Guides

51 simulators with a written guide and an example that has been run and checked. 7 also run in your browser; the others come with a container recipe that needs only Docker.

Run in your browser

• ArtistooCellular Potts model of cells and tissues: cell sorting by differential adhesion, or a single migrating cell (Act model).
• COPASIDeterministic (LSODA, RADAU5) and stochastic (Gillespie, Gibson-Bruck, tau-leap) time courses of SBML biochemical models.
• LAMMPSClassical molecular dynamics of atoms, polymers and coarse-grained or biomolecular systems, driven by a LAMMPS input script.
• msprimeSimulate a coalescent genealogy with recombination and mutation, and write a VCF, a tree sequence and summary statistics.
• NetLogo WebAgent-based models from the NetLogo Models Library, run by NetLogo Web (Tortoise) embedded from netlogoweb.org, with a seeded run and population chart.
• SimProtProtein sequence evolution with indels along a tree; writes the true alignment.
• R simulators (webR)R 4.6 in the browser: stochastic SIR epidemics with SimInf or adaptivetau, and random trees with ape.

Run with Docker

• BoquilaSelect reads from a pool of candidate reads so that their nucleotide (k-mer) composition matches a model read set, to serve as bias-matched controls.
• Bio++ bppseqgenSimulate DNA sequence alignments along a phylogenetic tree under an HKY85 substitution model with gamma rate variation.
• BygulSimulate tiled-amplicon sequencing reads from two sample genomes mixed at chosen proportions, given a reference and a primer BED scheme.
• CycSimSimulate context-aware long reads from a reference genome using a trained CycSim error model.
• Cytosim2D Brownian-dynamics simulation of flexible cytoskeletal filaments with molecular motors and crosslinkers, from a .cym config file.
• DFTB+Semiempirical density-functional tight-binding and xTB calculations (energies, geometry optimisation, MD) from an HSD input file.
• DWGSIMSimulate paired-end Illumina-like reads from a reference genome, with SNPs, indels, and sequencing errors.
• epydemixStochastic SIR or SEIR epidemic simulation in a well-mixed population, repeated over many runs with 5/50/95 percent bands per compartment.
• FaunusMetropolis Monte Carlo simulation of atomic and molecular systems (electrolytes, proteins, polymers) from a JSON input file.
• fwdpy11Forward-time neutral Wright-Fisher simulation with recombination and an optional population size change; returns a sampled VCF, the site frequency spectrum and diversity statistics.
• gargammelSimulate ancient DNA sequencing reads (short fragments with deamination damage and Illumina errors) from a reference FASTA.
• GillesPy2Simulate a mass-action biochemical reaction network with stochastic (SSA, tau-leaping) or deterministic (ODE) solvers.
• GROMACSClassical molecular dynamics of proteins, lipids and nucleic acids; upload a prepared run input (.tpr) and mdrun simulates it.
• InSilicoSeqSimulate Illumina metagenomic reads from a multi-FASTA of genomes using built-in error models and an abundance distribution.
• ipcoalSimulate gene genealogies and SNPs along a species tree under the multispecies coalescent with recombination and mutation.
• JAX MDDifferentiable molecular dynamics in JAX, run as a fixed Lennard-Jones fluid simulation (NVT Langevin or NVE) with a thermodynamic log and trajectory.
• LRSimSimulate 10x Genomics-style linked reads (barcoded molecules, two haplotypes with random variants) from a reference FASTA.
• NemoIndividual-based forward-time simulation of population genetics and life-history evolution in structured populations, driven by an ini-style configuration file.
• NWChemComputational chemistry package for quantum chemistry, QM/MM and molecular dynamics, driven by an NWChem input deck.
• openCARP (single-cell bench)Run a single-cell cardiac ionic model with periodic stimuli using openCARP's bench tool and return the transmembrane voltage and ionic current traces.
• OpenMMMolecular dynamics of a solvated structure with the AMBER or CHARMM force fields; upload a PDB, get a minimised, equilibrated trajectory back.
• OpenSimForward dynamics of an OpenSim musculoskeletal or mechanical model (.osim) from its default pose, returning coordinate trajectories as CSV.
• PBSIM2Simulate PacBio and Oxford Nanopore long reads from a reference genome using an HMM model of quality scores.
• PBSIM3Simulate Oxford Nanopore and PacBio RS II (CLR) long reads from a reference genome using built-in quality-score HMM error models.
• pIRSSimulate paired-end Illumina reads from a reference FASTA using empirical base-calling, indel and GC-bias profiles.
• PReFerSimForward simulation under the Poisson Random Field model with a two-epoch demography and a point or gamma distribution of selection coefficients; returns SFS, SNP counts and per-site output.
• pyafvActive finite Voronoi model of confluent epithelial tissue; simulates self-propelled cells and returns trajectories, tissue statistics and a final snapshot.
• PyLEMSRun a LEMS (Low Entropy Model Specification) model file, such as an ODE-based neuron or synapse model, and write its output files.
• PyvolveSimulate nucleotide, amino-acid or codon sequence alignments along an input phylogeny (Newick) under a continuous-time Markov substitution model.
• ReaDDyParticle-based reaction-diffusion of a reversible A + B <-> C reaction in a periodic box, returning particle counts over time.
• scrmSimulate genome-scale samples under the coalescent with recombination (ms-compatible output) using the sequential coalescent approximation.
• SELAMForward-time simulation of admixture between ancestral populations with optional selection, from a demography file and a sampling file.
• Seq-GenSimulate the evolution of nucleotide or amino-acid sequences along a phylogenetic tree under Markov substitution models.
• SimLoRDSimulate PacBio SMRT long reads (with pass-dependent insertion, deletion and substitution errors) from a reference FASTA.
• simuGSimulate a genome carrying random SNPs and indels relative to a reference FASTA, with the matching VCFs and coordinate map.
• simuPOPForward-time Wright-Fisher simulation of a diploid population with mutation, recombination and optional selection, returning allele-frequency trajectories and heterozygosity.
• SLiMForward-time, individual-based population genetics simulation scripted in Eidos. Upload a SLiM script; files it writes are returned.
• stdpopsimSimulate genomes under curated published demographic models (human, fly, Arabidopsis) with msprime, returning tree sequences, a VCF and summary statistics.
• treesimulatorSimulate a rooted phylogenetic tree under an epidemiological birth-death model with sampling.
• tyssueRelax a planar epithelium vertex model (line tension, contractility, area elasticity) to its energy minimum and return cell geometry and a picture.
• vcfsimSimulate all-sites VCF files with configurable missing data from msprime coalescent simulations.
• AutoDock VinaDock a small-molecule ligand into a rigid receptor inside a search box and return ranked binding poses with scores.
• wgsimSimulate paired-end Illumina-like reads from a reference genome, with sequencing errors, SNPs and small indels.
• XPPAUTIntegrate a user-supplied system of ODEs or difference equations in XPPAUT batch mode and return the time series as a table.