dynamicme

Dynamic simulation of models of Metabolism and macromolecular Expression

Installation

1. Run python setup.py install
2. Open notebooks/publication/start_here.ipynb to run your first dynamicME simulation.

Requirements

DynamicME requires

• Python version >= 2.7.
  • Note: Python 3 compatibility: scheduled Q4 2018.
• COBRApy versions <= 0.5.11. We recommend using 0.5.11
• COBRAme
• ECOLIme
• solvemepy

Note on version compatibility

We are working on bringing DynamicME up to date with the latest COBRApy. Please note that DynamicME is built on COBRAme, and work is underway to first make COBRAme compatible with the latest backend updates that were made in COBRApy after 0.5.11.

Citing:

If you find the module useful, please consider citing:

• L Yang, A Ebrahim, CJ Lloyd, MA Saunders, BO Palsson (2019). DynamicME: dynamic simulation and refinement of integrated models of metabolism and protein expression. BMC Systems Biology 13:2. doi: 10.1186/s12918-018-0675-6.