C | Species, locus and gene trees under incomplete lineage sorting, duplication/loss, horizontal gene transfer and gene conversion, plus sequences via INDELible. | Population genetics | Could be ported | GPL-2.0 | 2023-06 | 36 |
| Perl | Genomes carrying simulated SNPs, indels, CNVs, inversions and translocations (a variant-genome simulator, no reads). | Sequencing and omics data | Guide | MIT | 2025-06 | 105 |
| C++/Python | Python-scripted forward-time simulation of populations: mating schemes, selection, migration, recombination, linkage and pedigrees. | Population genetics | Guide | GPL-2.0 | 2026-02 | 37 |
| R | Phylogenetic network simulation under a birth-death-hybridization process | Phylogenetics and sequence evolution | Could be ported | GPL-3.0 | 2024-10 | 11 |
| C | Simplified Photosynthesis and EvapoTranspiration model: process-based ecosystem carbon and water cycling. | Ecology and agent-based models | Could be ported | BSD-3-Clause | 2026-10 | 41 |
| R/C++ | Stochastic age-structured SARS-CoV-2 transmission models (built on odin/dust) used for UK fitting. | Epidemiology | Could be ported | MIT | 2025-06 | 29 |
| C++ | Genetically explicit forward simulation: WF and non-WF models, selection, recombination, continuous space, multispecies eco-evolutionary dynamics and tree-sequence recording, scripted in Eidos. | Population genetics | Guide | GPL-3.0 | 2026-10 | 234 |
| C++ | Spatial stochastic Brownian-dynamics simulation of individual molecules diffusing and reacting, with surfaces and rule-based reactions | Systems biology | Could be ported | GPL-3.0 | 2026-10 | 34 |
| C++ | Forward-time simulation of asexual population dynamics with protein-level fitness landscapes from stability, expression or user-defined functions. | Population genetics | Could be ported | GPL-3.0 | 2020-10 | 7 |
| C | Raw nanopore signal (SLOW5/BLOW5) for DNA/RNA from a genome, transcriptome or reads. | Sequencing and omics data | Could be ported | MIT | 2026-03 | 83 |
| R | Age-structured SEIR COVID-19 transmission model with healthcare capacity and interventions. | Epidemiology | Could be ported | MIT | 2024-02 | 53 |
| R | R/Bioconductor package for random circuit perturbation: deterministic and stochastic (noise-driven) ensemble ODE simulation of gene regulatory circuits with randomized parameters. | Gene networks and synthetic biology | Could be ported | MIT | 2026-02 | 6 |
| C++ | Discrete stochastic (SSA, tau-leaping) simulation of well-stirred chemical kinetics, with events | Systems biology | Could be ported | GPL-3.0 | 2020-06 | 17 |
| C++ | Structural variants and reads for SV caller evaluation; also merging/comparison utilities. | Sequencing and omics data | Could be ported | MIT | 2023-12 | 426 |
| R | Simulation of reconstructed phylogenies under birth-death processes with rate shifts and mass extinctions, plus likelihood inference | Phylogenetics and sequence evolution | Could be ported | GPL-3 | 2022-01 | 3 |
| C | Artificial-life system: self-replicating machine-code organisms evolving in a virtual computer. | Ecology and agent-based models | Could be ported | — | — | |
| Fortran | Molecular modelling and dynamics with polarizable AMOEBA and other force fields. | Molecular simulation | Could be ported | Tinker licence (custom, LICENSE.pdf; free academic, commercial via licence) | 2026-10 | 164 |
| C++ | Cellular Potts model toolkit (Leiden) for tissue morphogenesis, cell sorting and related simulations. | Cells and tissues | Could be ported | GPL-2.0 | 2026-09 | 8 |
| R | Phylogenetic trees under birth-death processes with fixed extant species number, mass extinctions, rate shifts and incomplete sampling | Phylogenetics and sequence evolution | Could be ported | GPL-2 | 2019-04 | — |
| R | Phylogenetic trees under general Bellman-Harris models with arbitrary speciation/extinction waiting-time distributions and lineage-specific shifts | Phylogenetics and sequence evolution | Could be ported | GPL-2 | 2020-03 | — |
| C++ | Individual-based evolutionary simulation that generates trees and morphological character data for benchmarking phylogenetic methods. | Phylogenetics and sequence evolution | Could be ported | GPL-3.0 | 2026-07 | 8 |
| C++ | Agent-based tumor growth simulation on a lattice (C++ core, R package interface). | Cells and tissues | Could be ported | MIT | 2026-06 | 20 |
| Python | Python library for vertex-model simulation of epithelial tissue mechanics and morphogenesis. | Cells and tissues | Guide | GPL-3.0 | 2026-02 | 68 |
| C++ | Simulates sequencing read depth, genotype likelihoods and errors from input VCF/BCF genotypes (data simulator, not an evolutionary model). | Population genetics | Could be ported | GPL-3.0 | 2025-05 | 17 |
| Cython (Python package) | Forward hierarchical-Gillespie epidemic simulation with backward coalescent-like genealogy generation; supports population structure, epistasis and immune escape. | Population genetics | Could be ported | GPL-3.0 | 2026-04 | 17 |
| C | Paired-end/single-end Illumina-like reads from a reference, with SNP/indel mutations and sequencing errors. | Sequencing and omics data | Guide | MIT | 2021-09 | 290 |
| Fortran | WOFOST crop growth simulation model (Fortran version). | Physiology and organs | Could be ported | EUPL-1.1 | 2019-11 | 75 |
| C | Dynamical systems (ODEs, difference equations, delay, stochastic and boundary value problems) with bifurcation analysis via AUTO, used for models in neuroscience and biology | Systems biology | Guide | GPL-2.0 | 2020-05 | 27 |
| C++ | Yet Another BOOlean Network Simulator: C++ library to prototype and simulate Boolean networks (generic, used for gene regulatory network models). | Gene networks and synthetic biology | Could be ported | GPL-3.0 | 2018-05 | — |
| Genome evolution simulation: substitutions, indels, duplications, losses, rearrangements, LGT along a species tree. | Population genetics | Web service | — | — | ||
| C++ | Cardiac action potential prediction under drug-induced ion channel block (Chaste extension). | Physiology and organs | Web service | BSD-3-Clause | 2026-10 | 10 |
| Prolog/C (BIOCHAM 4; original BIOCHAM was SICStus/Prolog) | Environment for modeling biochemical systems with Boolean, ODE and stochastic simulation plus temporal-logic property checking and parameter search. | Systems biology | Web service | — | — | |
| Java | Systems biology platform simulating SBML and Simulink-like diagram models (ODE, stochastic) with data-analysis workflows. | Systems biology | Web service | AGPL-3.0 | 2026-10 | 7 |
| Web platform for building and real-time simulation of logical (Boolean) models of signalling/regulatory networks, including loss/gain-of-function what-if scenarios. | Gene networks and synthetic biology | Web service | — | — | ||
| Java | Digital evolution platform: self-replicating organisms with an assembly-like instruction set evolving in a 2D world, with full-tick recording, analytics and lineage tracking. | Ecology and agent-based models | Web service | MIT | 2026-10 | 28 |
| Individual-based simulation of yeast populations in liquid media: uptake, metabolism, budding reproduction and viability of cells on a 3D grid. | Ecology and agent-based models | Web service | — | — | ||
| C++ | Continuous-time Markov chain (Gillespie-style) simulation of Boolean regulatory networks; HPC/GPU implementations and the WebMaBoSS web front end exist. | Systems biology | Web service | BSD-3-Clause | 2026-10 | 3 |
| TypeScript | Web-based GUI for building and running NEST spiking networks (simulation executed by a NEST server). | Neuroscience | Web service | MIT | 2026-10 | 24 |
| Collaborative platform to share, visualize, analyze and simulate standardized (NeuroML) models of neurons and circuits | Neuroscience | Web service | — | — | ||
| R | Standard pipeline for running, parameter-estimating and evaluating 49 scRNA-seq and spatial transcriptomics simulation methods; the Simsite web tool exposes them. | Sequencing and omics data | Web service | GPL-3.0 | 2024-06 | 2 |
| Python | Simulates gene sequence evolution with exon-intron structure and alternative-splicing transcript evolution along a guide gene tree | Phylogenetics and sequence evolution | Web service | — | 2024-06 | 3 |
| JavaScript (frontend) with Python backend | Web and Jupyter platform for ODE, stochastic and spatial biochemical simulation, built on GillesPy2 and SpatialPy | Systems biology | Web service | GPL-3.0 | 2026-01 | 25 |
| Python | Large-scale brain network dynamics from connectomes and neural mass models, with EEG/MEG/fMRI forward models | Neuroscience | Web service | CeCILL-2.1 | 2026-10 | 193 |
| Java | Compartmental ODE, stochastic, spatial reaction-diffusion-advection and rule-based simulation of cell biological processes, with geometries from microscope images | Systems biology | Web service | MIT | 2026-10 | 140 |
| JavaScript (GitHub primary language; Python back end per requirements.txt) | Web platform for creating, running and viewing CellModeller individual-based simulations of multicellular bacterial populations and communities on a remote server. | Ecology and agent-based models | Web service | MIT | 2026-05 | 1 |
| JavaScript | Web interface for storing, converting, editing and stochastically simulating MaBoSS Boolean models, with import from BioModels/CellCollective and SBML-qual/GINsim/BNet. | Gene networks and synthetic biology | Web service | LGPL-3.0 | 2026-10 | 1 |
| Mathematica | Vertex model of 2D epithelial tissue mechanics, implemented in Mathematica. | Cells and tissues | Desktop or server only | — | 2022-02 | 8 |
| Mathematica | Vertex model of 3D biological tissue mechanics, implemented in Mathematica. | Cells and tissues | Desktop or server only | — | 2021-10 | 12 |
| GPU-accelerated production molecular dynamics engine for biomolecular systems. | Molecular simulation | Desktop or server only | — | — | ||
| Python (Django front end; C simulation engine in a companion repo) | Spatial stochastic simulation of animal (livestock) disease spread within and between herds, with detection, tracing and containment (successor to NAADSM). | Epidemiology | Desktop or server only | BSD-2-Clause (LICENSE file text; GitHub API reports NOASSERTION) | 2026-05 | 10 |
| C++ | Large-scale simulation of cytoskeletal filament and motor ensembles (active matter / mitotic spindle-like systems). | Cells and tissues | Desktop or server only | Apache-2.0 | 2025-11 | 17 |
| Darwin (.drw scripts) | Whole-genome evolution along a species tree: substitutions, indels, rearrangements, gene duplication, loss and transfer. | Phylogenetics and sequence evolution | Desktop or server only | — | 2020-04 | 4 |
| C++ | CUDA-powered artificial life engine with evolving particle-based digital organisms. | Ecology and agent-based models | Desktop or server only | BSD-3-Clause | 2026-10 | 5,538 |
| C++ | Agent-based simulation of animal populations in realistic agricultural landscapes with farm management. | Ecology and agent-based models | Desktop or server only | — | — | |
| Biomolecular molecular dynamics suite with force fields; PMEMD (CPU/GPU) for explicit-solvent PME MD, AmberTools provides sander and setup/analysis tools. | Molecular simulation | Desktop or server only | — | — | ||
| Python (C++ core, MATLAB interface) | Compiled ODE simulation of SBML/PEtab models with forward and adjoint sensitivity analysis (CVODES/IDAS). | Systems biology | Desktop or server only | BSD-3-Clause | 2026-10 | 144 |
| C++ | Coupled 3D phase-field tumor growth and 1D vascular network model for tumor angiogenesis. | Cells and tissues | Desktop or server only | BSL-1.0 | 2021-06 | 5 |
| Python | Rate-coded and spiking neural network simulation via C++/CUDA code generation. | Neuroscience | Desktop or server only | GPL-2.0 | 2026-10 | 46 |
| Inverse-dynamics musculoskeletal simulation of muscle and joint forces. | Physiology and organs | Desktop or server only | commercial | — | — | |
| CUDA/C++ | GPU-accelerated within-host simulator of viral evolution and infection dynamics across population, tissue and cell levels, scaling to hundreds of millions of genomes. | Epidemiology | Desktop or server only | MIT | 2026-04 | 16 |
| C# | Crop, soil and farm-system simulation (farming-systems modelling framework). | Physiology and organs | Desktop or server only | APSIM General Use Licence Agreement (custom, royalty-free for non-commercial research; not OSI) | 2026-10 | 216 |
| Java | Mechanical modeling system combining rigid bodies, finite elements and muscles for anatomical biomechanics. | Physiology and organs | Desktop or server only | BSD-2-Clause | 2026-10 | 85 |
| Python | Python framework that uses MaBoSS stochastic Boolean simulation to compare dynamics, logic functions and statistics across ensembles of Boolean models (e.g. from Bonesis). | Gene networks and synthetic biology | Desktop or server only | GPL-3.0 | 2026-09 | — |
| C | Spatially explicit end-to-end marine ecosystem model with dynamically coupled physics, ecology, fisheries, management and socio-economic modules, used for management strategy evaluation. | Ecology and agent-based models | Desktop or server only | none-found | — | |
| C++ | Fast event-driven spiking neural networks with synaptic plasticity (STDP). | Neuroscience | Desktop or server only | GPL-3.0 | 2025-03 | 112 |
| C++ | Stochastic ligand-receptor docking (AutoDock4 scoring function, selective receptor flexibility); AutoDock-GPU is the OpenCL/CUDA implementation. | Molecular simulation | Desktop or server only | GPL-2.0 | 2026-08 | 614 |
| Python | Coarse-grained protein folding and structure-prediction MD (AWSEM, plus Open3SPN2 for DNA) running on OpenMM. | Molecular simulation | Desktop or server only | MIT | 2025-05 | 39 |
| R | Individual-based metabolic modelling of microbes using genome-scale metabolic models (flux balance analysis) in a spatial grid with diffusing substrates. | Ecology and agent-based models | Desktop or server only | GPL-3.0 | 2024-08 | 39 |
| Python | Spike-in of synthetic SNVs, indels and SVs into real BAM files to simulate tumor genomes for somatic variant caller benchmarking | Sequencing and omics data | Desktop or server only | MIT | 2026-08 | 252 |
| Python | CUDA GPU-accelerated simulation, attractor detection and control of (probabilistic) Boolean networks; parses ASSA-PBN and SBML. | Gene networks and synthetic biology | Desktop or server only | Apache-2.0 | 2025-11 | 6 |
| Java | Synthetic short and long reads (with errors, indels and variants) from a reference via randomreads.sh, one tool in the BBTools suite. | Sequencing and omics data | Desktop or server only | BSD-3-Clause-LBNL (custom LBNL modified BSD) | 2026-10 | 97 |
| Perl, Python | Metagenomic whole-genome shotgun reads (Illumina, 454, Ion Torrent) with empirically derived read-length and quality distributions and automatic abundance generation. | Sequencing and omics data | Desktop or server only | Free for academic non-commercial use (custom; contact authors for commercial) | 2017-08 | — |
| Perl | RNA-seq reads (Illumina-like, with spliced and alternative isoforms, polymorphisms and errors) used to benchmark spliced aligners and isoform quantifiers. | Sequencing and omics data | Desktop or server only | — | 2015-12 | 5 |
| Scala | Scala agent-based modelling framework with an India-specific synthetic population (up to 50 million agents) used for COVID-19 school, variant and NPI scenarios. | Epidemiology | Desktop or server only | CC-BY-SA-4.0 | 2024-06 | 2 |
| Python | Spiking neural networks with local learning rules (machine-learning oriented) in PyTorch. | Neuroscience | Desktop or server only | AGPL-3.0 | 2026-10 | 1,704 |
| C++ | Modular high-performance agent-based simulation platform for biology (neuroscience, oncology, epidemiology). | Ecology and agent-based models | Desktop or server only | Apache-2.0 | 2026-10 | 137 |
| Julia | Bio-energetic (Yodzis-Innes) food web biomass dynamics, solved as ODEs on a food web network. | Ecology and agent-based models | Desktop or server only | MIT | 2022-03 | 28 |
| Java | Java toolkit for multi-valued logical qualitative models: SBML-qual I/O, perturbations, reduction, simulation under synchronous/asynchronous/random updating, attractor search. | Gene networks and synthetic biology | Desktop or server only | LGPL-3.0 | 2026-04 | 20 |
| Java | Cytoscape app simulating dynamics of KEGG-derived regulatory/signalling networks with a simple discrete-time model using expression data. | Gene networks and synthetic biology | Desktop or server only | — | — | |
| Python | Optimal control and predictive simulation of musculoskeletal models (CasADi, Ipopt, biorbd). | Physiology and organs | Desktop or server only | MIT | 2026-10 | 120 |
| Python | API for biologically detailed single-cell and small-network simulations, running on the NEURON simulator. | Neuroscience | Desktop or server only | Apache-2.0 | 2025-02 | 15 |
| Python | Building and simulating brain circuit models at biophysical, point-neuron and population levels via NEURON, NEST, DiPDE and its own back ends. | Neuroscience | Desktop or server only | BSD-3-Clause | 2026-10 | 336 |
| Python | Biologically detailed multi-compartment brain cell models in JAX. | Neuroscience | Desktop or server only | Apache-2.0 | 2026-09 | 14 |
| Python | Whole-brain neural mass models, differentiable, built on the BrainPy/JAX ecosystem. | Neuroscience | Desktop or server only | Apache-2.0 | 2026-07 | 9 |
| Python | Spiking, rate and neural-mass brain dynamics models, JIT-compiled with JAX. | Neuroscience | Desktop or server only | GPL-3.0 | 2026-08 | 715 |
| Python | CUDA GPU backend (code-generation device) for Brian 2 spiking network simulation. | Neuroscience | Desktop or server only | GPL-3.0 | 2026-09 | 84 |
| Python | Brian 2 frontend that runs models on the GeNN GPU simulator. | Neuroscience | Desktop or server only | GPL-2.0 | 2026-03 | 51 |
| Java | Agent-based simulation of bacterial populations (growth, chemotaxis, signalling) in microfluidic/synthetic-biology settings. | Physiology and organs | Desktop or server only | MIT | 2021-10 | 15 |
| Java | Agent-based simulator of bacterial populations (capsule-shaped cells, growth, chemotaxis, quorum sensing, DDEs, microfluidic chemostat geometries). | Ecology and agent-based models | Desktop or server only | MIT | 2021-10 | 15 |
| Python | Generates NeuroML multiscale network models of the C. elegans nervous system, run through jNeuroML/NEURON/other engines. | Neuroscience | Desktop or server only | MIT | 2026-10 | 158 |
| Python | Residue-level coarse-grained simulation of intrinsically disordered proteins, conformations and phase separation, run through OpenMM. | Molecular simulation | Desktop or server only | GPL-3.0 | 2026-09 | 101 |
| Python | Microbial communities with abundance profiles, time series and strain diversity, producing second- and third-generation metagenome reads plus gold standards. | Sequencing and omics data | Desktop or server only | Apache-2.0 | 2026-07 | 233 |
| C++ | Large-scale cardiac electrophysiology and mechanics simulation on HPC systems (LLNL). | Physiology and organs | Desktop or server only | MIT | 2024-05 | 66 |
| C++ | Finite element framework for cardiac electromechanics. | Physiology and organs | Desktop or server only | GPL-3.0 | 2026-10 | 11 |
| C++ | GPU-accelerated large-scale spiking neural networks with biological detail and plasticity. | Neuroscience | Desktop or server only | MIT | 2025-11 | 59 |
| Julia | Symbolic chemical reaction networks compiled to ODE, SDE and jump (Gillespie) simulations. | Systems biology | Desktop or server only | MIT | 2026-09 | 530 |
| Python | Adjoint-enabled cardiac electrophysiology (monodomain/bidomain) simulation with FEniCS. | Physiology and organs | Desktop or server only | LGPL-3.0 | 2023-09 | 7 |
| C++ | EMG-driven neuromusculoskeletal modelling toolbox predicting muscle excitation, forces and joint moments (OpenSim-based). | Physiology and organs | Desktop or server only | Apache-2.0 | 2026-08 | 33 |
| Java | SBML process-diagram editor for biochemical networks with built-in ODE simulation and COPASI integration. | Systems biology | Desktop or server only | Freeware (proprietary terms, source not public) | — | |
| C++ | GPU-accelerated dynamic Voronoi and vertex models of confluent cells. | Cells and tissues | Desktop or server only | MIT | 2025-07 | 27 |
| Python (OpenCL) | GPU-accelerated agent-based simulation of growing bacterial colonies with 3D cell biophysics, gene regulation and intercellular signaling. | Systems biology | Desktop or server only | BSD-3-Clause | 2026-10 | 75 |
| Java | Compiles Verilog logic into genetic circuit DNA designs and predicts circuit response with gate response-function models. | Gene networks and synthetic biology | Desktop or server only | BSD-2-Clause | 2022-09 | 877 |
| Java | Rewritten Cello for genetic circuit design (Verilog to DNA) with predicted circuit performance simulation; command-line core with a separate webapp repo. | Gene networks and synthetic biology | Desktop or server only | — | 2022-05 | 74 |
| Julia | Cellular Potts model simulation of biological cells in Julia. | Cells and tissues | Desktop or server only | MIT | 2025-10 | 22 |
| Fortran | Macromolecular energy, minimization and MD program with free-energy methods. | Molecular simulation | Desktop or server only | Proprietary (free for academic/non-profit users, per homepage) | — | |
| C++ | Cell-based and continuum simulation of tissues for computational physiology and biology (cardiac electrophysiology, cancer, crypt dynamics) with ODE/PDE solvers. | Ecology and agent-based models | Desktop or server only | BSD-3-Clause | 2026-10 | 155 |
| Python | Fast scalable breeding program simulator on JAX. | Population genetics | Desktop or server only | BSD-3-Clause | 2025-06 | 10 |
| Agent-based simulation of COVID-19 transmission, hospitalisation and death among about 2.7 million synthetic Chicago residents moving among about 1.2 million places, run on HPC. | Epidemiology | Desktop or server only | none-found | — | ||
| R | Forward-in-time simulation of age-structured populations (via SLiM) and tabulation of pairwise kin relationships for close-kin mark-recapture. | Ecology and agent-based models | Desktop or server only | CC0-1.0 | 2026-04 | 4 |
| Python | Functional structural plant model of grasses integrating shoot morphogenesis, carbon/nitrogen metabolism and water fluxes in 3D. | Physiology and organs | Desktop or server only | CeCILL-C | 2026-10 | 14 |
| Python | GUI for constraint-based metabolic modeling (FBA, FVA, elementary flux modes, OptKnock, minimal cut sets) of genome-scale networks | Systems biology | Desktop or server only | Apache-2.0 | 2026-09 | 70 |
| Python | Copy number variations (amplifications and deletions) introduced into reads generated by existing NGS read simulators. | Sequencing and omics data | Desktop or server only | — | 2018-07 | 11 |
| MATLAB | MATLAB suite for constraint-based reconstruction and analysis (FBA, FVA, sampling) of metabolic networks | Systems biology | Desktop or server only | GPL-3.0 | 2026-10 | 291 |
| Python | Genome-scale models of metabolism and gene expression (ME-models) solved by constrained optimization (COBRApy extension) | Systems biology | Desktop or server only | MIT | 2019-01 | 40 |
| MATLAB | Compartmental transmission model of lymphatic filariasis infection, disease (lymphoedema, hydrocele) and mass-drug-administration elimination strategies, with a meta-population migration extension. | Epidemiology | Desktop or server only | none-found | 2025-08 | — |
| Java | Spatiotemporal dynamic FBA simulation of microbial communities in structured environments | Systems biology | Desktop or server only | MIT | 2026-09 | 30 |
| GAML | Agent-based epidemic model of COVID-19 transmission, individual epidemiological status and mobility, to compare mitigation policies at city scale. | Ecology and agent-based models | Desktop or server only | GPL-3.0 | 2023-09 | 26 |
| C++ | Cellular Potts (GGH) simulation of multicellular tissue morphogenesis with PDE fields and intracellular SBML networks | Systems biology | Desktop or server only | MIT | 2026-08 | 85 |
| C++ | Optimized compute engine for large NEURON network simulations on CPU/GPU (MPI, OpenMP, OpenACC). | Neuroscience | Desktop or server only | BSD-3-Clause | 2023-03 | 147 |
| Python | Agent-based SARS-CoV-2 transmission across household, school, work and community layers with testing, tracing, quarantine, vaccination and variants. | Epidemiology | Desktop or server only | MIT | 2026-10 | 291 |
| Fortran | DFT (Quickstep), QM/MM and ab initio MD, used for biomolecular QM/MM among condensed-phase systems. | Molecular simulation | Desktop or server only | GPL-2.0 | 2026-10 | 1,215 |
| C++ | Cardiovascular hemodynamics: 3D blood flow coupled to lumped-parameter models in patient-specific geometries. | Physiology and organs | Desktop or server only | GPL-3.0-or-later | 2021-05 | 25 |
| Julia | Declarative Julia framework for building and running process-based crop growth models (e.g. photosynthesis, phenology, plant architecture). | Physiology and organs | Desktop or server only | MIT | 2026-10 | 25 |
| Rust | Context-aware long reads (error profiles learned from real data) for optimizing long-read mapping parameters. | Sequencing and omics data | Guide | MIT | 2026-08 | 15 |
| Java | Stochastic simulator of membrane-enclosed hierarchies of biochemical processes based on a formal language model | Systems biology | Desktop or server only | — | — | |
| Interactive virtual laboratory for deterministic and stochastic simulation of SBML genetic logic circuits, with logic extraction, threshold and propagation-delay analysis. | Gene networks and synthetic biology | Desktop or server only | — | — | ||
| Java | Java 3D reaction-diffusion simulator for diffusion in neuropil-like geometries. | Cells and tissues | Desktop or server only | GPL-3.0 | 2023-07 | 3 |
| Python | Machine-learned Deep Potential many-body potentials that drive MD (via LAMMPS, GROMACS, i-PI etc.). | Molecular simulation | Desktop or server only | LGPL-3.0 | 2026-10 | 2,054 |
| Python (TensorFlow) / C | Oxford Nanopore raw current signals and basecalled reads generated with a context-dependent deep-learning pore model. | Sequencing and omics data | Desktop or server only | MIT | 2020-10 | 122 |
| C++ | Spatiotemporal dengue and Aedes aegypti vector dynamics, compartmental and individual-based, over a GIS database with human mobility. | Epidemiology | Desktop or server only | BSD-2-Clause | 2018-02 | 5 |
| Java | Agent-based simulation of how noise and other disturbances (pile driving, ships, bycatch) affect North Sea harbour porpoise populations via movement, foraging and energy balance. | Ecology and agent-based models | Desktop or server only | GPL-2.0-only | 2026-02 | 7 |
| GPU/CPU molecular dynamics engine for biomolecular systems from D. E. Shaw Research. | Molecular simulation | Desktop or server only | Proprietary (free for academic/non-profit use, per homepage) | — | ||
| MATLAB | Dynamic flux balance analysis of multi-species microbial cultures (LP-embedded ODE/DAE simulation) in MATLAB. | Physiology and organs | Desktop or server only | — | — | |
| Python | Fully differentiable cellular Potts model implemented in JAX. | Cells and tissues | Desktop or server only | — | 2023-11 | 2 |
| Python | Differentiable (PyTorch-based) implementation of the WOFOST crop growth model for gradient-based calibration and learning. | Physiology and organs | Desktop or server only | EUPL-1.1 | 2026-10 | 25 |
| Java | Stochastic and deterministic simulation of genetic regulatory, metabolic and signaling networks (Gillespie, tau-leap, ODE) | Systems biology | Desktop or server only | ISB Software License Agreement (custom, License.html) | 2018-04 | 1 |
| MATLAB | Neural dynamical systems and network models (ODE-based) in MATLAB. | Neuroscience | Desktop or server only | MIT | 2025-02 | 67 |
| Python | Agent-based forward-time simulator coupling pathogen transmission, molecular evolution and environment (compartmental models, contact networks, within-host and multi-strain features) to generate pathogen genomes. | Epidemiology | Desktop or server only | none-found | 2026-05 | 5 |
| C++ | Illumina sequencing reads from a reference genome (Enhanced Artificial Genome Engine). | Sequencing and omics data | Desktop or server only | BSD-3-Clause | 2020-05 | 33 |
| Mass-balance food-web model (Ecopath), time-dynamic simulation (Ecosim) and spatial-temporal simulation (Ecospace) of fisheries and marine ecosystems. | Ecology and agent-based models | Desktop or server only | Free software suite per homepage (not open source; professional licences also offered); no source licence file found | — | ||
| Fortran | Size- and age-structured forest dynamics with carbon, water and energy fluxes (Ecosystem Demography model version 2). | Ecology and agent-based models | Desktop or server only | CC-BY-4.0 | 2026-09 | 91 |
| C++ | Enhanced Green's Function Reaction Dynamics: exact event-driven particle-based reaction-diffusion in space and time. | Cells and tissues | Desktop or server only | GPL-2.0 | 2017-12 | 9 |
| C++ | Stochastic individual-based multi-disease transmission platform (malaria, HIV, TB, dengue, polio, typhoid) with shared vector, host and generic pathogen code. | Epidemiology | Desktop or server only | MIT | 2026-09 | 107 |
| C++ | High-performance network-based agent-based epidemic simulation over large dynamic social-contact networks with custom disease models and programmable interventions. | Epidemiology | Desktop or server only | MIT | 2026-07 | 6 |
| Large-scale interaction-based simulation of contagion diffusion (epidemics, immune-system models) over contact networks on HPC clusters, with GPU acceleration. | Epidemiology | Desktop or server only | none-found | — | ||
| C++ | Extensible MD/MC package for coarse-grained soft matter, polymers and charged systems (also lattice Boltzmann). | Molecular simulation | Desktop or server only | GPL-3.0 | 2026-09 | 273 |
| Fortran | Size- and trait-structured vegetation demography and competition (cohorts of trees) within Earth system land models. | Ecology and agent-based models | Desktop or server only | BSD-3-Clause-LBNL (modified BSD) | 2026-10 | 130 |
| Java | BEAST 2 package that adds tree and alignment simulators, plus other utilities such as input/output helpers. | Phylogenetics and sequence evolution | Desktop or server only | GPL-3.0 | 2026-08 | 13 |
| Python | Cardiac electrophysiology (monodomain/bidomain) PDE solver built on FEniCSx. | Physiology and organs | Desktop or server only | MIT | 2026-10 | 14 |
| Python | Finite-element hyperelastic cardiac mechanics (passive and active contraction) solver built on FEniCSx. | Physiology and organs | Desktop or server only | MIT | 2026-10 | 13 |
| GPU-powered deterministic ODE simulation (Dormand-Prince, Radau IIA) of large biochemical networks | Systems biology | Desktop or server only | — | — | ||
| Python | Finite-difference cardiac tissue electrophysiology simulations (reaction-diffusion, 2D/3D, several ionic models). | Physiology and organs | Desktop or server only | MIT | 2026-10 | 13 |
| Python/R | Stochastic metapopulation compartmental scenario and forecast modeling pipeline, successor of COVIDScenarioPipeline. | Epidemiology | Desktop or server only | GPL-3.0 | 2025-12 | 11 |
| R | Individual-based operating model of fish stock dynamics, recording stock state in FLR FLStock objects to generate length-based and age-based indices. | Ecology and agent-based models | Desktop or server only | GPL-3 | 2025-01 | 6 |
| Java | The whole RNA-seq experiment in silico: expression, reverse transcription, fragmentation, PCR amplification, size selection and sequencing. | Sequencing and omics data | Desktop or server only | BSD-3-Clause (per bundled README of v1.2) | — | |
| C++ | Volunteer distributed MD of protein folding and dynamics; the client runs OpenMM-based cores, the repo is the v8 client. | Molecular simulation | Desktop or server only | GPL-3.0 | 2026-09 | 175 |
| C++ | Agent-based epidemic simulation over census-based synthetic populations with households, schools and workplaces. | Epidemiology | Desktop or server only | University of Pittsburgh EULA (non-commercial, educational or research use only; not OSI open source) | 2024-05 | 83 |
| Python | Hi-C contact data simulated from real Hi-C data via empirical fragment-interaction estimation, for benchmarking and data augmentation. | Sequencing and omics data | Desktop or server only | MIT | 2021-04 | 9 |
| Commercial PBPK and oral absorption simulation (ACAT model) from Simulations Plus. | Physiology and organs | Desktop or server only | commercial | — | ||
| Julia | Mosquito population genetics and gene drive dynamics (inheritance, release, suppression) with optimisation of control strategies. | Ecology and agent-based models | Desktop or server only | MIT | 2026-08 | 22 |
| Java | Generates in silico GRN benchmarks and simulates expression data (ODE/SDE) used in DREAM3-5 challenges, with network-inference performance profiling. | Gene networks and synthetic biology | Desktop or server only | MIT | 2022-03 | 26 |
| Fortran | MD and enhanced sampling (REMD, string method, GaMD) of large biomolecular systems. | Molecular simulation | Desktop or server only | LGPL-3.0 | 2026-01 | 43 |
| C++ | Code-generation framework for GPU (CUDA/HIP) accelerated spiking neural network simulation. | Neuroscience | Desktop or server only | LGPL-2.1 | 2026-10 | 283 |
| Java | Construction and dynamical simulation/analysis of logical (Boolean/multivalued) regulatory network models | Systems biology | Desktop or server only | GPL-3.0 | 2026-09 | 6 |
| Stochastic global metapopulation (GLEaM) simulation of emerging human infectious disease spread using worldwide mobility data, run through a client-server tool. | Epidemiology | Desktop or server only | — | — | ||
| C++ | Molecular docking and scoring with convolutional neural network scoring functions. | Molecular simulation | Desktop or server only | Apache-2.0 | 2026-06 | 986 |
| Python | Blender-based library for modelling cells, tissues and embryo development with physical interactions (growth, division, adhesion). | Cells and tissues | Desktop or server only | BSD-3-Clause | 2026-03 | 71 |
| Multi-GPU reconstruction and simulation of the cerebellar granular layer network. | Neuroscience | Desktop or server only | — | — | ||
| C++ | GPU/CPU simulator of graph-based systems, applied to spiking neural networks (growth/connectivity) and emergency communications. | Neuroscience | Desktop or server only | Apache-2.0 | 2026-10 | 11 |
| Perl | Amplicon and shotgun (genomic, metagenomic, transcriptomic) reads from reference sequences with community abundance models, chimeras and copy-number bias. | Sequencing and omics data | Desktop or server only | GPL-2.0 | — | |
| Python | GPU-accelerated (JAX) RACIPE random-circuit ODE ensembles and Boolean Ising formalism for gene regulatory network dynamics and steady states. | Gene networks and synthetic biology | Desktop or server only | GPL-3.0 | 2026-01 | 8 |
| C++ | Multicellular bacterial colony growth and gene-circuit simulator (cell programming language) | Systems biology | Desktop or server only | UW Open Source License (custom) | 2026-05 | 53 |
| Java | Java modelling platform with the XL rule-based language (relational growth grammars) for functional-structural plant models. | Physiology and organs | Desktop or server only | — | — | |
| Python | Information-driven integrative docking of biomolecular complexes with rigid-body, flexible and MD-style refinement; HADDOCK3 is the modular Python rewrite. | Molecular simulation | Desktop or server only | Apache-2.0 | 2026-10 | 276 |
| Java | Java framework for hybrid on/off-lattice agent-based and PDE models in mathematical oncology. | Cells and tissues | Desktop or server only | MIT | 2024-08 | 39 |
| Spatially explicit individual-based wildlife population simulation on hexagonal landscapes (life history, movement, habitat, stressors) for conservation and population viability analysis. | Ecology and agent-based models | Desktop or server only | — | — | ||
| Python | Biophysical neocortical column model (NEURON-based) producing MEG/EEG current dipoles for interpreting cellular and circuit origins of signals. | Neuroscience | Desktop or server only | BSD-3-Clause | 2026-10 | 83 |
| C++ | GPU-accelerated particle MD and hard-particle Monte Carlo for coarse-grained and soft matter. | Molecular simulation | Desktop or server only | BSD-3-Clause | 2026-10 | 449 |
| Spiking neural network simulator for GPGPU clusters (real-time large-scale spiking nets). | Neuroscience | Desktop or server only | — | — | ||
| Large integrative whole-body human physiology model (about 5000 variables: cardiovascular, respiratory, renal, neural, endocrine, muscle, metabolic) defined in XML. | Physiology and organs | Desktop or server only | — | — | ||
| Hybrid multiscale stochastic simulation of large well-mixed biochemical systems, MPI-parallel | Systems biology | Desktop or server only | GPL | — | ||
| Java | CAD tool for modeling and simulating genetic circuits (ODE, SSA, hybrid; SBML/SBOL) | Systems biology | Desktop or server only | Apache-2.0 | 2026-04 | 69 |
| Rust | Real-time Oxford Nanopore MinION/PromethION run signal output (a MinKNOW endpoint emulator) for testing adaptive sampling. | Sequencing and omics data | Desktop or server only | MPL-2.0 | 2025-04 | 25 |
| Java | Individual-based simulation of microbial communities and biofilms with diffusing solutes (version 1). | Cells and tissues | Desktop or server only | CeCILL-2.0 | 2022-08 | 20 |
| Java | Individual-based simulation of microbial communities and biofilms with diffusion, kinetics, growth strategies and mechanical interactions. | Ecology and agent-based models | Desktop or server only | CeCILL-2.1 | 2026-09 | 13 |
| C++ | Individual-based forest landscape and disturbance model: tree growth, regeneration, competition, fire, wind and bark beetle disturbance. | Ecology and agent-based models | Desktop or server only | GPL-3.0 | 2026-09 | 30 |
| Stochastic spatial simulation of epidemic spread in livestock (foot-and-mouth disease and others) with control strategies. | Epidemiology | Desktop or server only | — | — | ||
| Python | Spatially structured, selection-driven tumor evolution with optional treatment, producing bulk and single-cell DNA, RNA, spatial data and reads with known ground truth. | Sequencing and omics data | Desktop or server only | MIT | 2026-09 | 7 |
| Python | Differentiable molecular dynamics and particle simulation written in JAX. | Molecular simulation | Guide | Apache-2.0 | 2026-08 | 1,464 |
| Java | GenPhyloData simulates host (species) trees and guest (gene) trees with duplication, loss and transfer. The rest of jPrIME does probabilistic inference. | Phylogenetics and sequence evolution | Desktop or server only | BSD-3-Clause | 2021-09 | 10 |
| Java | Physiological and biological ODE/PDE models written in MML or imported from SBML/CellML, with parameter fitting | Systems biology | Desktop or server only | Free for non-commercial use (homepage statement; paper calls it open source) | — | |
| Julia | Julia framework to build and run evolutionary and eco-evolutionary simulation models (population genetics, game-theoretic and individual-based dynamics). | Ecology and agent-based models | Desktop or server only | MIT | 2026-09 | 7 |
| Python | Gillespie-style stochastic jump process solvers (SSA variants for chemical kinetics) implemented in JAX. | Systems biology | Desktop or server only | Apache-2.0 | 2026-07 | 10 |
| Julia | Gillespie-type SSA variants (direct, next-reaction, etc.), tau-leaping and jump-diffusion solvers for chemical kinetics and point processes in Julia/SciML. | Systems biology | Desktop or server only | MIT | 2026-09 | 151 |
| Python | Open-source individual-based epidemic simulation on census-derived virtual populations (England COVID-19) with households, schools and workplaces. | Epidemiology | Desktop or server only | GPL-3.0 | 2026-04 | 56 |
| C++ | Python Lindenmayer-system simulator for plant growth and architecture (morphogenesis). | Cells and tissues | Desktop or server only | CECILL-C | 2026-06 | 99 |
| C# | Spatially explicit forest landscape succession and disturbance (fire, wind, harvest, insects) via extensions. | Ecology and agent-based models | Desktop or server only | Apache-2.0 | 2025-09 | 6 |
| C++ | GPU-accelerated stochastic simulation of cells: well-stirred CME and spatial reaction-diffusion master equation (RDME), with ODE and hybrid solvers, via pyLM. | Systems biology | Desktop or server only | — | 2026-09 | 45 |
| Python | Extracellular potentials (LFP, MUA, EEG) from multicompartment neuron models run on NEURON, via line-source approximation. | Neuroscience | Desktop or server only | GPL-3.0 | 2026-05 | 93 |
| Four-chamber human heart finite-element model coupling electrical excitation and mechanics, run in the commercial Abaqus solver. | Physiology and organs | Desktop or server only | commercial | — | ||
| C | Dynamic global vegetation, hydrology and crop growth model (carbon, water and nitrogen cycles). | Physiology and organs | Desktop or server only | AGPL-3.0 | 2026-09 | 98 |
| Stochastic individual-based simulation of lymphatic filariasis transmission and control (LYMFASIM). TRANSFIL appears to be a related end-user version. | Epidemiology | Desktop or server only | — | — | ||
| Python | Mass-action kinetic simulation of metabolic networks (ODE via libRoadRunner), built on COBRApy. | Systems biology | Desktop or server only | MIT | 2022-12 | 27 |
| Java | Exact stochastic simulation of population dynamics models (birth-death-sampling and other master-equation models), producing trajectories and phylogenetic trees. | Phylogenetics and sequence evolution | Desktop or server only | GPL-3.0 | 2022-11 | 23 |
| MATLAB | Mechanistic and PK/PD models as ODE or stochastic reaction systems with parameter estimation and sensitivity analysis. | Systems biology | Desktop or server only | commercial | — | |
| Java | Agent-based epidemic (COVID-19) simulation built on the MATSim transport and mobility model. | Epidemiology | Desktop or server only | AGPL-3.0 | 2026-10 | 25 |
| C++ | Stochastic reaction-diffusion coupled with mechanics of actin, crosslinker and myosin II filament networks. | Cells and tissues | Desktop or server only | Custom academic/research-only license (not OSI) | 2022-10 | 1 |
| C++ | FFT-based rigid-body protein-protein docking and interaction prediction (GPU/MPI accelerated). | Molecular simulation | Desktop or server only | CC-BY-NC-4.0 | 2023-12 | 74 |
| Python | Shotgun metagenomic samples (Illumina/ONT/PacBio) via a Snakemake workflow that fetches genomes and runs read simulators. | Sequencing and omics data | Desktop or server only | MIT | 2026-03 | 32 |
| Teaching program simulating single-neuron physiology: resting potential, time/length constants, action potential, voltage clamp, synaptic potential. | Neuroscience | Desktop or server only | — | — | ||
| Julia | Population dynamics across space (metapopulation models) in Julia. | Ecology and agent-based models | Desktop or server only | MIT | 2023-03 | 6 |
| Java | Sequencing reads (Sanger, 454, Illumina-like) from genomes and taxonomy-defined metagenomes with abundance profiles. | Sequencing and omics data | Desktop or server only | — | — | |
| Python | Community-level flux balance (cooperative trade-off FBA) metabolic modeling and growth simulation of microbiomes. | Systems biology | Desktop or server only | Apache-2.0 | 2026-10 | 138 |
| Julia | Julia implementation of the microbial consumer-resource model (dynamics of microbes competing for and cross-feeding on resources). | Physiology and organs | Desktop or server only | MIT | 2023-01 | 3 |
| MATLAB | Dynamic flux-balance-analysis simulation of growth and metabolic cross-feeding in well-mixed microbial communities. | Ecology and agent-based models | Desktop or server only | GPL-3.0 | 2024-07 | 4 |
| C++ | Population-density simulation of interacting neural populations governed by arbitrary 1D/2D point-neuron dynamical systems. | Neuroscience | Desktop or server only | MIT | 2024-07 | 14 |
| Java | Genome-wide forward simulations of adapting populations for evolve-and-resequence experiments. | Population genetics | Desktop or server only | none declared | 2019-04 | 1 |
| Julia | Molecular dynamics in Julia, including protein force fields and differentiable simulation. | Molecular simulation | Desktop or server only | MIT | 2026-10 | 496 |
| C | Extensible monodomain simulator for 3D cardiac tissue electrophysiology with CPU and CUDA GPU solvers. | Physiology and organs | Desktop or server only | MIT | 2026-09 | 40 |
| C++ | Multiscale, multicellular systems biology models combining cellular Potts models, ODEs and reaction-diffusion PDEs. | Ecology and agent-based models | Desktop or server only | BSD-3-Clause | — | |
| MATLAB | Discrete-time Markov chain stochastic epidemic simulator (SEQIJR compartments) in Matlab. | Epidemiology | Desktop or server only | — | — | |
| Java | ms-compatible coalescent with recombination, population structure and demography plus single-locus selection via forward simulation. | Population genetics | Desktop or server only | GPL-3.0 | — | |
| MATLAB | Integrated whole-cell model of the M. genitalium life cycle with 28 submodels (MATLAB code from the Covert Lab). | Systems biology | Desktop or server only | MIT | 2015-10 | 131 |
| Stochastic, spatial, state-transition simulation of highly contagious animal disease spread (such as foot-and-mouth) with destruction and vaccination controls. | Epidemiology | Desktop or server only | GPL-2.0 | 2022-11 | — | |
| C++ | Scalable parallel molecular dynamics of large biomolecular systems on CPU and GPU. | Molecular simulation | Desktop or server only | — | — | |
| Python | Oxford Nanopore reads from error models learned from real data (genomic, transcriptomic, metagenomic). | Sequencing and omics data | Desktop or server only | GPL-3.0 | 2026-03 | 313 |
| Python | Raw nanopore current signals (DNA R10.4.1 and direct RNA) from sequences using a basecaller-guided Transformer. | Sequencing and omics data | Desktop or server only | Apache-2.0 | 2026-06 | 4 |
| C++ | Large networks of point-neuron and few-compartment spiking neurons with synapses and plasticity, parallelized with OpenMP/MPI. | Neuroscience | Desktop or server only | GPL-2.0 | 2026-10 | 671 |
| C++ | CUDA GPU library for large-scale spiking network simulation, NEST-compatible; benchmarked on macaque multi-area cortex model with MPI-GPU. | Neuroscience | Desktop or server only | GPL-2.0 | 2026-10 | 28 |
| Python | Declaratively specified, biophysically detailed multiscale network models executed on NEURON (with GUI). | Neuroscience | Desktop or server only | MIT | 2026-09 | 175 |
| Python | Deep neural cellular Potts models: learned CPM Hamiltonians for cell and tissue morphogenesis (ICML 2025 paper code). | Cells and tissues | Desktop or server only | — | 2025-07 | 4 |
| Julia | Brain circuit modeling from neuron, assembly and neural-mass blocks, for in silico evaluation of drugs and interventions. | Neuroscience | Desktop or server only | Proprietary EULA (academic and non-commercial trial use only) | 2026-09 | 9 |
| Java | Generates and runs 3D networks of multicompartmental neurons by producing NEURON or GENESIS scripts from NeuroML models. | Neuroscience | Desktop or server only | GPL-2.0 | 2026-09 | 54 |
| Python | Driver that builds and runs NEURON/CoreNEURON simulations of Blue Brain detailed circuit models (SONATA). | Neuroscience | Desktop or server only | Apache-2.0 | 2026-10 | 2 |
| C++ | Biophysically detailed neurons and networks (cable equation, ion channels, NMODL mechanisms, reaction-diffusion via RxD). | Neuroscience | Desktop or server only | BSD-3-Clause | 2026-10 | 551 |
| Experimental scalable parallel simulator for large firing-rate and ML-inspired neural network models with integrated analysis and visualization. | Neuroscience | Desktop or server only | — | — | ||
| Python | Predictive-coding and spiking neural circuits with local (biologically motivated) learning rules, built on JAX | Neuroscience | Desktop or server only | BSD-3-Clause | 2026-10 | 210 |
| Python | Phylogenomic simulation of Illumina reads/read counts from gene families evolving along a species tree, orchestrating SimPhy, INDELible and ART | Phylogenetics and sequence evolution | Desktop or server only | GPL-3.0 | 2018-03 | 14 |
| Python | Bio-inspired spiking neuron models (LIF, LSNN etc.) as PyTorch modules | Neuroscience | Desktop or server only | LGPL-3.0 | 2026-07 | 824 |
| MATLAB | PacBio continuous long reads using a log-normal read-length distribution and an empirical per-base error model. | Sequencing and omics data | Desktop or server only | none-found | 2018-03 | 3 |
| C++ | Massively parallel 3D individual-based simulation of microbial communities and biofilms, built as a LAMMPS extension. | Cells and tissues | Desktop or server only | GPL-2.0 | 2025-09 | 9 |
| C++ | Massively parallel 3D individual-based simulation of microbial communities and biofilms, built on LAMMPS. | Ecology and agent-based models | Desktop or server only | GPL-3.0 | 2023-04 | 25 |
| Python | GPU-accelerated ODE solvers for quantitative systems pharmacology models | Physiology and organs | Desktop or server only | NVIDIA Software License Agreement plus Product-Specific Terms for AI Products (proprietary) | 2026-08 | 19 |
| Fortran | Computational chemistry: quantum chemistry, QM/MM and classical molecular dynamics for large molecular systems. | Molecular simulation | Guide | ECL-2.0 | 2026-10 | 628 |
| Julia | 1D finite-volume blood flow in arterial networks | Physiology and organs | Desktop or server only | Apache-2.0 | 2026-07 | 45 |
| C++/Python | Multiscale cardiac electrophysiology (ionic cell models, tissue monodomain/bidomain, whole heart, body surface) | Physiology and organs | Guide | — | — | |
| Fortran | Multi-scale physiology simulation (finite element, bioelectrics, continuum mechanics) with embedded CellML models. | Systems biology | Desktop or server only | — | 2024-03 | 9 |
| C++ | Open source environment to edit and simulate CellML and SED-ML models (ODE/DAE/NLA) of cellular electrophysiology and biochemistry. | Systems biology | Desktop or server only | GPL-3.0 | 2025-07 | 42 |
| Python | Relative binding free energy calculation protocols driving MD engines (OpenMM). | Molecular simulation | Desktop or server only | MIT | 2026-10 | 338 |
| C++ | High-performance molecular dynamics toolkit with GPU platforms, Python API and custom forces/integrators. | Molecular simulation | Guide | MIT (API, reference and CPU platforms) plus LGPL for CUDA/OpenCL platforms; mixed | 2026-10 | 1,992 |
| Python | Replica exchange, alchemical and Monte Carlo move sets built on OpenMM. | Molecular simulation | Desktop or server only | MIT | 2026-10 | 342 |
| Python | Transition path and interface sampling of rare events on top of MD engines. | Molecular simulation | Desktop or server only | MIT | 2026-06 | 118 |
| C++ | Musculoskeletal optimal control (predictive simulation of movement) via direct collocation on OpenSim models | Physiology and organs | Desktop or server only | Apache-2.0 | 2025-04 | 73 |
| Python | Integrated C. elegans whole-organism simulation (neuronal c302 model, Sibernetic body physics, Docker-based stack) | Neuroscience | Desktop or server only | MIT | 2026-08 | 3,066 |
| Python | OpenSim musculoskeletal model environments (Learning to Run, AI for Prosthetics) for reinforcement learning | Physiology and organs | Desktop or server only | MIT | 2022-01 | 948 |
| Java | Multispecies, size-based individual-based model of exploited marine ecosystems and fish communities. | Ecology and agent-based models | Desktop or server only | GPL-3.0 | 2026-06 | 26 |
| R | R interface for loading, modifying and running PBPK/QSP simulations of the Open Systems Pharmacology Suite | Physiology and organs | Desktop or server only | GPL-2.0 with clarifying addendum (OSP license) | 2026-10 | 58 |
| CUDA C/C++ | GPU (CUDA) forward Wright-Fisher simulation of allele trajectories and SFS under arbitrary demography and selection (GO Fish API plus Spectrum API). | Population genetics | Desktop or server only | MIT | 2023-04 | 9 |
| Java | Meiosis and offspring genotypes along pedigrees in diploid and tetraploid organisms, with chiasma interference, bivalent/quadrivalent pairing and double reduction. | Population genetics | Desktop or server only | GPL-2.0-or-later | 2021-04 | 14 |
| Python | Relative alchemical free energy and expanded-ensemble simulations using OpenMM. | Molecular simulation | Desktop or server only | MIT | 2025-10 | 203 |
| Julia | Gene-tree simulation within species networks under the network multispecies coalescent, including correlated inheritance of gene flow | Phylogenetics and sequence evolution | Desktop or server only | MIT | 2026-06 | 16 |
| C++ | Multiscale agent-based multicellular simulation (PhysiCell) coupled with intracellular stochastic Boolean networks (MaBoSS). | Systems biology | Desktop or server only | — | 2026-10 | 2 |
| C# | Whole-body physiologically based pharmacokinetic (PBPK) modelling and simulation, with MoBi for custom systems pharmacology models | Physiology and organs | Desktop or server only | GPL-2.0 with clarifying addendum (OSP license) | 2026-10 | 180 |
| Julia | Julia framework to define and run multi-scale plant process models (photosynthesis, growth, etc.) | Physiology and organs | Desktop or server only | MIT | 2026-10 | 27 |
| Julia | Generates simulated genotype datasets by resampling alleles from empirical population genotype data (simulates samples, not evolutionary processes); borderline simulator. | Population genetics | Desktop or server only | MIT | 2026-07 | 5 |
| Python | Spatially and temporally explicit forward Wright-Fisher simulation of range expansion, selection and demography producing genetic data. | Population genetics | Desktop or server only | MIT | 2014-10 | — |
| C++ | Spatiocyte lattice-based particle reaction-diffusion simulator of intracellular systems (hexagonal close-packed lattice); pSpatiocyte is the MPI-parallel version. | Cells and tissues | Desktop or server only | GPL-2.0 with special exception for dynamically loadable subclasses | 2019-07 | 3 |
| High-performance parallel (MPI) spatial lattice reaction-diffusion simulator for intracellular systems, in the Spatiocyte/E-Cell lineage. | Systems biology | Desktop or server only | — | — | ||
| C++ | Spatial individual-based model of Plasmodium falciparum malaria transmission and drug resistance evolution (MaSim). | Ecology and agent-based models | Desktop or server only | BSD-3-Clause | 2024-02 | 5 |
| Julia | Pharmacometric PK/PD modelling, nonlinear mixed effects estimation and simulation in Julia | Physiology and organs | Desktop or server only | commercial | — | |
| Python | Simulator-independent Python API for spiking network models, run on NEURON, NEST, Brian 2 and neuromorphic back-ends | Neuroscience | Desktop or server only | CeCILL-2.1 | 2026-09 | 313 |
| Python | Opsin photocycle kinetic models (3-, 4-, 6-state) simulated at channel, neuron and network levels for optogenetics | Neuroscience | Desktop or server only | BSD-3-Clause | 2023-07 | 44 |
| Python | GPU-accelerated advanced-sampling methods (ABF, metadynamics etc.) for MD engines, written with JAX. | Molecular simulation | Desktop or server only | GPL-3.0-or-later overall; MIT for most files except abf.py | 2026-10 | 109 |
| Large-scale livestock genome and population simulation: historical population to mutation-drift equilibrium, recent complex pedigrees, QTL, markers, selection and mating, producing pedigree, genotype and phenotype data. | Population genetics | Desktop or server only | — | — | ||
| C++ | Spatially explicit individual-based platform for eco-evolutionary range dynamics, dispersal and population dynamics on landscapes. | Ecology and agent-based models | Desktop or server only | GPL-3.0 | 2023-11 | 17 |
| MATLAB | MATLAB toolbox for genome-scale metabolic model reconstruction, curation and constraint-based simulation (FBA) | Systems biology | Desktop or server only | GPL-3.0 | 2026-10 | 131 |
| C++ | Particle-based reaction-diffusion dynamics with interacting particles in crowded cellular environments | Systems biology | Guide | BSD-3-Clause | 2026-03 | 65 |
| Java | Stochastic simulation of phylodynamic (birth-death, structured, reaction-network) trees for BEAST 2.7 | Phylogenetics and sequence evolution | Desktop or server only | GPL-3.0 | 2026-08 | 9 |
| Smalltalk (Pharo) | Multi-agent simulator for individual-based modeling in population dynamics and ecotoxicology. | Ecology and agent-based models | Desktop or server only | MIT | 2026-08 | 15 |
| Java | General-purpose Java agent-based modeling toolkit with GIS support, used for ecology and social science models. | Ecology and agent-based models | Desktop or server only | — | 2026-09 | 102 |
| C++ | Illumina genomic DNA reads learned from a real sample, including systematic errors and a fragment-based coverage model. | Sequencing and omics data | Desktop or server only | MIT | 2022-08 | 52 |
| Python | Spiking neural networks simulated and trained for deployment on neuromorphic hardware | Neuroscience | Desktop or server only | AGPL-3.0 | 2026-07 | 92 |
| C++ | Monte Carlo conformational sampling for protein structure prediction, design and docking; PyRosetta is the Python interface. | Molecular simulation | Desktop or server only | Rosetta license (non-OSI; free for academic/non-commercial use, commercial licence needed) | 2026-09 | 474 |
| C++ | RNA-seq reads simulated from an expression model fitted by RSEM; the package is primarily a quantifier and simulation is a secondary tool. | Sequencing and omics data | Desktop or server only | GPL-3.0 | 2026-08 | 479 |
| Java | Birth-death simulation of species trees, gene trees (duplication, transfer, loss) and subgene/domain trees | Phylogenetics and sequence evolution | Desktop or server only | BSD (revised) | — | |
| Perl | NGS reads from genomes and transcriptomes, with expression profiles and quality profiles. | Sequencing and omics data | Desktop or server only | GPL-3.0 | 2024-02 | 22 |
| Java | Forward-time simulation of gene sequence populations with replication, recombination, point mutation, indels and selection under fitness models; extended with multiple compartments for within-host HIV-1 reservoir evolution. | Population genetics | Desktop or server only | Apache-2.0 | 2023-08 | 23 |
| Java | Java GUI tool for ODE time-course simulation of SBML models and parameter estimation | Systems biology | Desktop or server only | LGPL-3.0 | 2020-06 | 4 |
| Java | Java library implementing SBML interpretation and numerical solution (ODE) of SBML models, including events and rules | Systems biology | Desktop or server only | LGPL-3.0 | 2026-09 | 26 |
| C++ | Epithelial sub-cellular element method (SCE) CUDA package for developmental biology simulations. | Cells and tissues | Desktop or server only | MIT | 2018-06 | 2 |
| C++ | Predictive simulation of biological motion with muscle-driven musculoskeletal models and optimization | Physiology and organs | Desktop or server only | GPL-3.0 | 2021-03 | 68 |
| Python | scRNA-seq and scATAC-seq reads (FASTQ/BAM) mimicking real data with UMI counts and open-chromatin ground truth. | Sequencing and omics data | Desktop or server only | MIT | 2024-10 | 34 |
| Fortran | Brownian dynamics simulation of diffusional association and crowding of proteins. | Molecular simulation | Desktop or server only | — | — | |
| Python | Copy number variants and whole-exome sequencing reads from reference genomes. | Sequencing and omics data | Desktop or server only | MIT | 2020-02 | 17 |
| MATLAB | MATLAB toolbox for simulation of stochastic gene regulatory networks, giving population-level distributions of gene expression via the chemical master/Fokker-Planck-type framework with cell growth and division. | Gene networks and synthetic biology | Desktop or server only | — | — | |
| Julia | Forward population-genetic simulation and numerical approximations for multilocus mainland-island and finite-island models. | Population genetics | Desktop or server only | GPL-3.0 | 2025-10 | 1 |
| Kotlin | Visual neural network simulator (rate and spiking networks) with embodied agents in simulated environments | Neuroscience | Desktop or server only | GPL-2.0 | 2026-10 | 119 |
| Python | Cardiac electromechanics: coupled cell electrophysiology and tissue mechanics (finite element) | Physiology and organs | Desktop or server only | LGPL-2.1 | 2026-10 | 17 |
| Commercial population-based PBPK simulator for ADME and drug-drug interaction prediction | Physiology and organs | Desktop or server only | proprietary | — | ||
| Python | Finite-element simulation of electric fields from TMS, tDCS and other non-invasive brain stimulation in individualized head models | Neuroscience | Desktop or server only | GPL-3.0 | 2026-03 | 200 |
| C++ | Patient-specific cardiovascular blood flow (3D finite-element CFD with lumped-parameter boundary conditions) from image-derived models. | Physiology and organs | Desktop or server only | BSD-style (Stanford/UC Regents terms in LICENSE.md) | 2026-06 | 351 |
| C++ | Molecular simulation toolkit: molecular modelling, free energy calculations and Monte Carlo moves. | Molecular simulation | Desktop or server only | GPL-3.0 | 2026-10 | 69 |
| C++ | Hydrodynamic cytoskeleton simulator: flexible fibres in Stokes flow with bodies and periphery. | Cells and tissues | Desktop or server only | Apache-2.0 | 2024-05 | 30 |
| R | R framework for spatio-temporal population genomic simulation on real or abstract landscapes, with SLiM and msprime backends and tree-sequence analysis. | Population genetics | Desktop or server only | MIT | 2026-10 | 64 |
| Python (wraps SLiM; R helper scripts) | Generates and runs SLiM scripts from a Newick tree to simulate forward-time population genetics (substitutions and polymorphism) across a whole clade under sequence-fitness models. | Population genetics | Desktop or server only | none-found | 2026-10 | 5 |
| R | R interface to build, run and analyze SLiM forward population genomic simulations (requires external SLiM). | Ecology and agent-based models | Desktop or server only | MIT + file LICENSE | 2025-11 | 10 |
| C++ | GUI tool to construct and simulate hybrid (Petri net) biological models, combining stochastic and continuous parts | Systems biology | Desktop or server only | — | — | |
| Python | Spike-in of simulated somatic SNVs (with chosen VAF) into existing BAM files. | Sequencing and omics data | Desktop or server only | — | 2022-06 | 7 |
| Java | Spatially explicit individual-tree forest simulator for growth, mortality, recruitment and disturbance. | Ecology and agent-based models | Desktop or server only | — | — | |
| C++ | Genetic data under spatially explicit demographic scenarios with long-distance dispersal (forward demography plus backward coalescent). | Ecology and agent-based models | Desktop or server only | Free for non-commercial use (proprietary) | — | |
| Python | Runs PyNN-defined spiking neural network simulations on SpiNNaker neuromorphic hardware | Neuroscience | Desktop or server only | Apache-2.0 | 2026-10 | 121 |
| Python | Long-read RNA-seq (ONT/PacBio) with controlled transcript novelty classes, plus matched Illumina/CAGE; wraps NanoSim, PBSIM3, IsoSeqSim. | Sequencing and omics data | Desktop or server only | GPL-3.0 | 2025-09 | 10 |
| MATLAB | Steady-state microbial community composition and growth rates predicted by community flux balance analysis. | Physiology and organs | Desktop or server only | — | — | |
| Java | Spatiotemporal compartmental epidemic simulation across geographic regions with mobility and interventions. | Epidemiology | Desktop or server only | EPL-1.0 | — | |
| Python | Within-strain short-term evolutionary mutations in longitudinal metagenomic sequencing data (simulated reads). | Sequencing and omics data | Desktop or server only | Apache-2.0 | 2024-09 | 1 |
| C++ | Stochastic reaction-diffusion simulation in tetrahedral meshes of realistic cellular morphologies, including membrane potential and channels | Systems biology | Desktop or server only | GPL-3.0 | 2026-08 | 45 |
| MATLAB / CUDA | GPU-parallel stochastic simulation (SSA) of biochemical networks for the Systems Biology Toolbox 2 for MATLAB | Systems biology | Desktop or server only | — | — | |
| Python | Strain-resolved in silico mock metagenome (the DESMAN 'complex strain' community), via scripts built on meta-sweeper. | Sequencing and omics data | Desktop or server only | — | 2018-08 | 13 |
| Java | Lifespans of synthetic patients with disease-progression and care-pathway modules, producing synthetic EHRs (FHIR, C-CDA, CSV). | Epidemiology | Desktop or server only | Apache-2.0 | 2026-08 | 3,378 |
| Java | Generator of synthetic microarray gene expression data from subnetworks sampled from E. coli and S. cerevisiae regulatory networks, with Michaelis-Menten/Hill kinetics and noise models. | Gene networks and synthetic biology | Desktop or server only | — | — | |
| Python | Genomes with polymorphic transposable-element insertions/deletions, with optional short/long-read simulation and population-scale VCFs. | Sequencing and omics data | Desktop or server only | — | 2026-04 | 5 |
| Fortran | Massively parallel (MPI/GPU) polarizable-force-field molecular dynamics. | Molecular simulation | Desktop or server only | Tinker licence (custom; free for academic institutions, contact for commercial) | 2026-06 | 103 |
| C++ | Computer-aided design application for building biological networks from parts and modules with plug-ins for simulation (ODE/stochastic) and analysis of synthetic circuits. | Gene networks and synthetic biology | Desktop or server only | — | — | |
| C++ | Interactive particle-based physics, chemistry and biology (multicellular, subcellular) simulation environment | Systems biology | Desktop or server only | LGPL-3.0-or-later with additional conditions | 2025-07 | 28 |
| C++ | Modular long-read RNA-seq library prep and sequencing, including PCR and single-cell designs. | Sequencing and omics data | Desktop or server only | MIT | 2025-08 | 9 |
| C++ | Multi-cellular framework on TOPAS/Geant4 simulating biological response to ionizing radiation. | Cells and tissues | Desktop or server only | — | — | |
| Python | GPU-accelerated cardiac electrophysiology tissue simulation in PyTorch. | Physiology and organs | Desktop or server only | MIT | 2026-09 | 101 |
| Python | PyTorch-based end-to-end molecular dynamics for biomolecules with ML potentials. | Molecular simulation | Desktop or server only | MIT | 2026-04 | 719 |
| Java | Flexible forward-time population genetic simulator that tracks genealogies and allows selection, recombination and demography. | Population genetics | Desktop or server only | none-found | 2012-01 | 3 |
| C++ | Simulation of vascularized tumors including angiogenesis, oxygen transport, drugs and interstitial fluid flow. | Cells and tissues | Desktop or server only | — | 2023-04 | 10 |
| Python | Co-simulation of TVB mean-field network models with NEST/ANNarchy/NetPyNE spiking networks | Neuroscience | Desktop or server only | GPL-3.0 | 2026-08 | 47 |
| MATLAB | MATLAB (SimBiology-based) toolbox for modelling cell-free TX-TL gene expression circuits. | Gene networks and synthetic biology | Desktop or server only | — | 2022-05 | — |
| Python | UMI-tagged paired-end targeted-sequencing reads with estimated background error noise and inserted SNVs/CNVs. | Sequencing and omics data | Desktop or server only | MIT | 2025-09 | 2 |
| C++ | GPU-accelerated high-throughput molecular docking of ligands to protein targets. | Molecular simulation | Desktop or server only | Apache-2.0 | 2026-07 | 313 |
| MATLAB | Stochastic reaction-diffusion master equation (RDME) simulation on unstructured meshes. | Cells and tissues | Desktop or server only | GPL-3.0 | 2026-02 | 30 |
| Java | Diploid genomes with germline/somatic SNVs, indels and SVs, plus read simulation and validation. | Sequencing and omics data | Desktop or server only | BSD-2-Clause | 2024-10 | 93 |
| Python (GitHub shows Jupyter Notebook) | Whole-cell model of E. coli (gene expression, metabolism, growth) implemented on the Vivarium framework | Systems biology | Desktop or server only | MIT | 2026-10 | 34 |
| MATLAB | Large-scale spiking cortical tissue simulation with extracellular potentials (LFP) and virtual multi-electrode recording/stimulation | Neuroscience | Desktop or server only | Non-Commercial Software License Agreement (research use) | — | |
| R | Spatiotemporal agent-based genome-scale metabolic simulation of host colonic cells and gut microbes (SIHUMIx) in a virtual crypt, mucus and lumen with fluid flow, built on BacArena. | Ecology and agent-based models | Desktop or server only | GPL-3.0 | 2025-12 | 3 |
| C++ | Cell-based vertex-style framework for plant tissue growth and morphogenesis with intracellular reaction networks. | Cells and tissues | Desktop or server only | GPL-2.0 | 2026-07 | 8 |
| C++ | Cell-based (cellular Potts-like vertex) modelling of plant tissue growth and morphogenesis. | Physiology and organs | Desktop or server only | — | — | |
| Java | Within-host virus phylogenies (coalescent with demography) simulated inside a given transmission tree. | Phylogenetics and sequence evolution | Desktop or server only | GPL-2.0 | 2019-12 | 7 |
| Python | Virtual extracellular spiking activity from biophysical multicompartment neuron models (NEURON + LFPy) to benchmark spike sorting | Neuroscience | Desktop or server only | GPL-2.0 | 2020-10 | 22 |
| Python | Haplotype-aware structural variants with short-read, long-read, single-cell and linked-read sequencing. | Sequencing and omics data | Desktop or server only | LGPL-3.0 | 2024-10 | 54 |
| C++ | Virtual Iterative Angiogenesis library generating synthetic vascular trees by constrained optimisation. | Cells and tissues | Desktop or server only | Apache-2.0 | 2022-01 | 12 |
| Individual-based stochastic simulation of wildlife population viability, including demographic, environmental and genetic stochasticity (extinction vortices). | Ecology and agent-based models | Desktop or server only | CC BY-ND 4.0 (per homepage; source code not stated to be public) | — | ||
| Python | Whole-cell mechanistic model of E. coli (gene expression, metabolism via FBA, replication, cell cycle) integrating heterogeneous datasets | Systems biology | Desktop or server only | Stanford Academic Software License (non-commercial academic use only, no redistribution; not open source) | 2026-10 | 44 |
| Python | Weighted-ensemble path sampling of rare events by orchestrating MD or other dynamics engines. | Molecular simulation | Desktop or server only | MIT | 2026-10 | 220 |
| Python | Differentiable whole-brain network (neural mass) models fitted to neuroimaging data in PyTorch | Neuroscience | Desktop or server only | MIT | 2026-07 | 42 |
| Windows biochemical reaction simulator for ODE-based kinetic models of large biochemical reaction networks, with user-defined equations and events as GUI components and SBML import/export | Systems biology | Desktop or server only | — | — | ||
| C++ | Conductance-based single-neuron and small network models, MATLAB front-end with C++ core | Neuroscience | Desktop or server only | GPL-3.0 | 2023-04 | 46 |
| Python | Synthetic cancer exomes with subclones, somatic variants and CNAs, built by blending real reads. | Sequencing and omics data | Desktop or server only | GPL-3.0 | 2020-09 | 11 |
| Java | Generic 3D root-system architecture growth model (DigR) run in the Xplo software. | Physiology and organs | Desktop or server only | — | — | |
| Julia | Genotypes and phenotypes of descendants from ancestors with sequence data for breeding populations and genomic selection studies; v2 simulates modern breeding programs. | Population genetics | Desktop or server only | GPL-2.0 | 2023-04 | 16 |
| Cuda | GPU-powered centre-based (spheroid) models of mesenchyme and epithelium morphogenesis. | Cells and tissues | Desktop or server only | MIT | 2025-10 | 46 |
| Python | Alchemical binding free energy calculations built on OpenMM. | Molecular simulation | Desktop or server only | MIT | 2023-07 | 203 |
| Python | General-purpose Python agent-based modelling framework with experiments and sensitivity analysis; not biology-specific. | Ecology and agent-based models | Not assessed | BSD-3-Clause | 2025-02 | 388 |
| Julia | General Julia agent-based modelling framework (discrete, continuous, graph and OSM spaces) used for ecology and epidemiology models. | Ecology and agent-based models | Not assessed | MIT | 2026-09 | 919 |
| Python | Python implementation of the AquaCrop-OS crop water productivity model. | Physiology and organs | Not assessed | Apache-2.0 | 2026-09 | 169 |
| Python | General compartmental disease-model simulation engine (TB, HIV, malaria and others) with cascades, programs and optimisation. | Epidemiology | Not assessed | MIT | 2026-10 | 17 |
| Automated design of gene regulatory circuits with evolutionary strategies and simulation (including stochastic effects) of circuit dynamics from part-level models. | Gene networks and synthetic biology | Not assessed | — | — | ||
| Python | Imperfect ONT/PacBio long reads with realistic errors, chimeras, junk and random reads, glitches and adapter artifacts | Sequencing and omics data | Not assessed | GPL-3.0 | 2026-07 | 306 |
| Brownian dynamics of macromolecules with hydrodynamic interactions, on CPU and GPU. | Molecular simulation | Not assessed | — | — | ||
| Python | Trees simulated under birth-death-mutation-sampling processes, with user-defined type-dependent rates and mutation models. | Phylogenetics and sequence evolution | Not assessed | MIT | 2025-10 | 3 |
| Python | Compiler that builds chemical reaction network models (SBML) of biomolecular parts, mechanisms and contexts; simulation is delegated to Bioscrape/other tools. | Gene networks and synthetic biology | Not assessed | BSD-3-Clause | 2026-09 | 55 |
| Python | Python framework for ODE modeling, simulation, parameter estimation and sensitivity analysis of cell signaling systems. | Systems biology | Not assessed | Apache-2.0 | 2026-10 | 30 |
| Stochastic simulation (Gillespie-type and Langevin) of biochemical networks. | Systems biology | Not assessed | — | — | ||
| Python/Cython | Fast stochastic (SSA) and deterministic (ODE) simulation of biological circuits with delays, rules and cell lineages. | Systems biology | Not assessed | MIT | 2026-09 | 30 |
| Python | Python package for analysis and simulation of Boolean and semi-quantitative Boolean networks. | Gene networks and synthetic biology | Not assessed | GPL-3.0 | 2026-10 | — |
| Python | Boolean network simulation of gene regulatory networks with synchronous, asynchronous and piecewise-linear differential (Boolean-to-ODE) update rules. | Gene networks and synthetic biology | Not assessed | MIT | 2026-10 | 41 |
| Python | Converts Boolean GRN models into ODE/SDE systems and simulates single-cell expression with dropouts; generator for BEELINE GRN-inference benchmarks. | Gene networks and synthetic biology | Not assessed | GPL-3.0 | 2025-11 | 41 |
| Python | Command-line tool for distributed (MPI optional) simulations and attractor/statistical analysis of synchronous Boolean networks. | Gene networks and synthetic biology | Not assessed | MIT | 2025-09 | 9 |
| Python | Equation-oriented spiking neural network simulator with code generation (numpy, Cython, C++ targets). | Neuroscience | Not assessed | CECILL-2.1 | 2026-10 | 1,241 |
| Python | Emulator of the Intel Loihi neuromorphic chip's neuron/synapse behavior on top of Brian 2. | Neuroscience | Not assessed | MIT | 2021-12 | 31 |
| Brownian dynamics simulation of diffusional association of biomolecules, computing association rate constants (BrownDye 1/2). | Molecular simulation | Not assessed | — | — | ||
| Python | Genomic variation (SNPs, small indels, simple and complex structural variants) mimicking the human variation spectrum, for benchmarking variant callers. | Sequencing and omics data | Not assessed | GPL-3.0 | 2025-06 | 2 |
| Python | Amplicon sequencing reads (tiled amplicon schemes such as viral genomes) from a reference and primer scheme. | Sequencing and omics data | Guide | BSD-2-Clause | 2026-09 | 4 |
| Converts biochemical network diagrams into dynamic (ODE) models and simulates them. | Systems biology | Not assessed | — | — | ||
| Coarse-grained MD of proteins and nucleic acids (Go-like, AICG2+, 3SPN models). | Molecular simulation | Not assessed | — | — | ||
| Python | Strain-design simulation on top of COBRApy: FBA, MOMA, knockout enumeration and heterologous pathway predictions for genome-scale metabolic models. | Systems biology | Not assessed | Apache-2.0 | 2022-11 | 129 |
| Python | Genome evolution along a phylogeny where genes have evolving regulatory interactions that determine fitness. A genetic algorithm evolves populations, linking sequence mutation to regulatory change. | Phylogenetics and sequence evolution | Not assessed | GPL-3.0 | 2023-07 | 1 |
| Python/Cython | Stochastic simulation of reaction systems with Gillespie direct, tau-leaping and adaptive tau-leaping algorithms. | Systems biology | Not assessed | Apache-2.0 | 2026-10 | 18 |
| Python | Python platform for constraint-based modelling: FBA, FVA and related flux analyses of metabolic networks. | Systems biology | Not assessed | GPL-3.0 | 2026-05 | 20 |
| Python | Spatially explicit individual-based demo-genetic metapopulation model with landscape change, now with a host-pathogen disease module. | Ecology and agent-based models | Not assessed | none-found | 2026-10 | 15 |
| Python | Spatially explicit individual-based population genetics on cost-distance landscapes: movement, reproduction, mortality, dispersal, Mendelian inheritance and k-allele mutation. | Ecology and agent-based models | Not assessed | none-found | 2024-09 | 5 |
| Python | Spatially explicit individual-based simulation of gene flow, mating, mortality and dispersal on cost-distance landscapes. | Population genetics | Not assessed | — | — | |
| JavaScript | Real-time type 1 diabetes glucose simulation under multiple daily injections or insulin pump therapy, linked to Nightscout. | Physiology and organs | Not assessed | MIT | 2022-04 | 31 |
| R | Individual-based simulation of genetic diversity loss to drift, translocation (augmentation), targeted removals and catastrophes in managed wildlife populations. | Ecology and agent-based models | Not assessed | none-found | — | |
| Python | COVID-19 Hospital Impact Model for Epidemics: SIR-based projection of hospital admissions, ICU and ventilator demand. | Epidemiology | Not assessed | MIT | 2023-03 | 210 |
| Python | Auto-assembles CellML modules into circulatory/cardiac/neuron system models for simulation and parameter identification. | Physiology and organs | Not assessed | Apache-2.0 | 2026-10 | 5 |
| Scalable forward-time population genetic simulation. | Population genetics | Not assessed | — | — | ||
| Python | Structural variants (deletions, insertions, duplications, inversions, translocations) introduced into BAM/sequence data. | Sequencing and omics data | Not assessed | Apache-2.0 | 2022-09 | 11 |
| R | R framework giving one model interface to several coalescent simulators (ms, msms, scrm, fastsimcoal). | Population genetics | Not assessed | MIT | 2024-03 | 24 |
| Python | Python package for classic constraint-based analysis (FBA) and COBRA with kinetics (COBRA-k) | Systems biology | Not assessed | Apache-2.0 | 2026-09 | 22 |
| Python | FBA, FVA and related constraint-based flux simulation of genome-scale metabolic models in Python | Systems biology | Not assessed | GPL-2.0 | 2026-10 | 589 |
| Julia | Julia package for large-scale (HPC) constraint-based reconstruction and analysis of metabolic models (FBA and variants) | Systems biology | Not assessed | Apache-2.0 | 2025-09 | 19 |
| Python | Python toolbox for conditional flux balance analysis of metabolism with resource allocation in cyclic environments | Systems biology | Not assessed | free for non-commercial use (per paper) | — | |
| Python | Forward-in-time simulation of prokaryotic core genome evolution with homologous recombination, guided by a phylogenetic tree and including codon-selection models. | Phylogenetics and sequence evolution | Not assessed | — | 2025-02 | 6 |
| Python | Forward-in-time simulation of prokaryote genome evolution with homologous recombination. | Population genetics | Not assessed | none-found | 2025-02 | 6 |
| Python | Agent-based COVID-19 epidemic model coupling health outcomes with economic effects of social-distancing scenarios. | Epidemiology | Not assessed | GPL-3.0 | 2022-09 | 94 |
| Python | Spatiotemporal stochastic epidemic model quantifying the effect of contact tracing, testing and containment measures (Tracing-Testing-Containment, continuous-time event simulation). | Epidemiology | Not assessed | MIT | 2026-06 | 74 |
| Python | Functional-structural plant model: 3D root and shoot architecture growth with water and carbon transport. | Cells and tissues | Not assessed | GPL-3.0 | 2026-10 | 77 |
| Python | GPU-optimized Gillespie/SSA simulation of chemical reaction networks in JAX | Systems biology | Not assessed | MIT | 2026-05 | 2 |
| Julia | Exact stochastic simulation (delay SSA) of reaction systems with time delays in Julia | Systems biology | Not assessed | MIT | 2026-06 | 17 |
| Python | Automatically generates reduced dendritic compartment models for Brian 2 spiking networks. | Neuroscience | Not assessed | GPL-3.0 | 2026-08 | 44 |
| Python | Very simple cis-regulatory gene regulatory network simulation of developmental gene expression. | Gene networks and synthetic biology | Not assessed | AGPL-3.0 | 2025-06 | — |
| C++ | Coalescent simulator for microsatellite/sequence/SNP data under user scenarios, used for ABC and ABC-RF inference. | Population genetics | Not assessed | none-found | 2025-03 | 8 |
| Ligand docking with sampling, scoring and flexible ligand handling. | Molecular simulation | Not assessed | — | — | ||
| Python | Multi-algorithm, multi-timescale cell simulation (ODE, Gillespie, spatial particle methods); lineage of the 1999 E-CELL system | Systems biology | Not assessed | GPL-3.0 | 2026-09 | 20 |
| C++ | High-performance general-purpose NeuroML-based neural simulator (compartmental and point neurons). | Neuroscience | Not assessed | GPL-3.0 | 2026-06 | — |
| Python and C++ | Agent-based epidemic model with household, place and age structure, available as a Python implementation (pyEpiabm) and a C++ one (cEpiabm). | Epidemiology | Not assessed | BSD-3-Clause | 2025-09 | 22 |
| R | Single-cell RNA-seq expression with gene co-expression structure. | Sequencing and omics data | Not assessed | GPL-3.0 | 2021-05 | 8 |
| Python | Fast simulation of sequences (substitutions and indels) along a phylogenetic tree, with data structures that make indel handling efficient. It is integrated into the SpartaABC web server. | Phylogenetics and sequence evolution | Not assessed | AFL-3.0 | 2025-09 | 3 |
| R | Classroom population genetics simulations (drift, selection) in R. | Population genetics | Not assessed | GPL-3.0 | 2021-01 | 1 |
| Evolution of intact DNA coding sequences along a tree, with separate mutation and selection, substitutions, insertions and deletions. It outputs the true tree and true alignment. | Phylogenetics and sequence evolution | Not assessed | — | — | ||
| Event-driven spiking neural network simulator optimized by population and pre-filtering. | Neuroscience | Not assessed | — | — | ||
| Bacterial genome evolution under the bacterial sequential Markov coalescent with structure, migration and recombination. | Population genetics | Not assessed | — | — | ||
| C++ | Continuous-time coalescent simulation of genomic diversity under complex demographic scenarios; fastsimcoal2 also does SFS-based inference. | Population genetics | Not assessed | — | — | |
| Python | Contact networks, transmission, phylogenies and sequence evolution for viral outbreaks. | Population genetics | Not assessed | GPL-3.0 | 2023-11 | 40 |
| Python | Lightweight simulation of viral transmission: contact networks, transmission networks, phylogenies and sequence evolution. | Epidemiology | Not assessed | GPL-3.0 | 2026-03 | 8 |
| C++ | Simulator for biological and physiological models described in SBML, CellML and PHML | Systems biology | Not assessed | MIT | 2026-10 | 7 |
| Java | Event-driven spiking network simulator based on the leaky integrate-and-fire-with-latency (LIFL) neuron model, multi-threaded. | Neuroscience | Not assessed | GPL (version not stated) | — | |
| Forward evolutionary simulation of the genetic architecture of complex traits under demography, chance and selection. | Population genetics | Not assessed | — | — | ||
| C++ | Forward-in-time simulation of sequence-level data over large genomic regions with selection, demography, recombination hotspots and gene conversion; companion SAMPLE replicates association study datasets. | Population genetics | Not assessed | GPL (stated for invertFREGENE derivative in paper abstract; FREGENE itself not verified) | — | |
| Python/C++ | Python package for forward-time Wright-Fisher simulation (built on fwdpp) with selection, demography and tree-sequence recording. | Population genetics | Guide | GPL-3.0 | 2026-09 | 34 |
| Python | Individual-tree forest gap model: establishment, growth and mortality of trees in plots under climate drivers. | Ecology and agent-based models | Not assessed | MIT | 2026-03 | 5 |
| C++, Perl | Ancient DNA sequencing reads (fragmentation, deamination damage, present-day contamination). | Sequencing and omics data | Guide | GPL-3.0 | 2026-09 | 39 |
| Python | Illumina and 454 reads (single and paired end) from empirical error models, including multi-genome, metagenome and haplotype simulation. | Sequencing and omics data | Not assessed | GPL-3.0 | — | |
| R | Scale-free transcriptional network topology with fuzzy-logic regulation integrated with ODEs to generate expression data for testing reverse-engineering algorithms (R package). | Gene networks and synthetic biology | Not assessed | — | — | |
| C | Compartmental neuron and network models with Hodgkin-Huxley-type channels, synapses and subcellular biochemistry. | Neuroscience | Not assessed | — | — | |
| Forward simulation of genomes/SNPs in populations with mutation (GTR/codon models), recombination, selection, migration and demography. | Population genetics | Not assessed | GNU license (version not verified) | — | ||
| Python | Biochemical models solved by ODE and SSA, tau-leaping and hybrid solvers | Systems biology | Guide | GPL-3.0 | 2025-01 | 84 |
| Three-dimensional stochastic particle-based simulation of biochemical networks with crowding and localization | Systems biology | Not assessed | — | — | ||
| Python | Spatially explicit coalescent simulation on a 2D grid of demes with varying deme sizes and migration, as a wrapper for msprime. | Population genetics | Not assessed | none declared | 2023-02 | 1 |
| Generation-by-generation exact coalescence of recombining genomes with small population size and isolation by distance. | Phylogenetics and sequence evolution | Not assessed | — | — | ||
| NetLogo | NetLogo agent-based model of spatial and temporal development of four bacterial genera populations in the ileum under flow, nutrition and probiotic perturbations. | Ecology and agent-based models | Not assessed | none found | 2018-05 | 2 |
| Python | Gymnasium environments simulating Probabilistic Boolean Networks and PBCNs for reinforcement-learning-based control toward target attractors. | Gene networks and synthetic biology | Not assessed | MIT | 2026-04 | 4 |
| C++ | Case-control haplotype/genotype data with multiple disease SNPs, resampled from reference haplotypes with a recombination-based copying model. | Population genetics | Not assessed | — | — | |
| Python | Mechanistic stochastic gene regulatory network model based on transcriptional bursting (two-state promoter, mRNA, protein) with fast simulation and network inference (CARDAMOM). | Gene networks and synthetic biology | Not assessed | BSD-3-Clause | 2026-04 | 13 |
| Python | Horizontal gene transfer events among members of a simulated microbial community, producing metagenomic benchmarking data. | Sequencing and omics data | Not assessed | GPL-3.0 | 2020-10 | 10 |
| Python | Agent-based HPV transmission, cervical disease progression, screening and vaccination. | Epidemiology | Not assessed | MIT | 2026-10 | 18 |
| Protein and DNA sequence evolution with insertions and deletions, lineage-specific evolution, and motif conservation via PROSITE-like regular expressions. | Phylogenetics and sequence evolution | Not assessed | — | — | ||
| Spatially explicit individual-based model of bacterial motility and growth using dynamic flux balance analysis on soil pore networks with nutrient diffusion. | Ecology and agent-based models | Not assessed | — | — | ||
| Integrated environment for synthetic biology: Infobiotics Language (P-system) model specification, stochastic multi-compartment simulation, model checking and biocompilation to DNA. | Gene networks and synthetic biology | Not assessed | GPL-3.0 | — | ||
| Python | Structural variants, simulated from a flexible grammar with placement constraints on a genome. It also supports small variants, genome mixtures and read simulation. | Phylogenetics and sequence evolution | Not assessed | MIT | 2026-09 | 18 |
| C++ | Extension of FREGENE simulating an inversion polymorphism of given length, location, frequency and age in a population of sequences. | Population genetics | Not assessed | GPL | — | |
| Python | Gene-tree and sequence simulation on species trees or networks via msprime, with tools to analyze genealogies. | Population genetics | Guide | MIT | 2026-07 | 14 |
| C++ | ChIP-seq (and ChIP-exo) sequencing data from a user-defined binding template, with Illumina/454/IonTorrent/SOLiD read models. | Sequencing and omics data | Not assessed | GPL-3.0 | 2025-03 | 9 |
| Python | PacBio Iso-Seq / ONT full-length isoform sequencing reads from a transcript annotation. | Sequencing and omics data | Not assessed | Apache-2.0 | 2022-03 | 16 |
| Python | Builds, simulates and trains SBML kinetic ODE models with JAX/Diffrax | Systems biology | Not assessed | Apache-2.0 | 2026-06 | 13 |
| Python | Differentiable biophysical (multi-compartment Hodgkin-Huxley) neuron and network simulation in JAX on CPU/GPU, for gradient-based parameter fitting. | Neuroscience | Not assessed | Apache-2.0 | 2026-09 | 215 |
| R | Landscape forest succession and disturbance modules (LANDIS-II-like cohort dynamics) in R on the SpaDES framework. | Ecology and agent-based models | Not assessed | GPL-3.0 | 2026-10 | 20 |
| Python | Neuromorphic software framework: spiking/process models simulated on CPU or deployed to Intel Loihi. | Neuroscience | Not assessed | BSD-3-Clause (core) / LGPL-2.1-or-later (compiler, runtime) | 2026-05 | 741 |
| C++ | LLVM-JIT-compiled deterministic (ODE), stochastic and steady-state simulation and analysis of SBML models. | Systems biology | Not assessed | Apache-2.0 | 2026-10 | 63 |
| Python | Macromolecular docking (protein-protein, protein-peptide, protein-DNA) using a glowworm swarm optimization framework. | Molecular simulation | Not assessed | GPL-3.0 | 2026-09 | 409 |
| C | 10x-style linked reads, emulating library prep (fragmentation, partitioning, barcoding) and short-read sequencing. | Sequencing and omics data | Guide | MIT | 2026-08 | 46 |
| C++ | Authentic, ultrafast ONT-style long-read simulation using real read-length distributions and indel ratios. | Sequencing and omics data | Not assessed | none-found | 2025-05 | 2 |
| R | Educational open-source PBPK model with ACAT absorption for bottom-up simulations, delivered as an R Shiny app. | Physiology and organs | Not assessed | MIT | 2026-06 | 15 |
| Tool for building next-generation individual-based models of microbial consumer-resource systems from pre-implemented physical and biological building blocks. | Ecology and agent-based models | Not assessed | — | — | ||
| R | R package to build and run MCSim-syntax ODE models (toxicokinetics/PBPK) from R. | Physiology and organs | Not assessed | GPL-3.0 | 2026-01 | 11 |
| Python | Simulated microbial communities from real community structure, plus PacBio HiFi and ONT long reads for community members. | Sequencing and omics data | Not assessed | GPL-3.0 | 2024-03 | — |
| Python | Ground-truth extracellular spiking recordings (templates from biophysical models via LFPy/NEURON, plus spike trains and noise) for spike-sorting benchmarks. | Neuroscience | Not assessed | GPL-3.0 | 2023-10 | 4 |
| Stochastic individual-based simulation of tree population evolution with quantitative genetics, phenotypic plasticity and assortative mating in heterogeneous landscapes. | Population genetics | Not assessed | — | — | ||
| Python/Cython | Stochastic metapopulation (ward-level network) epidemic simulation with movement models, used in UK COVID-19 modelling. | Epidemiology | Not assessed | GPL-3.0 | 2024-07 | 14 |
| Python | PacBio HiFi microbiome amplicon sequencing datasets with genome-aware abundances, dual barcodes and empirical pass-number distributions. | Sequencing and omics data | Not assessed | MIT | 2025-12 | 2 |
| R | Simulates microbial community time series with generalized Lotka-Volterra, consumer-resource, Hubbell and related models. | Physiology and organs | Not assessed | Artistic-2.0 | 2025-10 | 22 |
| Python | Simulation, Bayesian inference and prediction of microbial community dynamics (generalized Lotka-Volterra, Gaussian process, VAR and consumer-resource models). | Ecology and agent-based models | Not assessed | MIT | 2025-12 | 12 |
| Python | Multilocus multispecies coalescent with gene duplication and loss (copy number hemiplasy) for gene-tree simulation | Phylogenetics and sequence evolution | Not assessed | GPL-3.0 | 2023-08 | — |
| Stochastic simulation and analysis of Petri net models of biochemical systems. | Systems biology | Not assessed | — | — | ||
| R | Bulk and single-cell multi-omics data (RNA-seq, ATAC, miRNA, ChIP, methyl-seq, scRNA/scATAC) with regulatory relationships. | Sequencing and omics data | Not assessed | GPL-3 | 2026-02 | 14 |
| R | ODE-based population PK/PD and quantitative systems pharmacology (QSP/PBPK) model simulation from R. | Physiology and organs | Not assessed | GPL-2.0 | 2026-09 | 171 |
| Python | Coalescent simulation with chromosomal inversions. | Population genetics | Not assessed | MIT | 2026-10 | 1 |
| C++ | Couples Markov state models of molecular kinetics with particle-based reaction-diffusion. | Cells and tissues | Not assessed | — | 2023-05 | 3 |
| Multi-formalism interaction network simulator combining constraint-based (flux balance) modelling with regulatory logic and Quasi-Steady State Petri Nets for gene regulation, signalling and metabolism. | Gene networks and synthetic biology | Not assessed | — | — | ||
| R | Multi-sample, multi-condition scRNA-seq with subpopulation-specific state transitions, via simData inside an analysis package. | Sequencing and omics data | Not assessed | GPL-3 | 2026-07 | 246 |
| Python | Random SNPs, indels and structural variants introduced into a reference genome, with region-specific rates. | Sequencing and omics data | Not assessed | GPL-3.0 | 2024-02 | 43 |
| Python | Single and multi-cell cardiac ionic model and action potential simulation, 0D/1D tissue, voltage-clamp protocols, with a Python interface. | Physiology and organs | Not assessed | BSD-3-Clause | 2026-08 | 46 |
| Python | NGS reads with empirical error models plus variant insertion (germline/tumor) and golden BAM/VCF truth sets. | Sequencing and omics data | Not assessed | BSD-3-Clause | 2026-09 | 72 |
| R | Simulates DNA sequence evolution on trees under relaxed molecular-clock models (autocorrelated and uncorrelated rates) | Phylogenetics and sequence evolution | Not assessed | GPL (>=2) | 2026-09 | 7 |
| Python/JavaScript/MATLAB | Network of regional SEIR models (Kazakhstan oblasts and cities) linked by transport edges, for evaluating region-specific COVID-19 policies. | Epidemiology | Not assessed | none-found | 2020-12 | 9 |
| Python | Whole-brain network models built from neural mass nodes coupled by structural connectivity, with exploration and optimization tools. | Neuroscience | Not assessed | MIT | 2025-11 | 495 |
| Python | NeuroML2/LEMS model description and tooling; runs models via jNeuroML/PyLEMS or exports to NEURON, NEST, Brian and others. | Neuroscience | Not assessed | LGPL-3.0 | 2026-07 | 53 |
| R (GitHub language tag says HTML) | Microclimate and ectotherm/endotherm biophysical (heat, water, energy budget) models. | Ecology and agent-based models | Not assessed | GPL-3.0 | 2026-09 | 89 |
| Python | Visual-programming, component-based platform for functional-structural plant modelling (plant architecture, growth, light, epidemics) | Physiology and organs | Not assessed | — | 2026-02 | 55 |
| Python | Lagrangian particle trajectory framework for ocean drift, including fish egg/larvae and other biological particle modules. | Ecology and agent-based models | Not assessed | GPL-2.0 | 2026-10 | 328 |
| Python | Reaction networks with compartments (pharmacokinetics, pharmacodynamics, reaction-diffusion) simulated stochastically (Gillespie) or deterministically (ODE). | Systems biology | Not assessed | MIT | 2026-02 | 13 |
| C++ | Functional-structural 3D root architecture model with nutrient uptake, carbon and water dynamics | Physiology and organs | Not assessed | — | — | |
| Python | Lagrangian simulation of virtual particles (plankton, larval dispersal, plastics) in ocean and atmosphere flow fields. | Ecology and agent-based models | Not assessed | MIT | 2026-10 | 366 |
| Python | Builds and simulates ODE signaling network models for patient-specific modeling (built on biomass). | Systems biology | Not assessed | Apache-2.0 | 2026-10 | 19 |
| Python | Crop growth simulation (WOFOST, LINTUL3 and related models) driven by weather and soil data | Physiology and organs | Not assessed | EUPL-1.1 | 2026-09 | 286 |
| Perl | Personal genomes with customizable known/novel SNVs, indels and SVs drawn from population variant databases. | Sequencing and omics data | Not assessed | MIT | 2020-03 | 6 |
| Python | Gillespie-based efficient sequence evolution along very large phylogenies (100,000+ tips) with indels and hypermutability models, for SARS-CoV-2-scale datasets. | Population genetics | Not assessed | GPL-3.0 | 2025-04 | 24 |
| R | Coalescent genealogy simulation (isochronous/heterochronous sampling) plus Bayesian nonparametric inference of effective population size. | Epidemiology | Not assessed | GPL-3 | 2021-11 | 20 |
| R | Monte Carlo (Gillespie) simulation of sequence evolution with substitutions and indels, site-specific rates and selective constraints | Phylogenetics and sequence evolution | Not assessed | GPL (>= 3) | 2023-10 | — |
| C++ | Illumina paired-end reads with empirical base-calling and GC-depth bias profiles, plus heterozygous diploid genome simulation. | Sequencing and omics data | Guide | GPL-2.0 | 2023-12 | 28 |
| R | RNA-seq reads with isoform-level differential expression across biological replicates. | Sequencing and omics data | Not assessed | Artistic-2.0 | 2021-09 | 100 |
| R | Spatially and temporally explicit forward Wright-Fisher simulator for range expansion, selection and demography. | Ecology and agent-based models | Not assessed | MIT + file LICENSE | — | |
| R | Bulk and single-cell RNA-seq count data for DE power analysis, with parameters estimated from real data. | Sequencing and omics data | Not assessed | Artistic-2.0 | 2023-08 | 108 |
| Python | Vivarium 2.0 compositional runtime for wiring and executing interoperable biological process models across timescales (a simulation framework, not a single model). | Systems biology | Not assessed | Apache-2.0 | 2026-10 | 9 |
| Modular, composable-parts ODE-based design and simulation of synthetic gene circuits using the Process Modeling Tool (ProMoT). | Gene networks and synthetic biology | Not assessed | — | — | ||
| Python | Phylogeny-guided tumor evolution and bulk/multi-sector/single-cell tumor NGS data. | Sequencing and omics data | Not assessed | GPL-3.0 | 2021-04 | 11 |
| Profile-based WGBS, RRBS and oxBS-seq bisulfite sequencing data for different cell types, modelling meQTLs, allele-specific methylation and DMRs. | Sequencing and omics data | Not assessed | — | — | ||
| Python | Python package for generation, modification and analysis of Boolean networks, including synchronous/asynchronous state-transition simulation, attractors, trap spaces and model checking. | Gene networks and synthetic biology | Not assessed | LGPL (PyPI classifier; no LICENSE file in repo) | 2026-03 | 56 |
| Python | Individual-level epidemic simulator with hierarchical random population structure, used to discover optimal containment policies (incl. RL). | Epidemiology | Not assessed | MIT | 2022-03 | 15 |
| Python | Python interface (PyPI package maboss) to MaBoSS for continuous/discrete time stochastic simulation of Boolean networks and population-level probabilities. | Gene networks and synthetic biology | Not assessed | — | 2026-07 | 9 |
| Python | Individual-based resource-competition model of mangrove and other vegetation stand dynamics. | Ecology and agent-based models | Not assessed | GPL-3.0 | 2026-10 | 12 |
| Python | Modular spiking neural network simulation (NumPy backend; PyTorch GPU backend in PymoNNtorch) | Neuroscience | Not assessed | MIT | 2024-10 | 20 |
| Python | Graph-based code generation and simulation of neural population (rate-based) and general dynamical systems models | Neuroscience | Not assessed | GPL-3.0 | 2026-06 | 93 |
| Python | Python DSL for rule-based biochemical models, simulated via BioNetGen, Kappa, ODE (scipy) or stochastic solvers. | Systems biology | Not assessed | BSD-2-Clause | 2026-05 | 201 |
| Python (with compiled C/Fortran extensions) | Python Simulator for Cellular Systems: time-course ODE simulation, steady-state analysis and metabolic control analysis of kinetic models | Systems biology | Not assessed | BSD-3-Clause | 2026-03 | 40 |
| Python | Python implementation of a simplified version of the STICS crop growth model | Physiology and organs | Not assessed | MIT | 2024-09 | 16 |
| Python | 3D vertex model of epithelial tissue and cell mechanics (scutoids, tissue repair simulations). | Cells and tissues | Not assessed | MIT | 2026-09 | 3 |
| Python | Python package for constraint-based metabolic modeling (FBA, pFBA, FVA, etc.) and some kinetic simulation of metabolic models | Systems biology | Not assessed | Apache-2.0 | 2026-06 | 63 |
| Protein sequence evolution simulation that preserves protein domain/constraint profiles | Phylogenetics and sequence evolution | Not assessed | GPL-3.0 | 2016-12 | — | |
| R | Simulation, visualization and estimation of stochastic SEIR epidemic models in R (ML and Bayesian inference). | Epidemiology | Not assessed | none-found | — | |
| Generates families of related RNA/DNA/protein sequences along a tree with substitutions, indels and site-specific rates, logging the true alignment | Phylogenetics and sequence evolution | Not assessed | — | — | ||
| R (with C++) | R implementation of Ecopath with Ecosim: mass-balance food web model and dynamic ecosystem simulation. | Ecology and agent-based models | Not assessed | Custom US Government (NOAA) public-domain notice (file LICENSE) | 2026-10 | 43 |
| R | Structural variations (deletions, insertions, inversions, tandem duplications, translocations) inserted into a genome, optionally biased to repeats or homology. | Sequencing and omics data | Not assessed | LGPL-3 | — | |
| C++ | Network-free stochastic simulation of rule-based models (BioNetGen language) | Systems biology | Not assessed | — | — | |
| Python | Python framework for defining and running SBML simulation experiments on top of libRoadRunner | Systems biology | Not assessed | MIT | 2026-10 | 12 |
| Python | Generates synthetic scRNA-seq data (including dropouts) from Boolean network traces and binarises scRNA-seq data; links expression statistics to Boolean dynamics. | Gene networks and synthetic biology | Not assessed | BSD-3 (PyPI metadata; no LICENSE file in repo) | 2026-09 | 16 |
| R | Protocol-dependent scRNA-seq count data for experimental design (sequencing depth, cell number) and DE-method evaluation. | Sequencing and omics data | Not assessed | GPL-2 | 2020-12 | 14 |
| R | High-fidelity single-cell gene expression count data with gene correlations via copulas. | Sequencing and omics data | Not assessed | MIT | 2024-11 | 30 |
| R | Multimodal single-cell and spatial omics data with cell states, trajectories and spatial locations from a unified probabilistic model. | Sequencing and omics data | Not assessed | MIT | 2025-09 | 126 |
| R | Single-cell multi-omics (expression, chromatin accessibility, RNA velocity) and spatial data guided by gene regulatory networks and cell-cell interactions. | Sequencing and omics data | Not assessed | Artistic-2.0 | 2026-06 | 69 |
| C++ | Single-cell genome sequencing data with MALBAC amplification, allele dropout and genomic variations. | Sequencing and omics data | Not assessed | BSD-3-Clause | 2019-12 | 10 |
| C++ | Forward-in-time simulation of molecular evolution in segmental duplications undergoing interlocus gene conversion and crossover, with copy-number selection. | Population genetics | Not assessed | — | — | |
| Perl | Bisulfite-converted FastQ reads (BiQRS). | Sequencing and omics data | Not assessed | GPL-3.0 | 2026-06 | 14 |
| Perl | Structural variants plus Nanopore/PacBio long reads with error profiles. | Sequencing and omics data | Not assessed | Apache-2.0 | 2026-05 | 28 |
| R | Genetic variants preserving LD from a phased VCF, for unrelated individuals and pedigrees. | Sequencing and omics data | Not assessed | GPL (>= 2) | 2021-09 | 19 |
| R | scATAC-seq count matrices resembling real data in library size, sparsity and accessibility signal. | Sequencing and omics data | Not assessed | GPL-3.0 | 2021-01 | 7 |
| Spatially explicit multiscale 3D simulation of bacterial populations, colonies and biofilms with intracellular genetic circuit models. | Gene networks and synthetic biology | Not assessed | — | — | ||
| Python | Type 1 diabetes glucose-insulin simulator (UVA/Padova model) for controller testing and RL | Physiology and organs | Not assessed | MIT | 2026-07 | 351 |
| Python | PacBio SMRT long reads with an empirical error model dependent on number of passes. | Sequencing and omics data | Guide | MIT | — | |
| Python | Agent-based multi-scale stochastic model of SARS-CoV-2 within-host evolution and between-host transmission with immune evasion. | Epidemiology | Not assessed | GPL-3.0 | 2026-10 | 4 |
| Python | Single-cell DNA sequencing data on a simulated cell lineage tree with SNVs and copy number aberrations. | Sequencing and omics data | Not assessed | none-found | 2023-04 | 7 |
| C | Illumina paired-end and mate-pair reads with site- and base-specific empirical error models, including chimeric reads. | Sequencing and omics data | Not assessed | MIT | 2014-09 | 68 |
| C++ | 3D simulation of tissue mechanics with deformable cells (cell shape, division, polarization). | Cells and tissues | Not assessed | BSD-3-Clause | 2024-06 | 6 |
| Python | Agent-based single-cell tumor evolution and metastasis under genotype-driven clonal selection, with mutation profiles and DNA-seq reads | Phylogenetics and sequence evolution | Not assessed | GPL-3.0 | 2026-05 | 4 |
| Perl | Generates structure-based (Go-like) models of proteins and RNA for folding and dynamics simulations in other MD engines. | Molecular simulation | Not assessed | GPL-2.0 | 2026-07 | 5 |
| C++ | Real-time multi-physics simulation with emphasis on medical simulation (soft tissue, deformable bodies). | Physiology and organs | Not assessed | LGPL-2.1 | 2026-10 | 1,269 |
| Python | Somatic SBS/DBS/ID mutations in an input sequence following COSMIC mutational-signature probabilities. | Sequencing and omics data | Not assessed | CC-BY-NC-SA-4.0 | 2023-05 | 6 |
| R (with C++/Rcpp) | scRNA-seq count matrices reproducing sparsity, variability and intensity of real data (gamma-multivariate hypergeometric model). | Sequencing and omics data | Not assessed | GPL-3.0 | 2026-07 | 5 |
| Simulator for rule-based modeling of biomolecular site dynamics on surfaces | Systems biology | Not assessed | — | — | ||
| R | scRNA-seq count data with the Splat gamma-Poisson model, plus a wrapper over other scRNA-seq simulators. | Sequencing and omics data | Not assessed | GPL-3.0 | 2026-05 | 234 |
| R | Spatially resolved transcriptomics counts that preserve spatial expression patterns. | Sequencing and omics data | Not assessed | GPL-3.0 | 2025-03 | 18 |
| R | Pharmacokinetic/pharmacodynamic simulation of anaesthetic drug effect-site concentrations and response (Shiny app). | Physiology and organs | Not assessed | MIT (R-style LICENSE file: YEAR/COPYRIGHT HOLDER) | 2026-10 | 25 |
| Python | Agent-based disease modelling framework (networks, demographics, interventions) for multiple pathogens; successor basis of Covasim. | Epidemiology | Not assessed | MIT | 2026-10 | 44 |
| Within-host hybrid PDE/cellular-automata simulation of sexually transmitted infection (Chlamydia trachomatis) in the female genital tract, incl. vaccination scenarios. | Epidemiology | Not assessed | none-found | — | ||
| Stochastic kinetic simulations of biochemical systems with the Gillespie algorithm | Systems biology | Not assessed | — | — | ||
| Python | Allele-specific, haplotype-aware structural variants with cancer clonal phylogeny, output as FASTA/FASTQ/BAM. | Sequencing and omics data | Not assessed | — | — | |
| R | scRNA-seq data with intrinsic transcriptional noise, extrinsic cell-state variation and technical noise. | Sequencing and omics data | Not assessed | Artistic-2.0 | 2024-09 | 28 |
| Python | Python environment for building and simulating SBML/Antimony kinetic models (ODE and stochastic, via libRoadRunner) | Systems biology | Not assessed | Apache-2.0 | 2026-08 | 146 |
| Simulates genomes carrying transposable-element insertion/deletion variants, with short/long-read data and VCFs | Phylogenetics and sequence evolution | Not assessed | — | — | ||
| Julia | Multiscale cardiac multiphysics (electrophysiology and mechanics) with finite elements. | Physiology and organs | Not assessed | MIT | 2026-09 | 26 |
| Python | Phylogenetic trees under epidemiological multi-type birth-death models (BD, BDEI, BDSS, MTBD, with contact tracing and skyline). | Phylogenetics and sequence evolution | Guide | GPL-3.0 | 2026-09 | 6 |
| Python | Quantitative trait phenotypes simulated on tskit tree sequences (ancestral recombination graphs) from msprime/SLiM. | Population genetics | Not assessed | MIT | 2026-09 | 9 |
| R | Tumor clonal evolution under the hallmarks-of-cancer model (Kato) linked to tumor-related gene mutation states. | Sequencing and omics data | Not assessed | GPL-3.0 | 2023-12 | 13 |
| Patient-specific cancer clonal dynamics under drug interventions, from patient NGS and imaging data. | Sequencing and omics data | Not assessed | — | — | ||
| Python | Stochastic simulation of transcription coupled to DNA supercoiling in bacteria | Systems biology | Not assessed | MIT | 2019-12 | — |
| Python | Agent-based/compartmental epidemic model on networks for 'what if' scenarios with public interventions (lockdown, testing, tracing); also integrated in NDlib as UTLDRModel. | Epidemiology | Not assessed | — | 2020-05 | 1 |
| Jupyter Notebook | Differentiable JAX-based vertex model of epithelial tissues for forward simulation and inverse design. | Cells and tissues | Not assessed | CC-BY-SA-4.0 | 2026-07 | 25 |
| Forward simulator for rapidly evolving (RNA) viral populations including compensatory mutations and synthetic lethal couples. | Population genetics | Not assessed | — | — | ||
| Visual tool built on the GEC (Genetic Engineering of Cells) language for designing genetic circuits and running deterministic and stochastic simulation of the compiled chemical reactions. | Gene networks and synthetic biology | Not assessed | unknown | — | ||
| Python | Interface and discrete-event engine for composing multi-algorithm integrative multiscale models (ODE, stochastic, FBA, agent-based, diffusion) from modular processes | Systems biology | Not assessed | Apache-2.0 | 2026-08 | 38 |
| R | Discrete-time individual-based simulation of within-host adaptive virus (HIV-1) sequence evolution with recombination, latent reservoir and conserved-site, replicative and immune selection. | Epidemiology | Not assessed | Triad National Security LANL custom license (GitHub API: NOASSERTION; DESCRIPTION says 'file LICENSE') | 2026-09 | 4 |
| R | Adaptive within-host viral sequence evolution (forward simulation with selection, recombination, immune escape). | Phylogenetics and sequence evolution | Not assessed | BSD-3-Clause | 2026-09 | 4 |
| Python | Multi-algorithmic (ODE, SSA, FBA) dynamic simulator for whole-cell models written in wc_lang, using a distributed discrete-event simulation core | Systems biology | Not assessed | MIT | 2025-01 | 7 |
| Computational whole-cell model of Saccharomyces cerevisiae S288C with 15 cellular states and 26 cellular processes, used to predict phenotypes and essential gene function | Systems biology | Not assessed | — | — | ||
| Reference-free FASTQ files (headers, sequences, qualities) for 454, Ion Torrent, Illumina and SOLiD. | Sequencing and omics data | Not assessed | — | — | ||
| Python | Phylogenetic simulator of species trees including extinct lineages, genomes with duplication/transfer/loss/inversion events, and sequences. | Population genetics | Not assessed | GPL-3.0 | 2025-04 | 25 |