How to obtain DFBSIM

DFBSIM is not in the public domain. However, we are glad to make it available, without charge, for both education and non-profit research purposes. For downloads please contact Suzane Cavalcanti and please use your academic email for correspondence.

DFBSIM uses DAEPACK for automatic code generation and numerical integration of the DAE system. DAEPACK and its component DSL48E are included in the DFBSIM files and the license is free for education and non-profit research purposes. DSL48LPR and the code for simulating dFBA models are currently available for Ubuntu Linux. A Windows version with integration to the COBRA toolbox is in progress and will be made available here. Additional annotated examples will be made available as they are completed.

In order to run DFBSIM, gcc and gfortran (version 4.4.3 or higher) are required.

Installing DFBSIM

After unpacking the zip file, the directory DFBASIM should include three directories: DAEPACK, examples, doc.

The current implementation uses CPLEX and includes a C program that uses the CPLEX Callable Library to construct the standard form LPs that are embedded in the system and subsequently solves them at events. Hence, the path of the CPLEX library has to be specified in the makefile for each example. However, the user can easily replace this with a call to their preferred LP solver. More information on how to interface different LP solvers can be found in the DSL48LPR Manual.