Welcome to the Vivarium Collective

The Vivarium Collective is a registry for open-source Vivarium-compatible simulation modules. These can be wired together to generate novel multi-scale simulations, with the most appropriate algorithm for each biological mechanism.

Featured Projects

Vivarium Core
Interface and Engine

This is the heart of the Vivarium Collective. Its modular interface allows for easy combination of systems biology models and simulators, which its engine executes as integrative simulations.

Documentation GitHub
BioSimulators

BioSimulators is a free registry of biosimulation tools. The simulators support a broad range of frameworks (e.g., logical, kinetic), simulation algorithms (e.g., FBA, SSA), and formats (e.g., BNGL, CellML, NeuroML/LEMS, SBML, Smoldyn). BiosimulatorProcess is a general-purpose wrapper for Biosimulators that adds the Vivarium interface, and allows multiple Biosimulators to be combined in hybrid simulations. ODE_FBA is a Composite simulator, that wires together any ODE-based biosimulator with any FBA-based biosimulator.

BioSimulators v-BioSimulators BioSimulators GitHub
Chemotaxis
Multiscale model of E. coli chemotaxis

Vivarium Chemotaxis is a library for the model of E. coli chemotaxis. Its processes include ReceptorCluster, which models the activity of a chemoreceptor cluster, MembranePotential based on internal and external ion concentrations, and FlagellaMotor, which generates thrust and torque based on number of flagella and their motor states.

GitHub Paper
Multibody

Lattice is a composite simulator for spatial environments in which cells can grow, divide, and interact -- through physical forces as well as by uptake and secretion of molecules in a shared chemical milieu. It includes the processes Multibody for solid-body multi-cell physics and DiffusionField for diffusion of molecular concentrations in 2D fields.

GitHub
Bioscrape

Bioscrape (Bio-circuit Stochastic Single-cell Reaction Analysis and Parameter Estimation) -- a Python package that supports deterministic and stochastic simulations.

GitHub
COBRA

COBRA_FBA is a wrapper process for the COBRApy FBA library, which can be loaded with BiGG models, and has been primarily used with BiGG model iAF1260b. The project includes CobraComposite, which adds auxiliary processes MassDeriver and VolumeDeriver to make a type of dynamic FBA. Other processes can constrain individual fluxes in COBRA_FBA through the flux_bounds port, allowing for a type of integrative FBA.

GitHub
Smoldyn

Smoldyn is a particle-based spatial stochastic simulator. Molecules are represented by point-like particles in 1-, 2-, or 3-dimensional continuous space. Molecules diffuse by Brownian motion, react when they collide into each other, and interact with surfaces in a variety of realistic ways.

Website GitHub
Convenience Kinetics

Convenience Kinetics is a generalized Michaelis-Menten-style enzyme kinetics process, which can implement any enzymatic mechanism as a function of the enzyme, substrates, co-factors, and competitors. This formulation is especially useful for generating rate laws for arbitrary chemical networks. ConvenienceKinetics is a process that takes stoichiometry and kinetic rates as parameters, generates the rate laws, and runs them.

GitHub
Vivarium Project Template

This is a template repository, which can be used to start a new Vivarium project. It includes the module structure with example processes, composites, and experiments, and scripts to simplify the release of the project on PyPI.

GitHub
Your Project

Want to add your project to the collective? Open a pull request! You can copy this card to get started.

Website