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Access to Biological Web Services from Python.
Core Interface and Engine for Vivarium
Whole cell model of E. coli implemented with Vivarium
Causal and probabilistic reasoning with continuous time dynamical systems
Python interface for running COMETS simulations and analyzing the results
Collection of tasks for running containerized models
An experimental language for causal reasoning
memote – the genome-scale metabolic model test suite
A latent text-to-image diffusion model
Tutorials for BioSimulators
active learning reusable workflows likelihood free inference
Deep universal probabilistic programming with Python and PyTorch
A platform for sharing and reusing biomodeling studies including models, simulations, and visualizations of their results
Registry of containerized biosimulation tools that support a standard command-line interface
Simulation Experiment Description Markup Language (SED-ML)
A tool for semantics-based annotation and composition of biosimulation models
Python Environment for Modeling and Simulating Biological Systems
Specification of the Functional Mock-up Interface (FMI)
Smoldyn is a particle-based biochemical simulator for modeling molecular diffusion, surface interactions, and chemical reactions
Repository for our project on exploring fundamental limits to bacterial growth
Computation of Microbial Ecosystems in Time and Space
A modular compiler for biological chemical reaction networks