This is the repository for the ModCell2 modular strain design framework.

If you use any part of this software, please cite:

Sergio Garcia and Cong T. Trinh,
Multiobjective strain design: A framework for modular cell engineering,
Metabolic Engineering, Volume 51, 2019, Pages 110-120, ISSN 1096-7176,
https://doi.org/10.1016/j.ymben.2018.09.003.

You may also find the following publications relevant:

Sergio Garcia and Cong T. Trinh,
Comparison of Multi-Objective Evolutionary Algorithms to Solve the Modular Cell Design Problem for Novel Biocatalysis,
Processes 7, (2019).
https://doi.org/10.3390/pr7060361

Sergio Garcia and Cong T. Trinh,
Modular design: Implementing proven engineering principles in biotechnology,
Biotechnology Advances, 2019,
https://doi.org/10.1016/j.biotechadv.2019.06.002.

Sergio Garcia and Cong T. Trinh,
Harnessing natural modularity of cellular metabolism to design a modular chassis cell for a diverse class of products by using goal attainment optimization,
(In preparation)

Download these references in BibTeX format.

Installation

Download or clone this repository, then add simply add the ModCell2 folder to your MATLAB path by running :

addpath(genpath(['<parent-directory>', filesep, 'ModCell2']))

Where <parent-directory> depends on your system. To verify your installation execute run_all_tests.m. ⚠️ Make sure the Requierements are met. ⚠️. You may need to run initCobraToolbox once within Matlab for certain methods to work correctly.

Quick start

All you need to use ModCell2 is a cobra model for your host organism, and the heterologus reactions required for each production pathway. Examples and more details are provided in the Documentation.

Questions and help

Open an issue if you encounter an error or need assitance.

Contributions

If you improve ModCell, please share your contribution creating a pull request. Remember to use google-style or numpy-style docstrings, and create a test for your code.

Requierements

• Matlab (>=2016a) together with the Global Optimization Toolbox and Parallel Computing Toolbox.
• The Cobratoolbox must be properly installed.

• Optimization solver:

  • GLPK: This is the best option for solving LPs. It should be working once you installed Cobratoolbox.
  • linprog (optional): This solver is included in the Matlab Optimization Toolbox and suported by ModCell but not recomended.
  • Gurobi (optional): Free licensces are available for academia. This may only be required for analysis methods solving quadratic programming (QP) problems.
  • Other (optional): Solvers can be easily added by modifying the method calc_basic_objectives.m