Menu
All By Tag
visualization strain-design general modeling cell-factories cobra community modeling metabolic model microbiome microbiota minimal cut sets models reconstruction web app algorithms dfba dynamic flux-balance analysis flux analysis gapfilling mathematical modeling me-models metabolic reconstruction modelseed sbml standardization synthetic biology thermodynamics thermodynamics-based flux analysis unit-testing

dfba

by David S. Tourigny and Moritz E. Beber

Tags: dynamic flux-balance analysis , dfba


The dfba project provides an object-oriented software package for dynamic flux-balance analysis (DFBA) simulations using implementations of the direct method or Algorithm 1 described in the paper Harwood et al., 2016. The main algorithms for solving embedded LP problems are written in C++ and use the GLPK (GNU Linear Programming (LP) Kit) and SUNDIALS (Suite of Nonlinear and Differential/Algebraic Equation Solvers) CVODE or IDA. Extension modules to cobrapy are provided for easy generation and simulation of DFBA models.

link Webpage code Repository