cameo mutant fba

Synopsis: Simulate a model after adding mutation(s) using Flux Balance Analysis (FBA), with Cameo.

Usage: python astools.py cameo-mutant-fba [option]

where [option] can be

• model: Model acceptable by Cameo (see http://cameo.bio/02-import-models.html).
• mutation: String to define mutation(s). Each mutation is defined as <reaction ID>:<upper bound>:<lower bound>. For example, RBFK,0,0 will represent a knock out. Multiple mutations are delimited using semicolon.
• result_type: Type of result to give. Allowable types are objective (objective value from FBA) or flux (table of fluxes). Default value = objective.

For example:

python astools.py cameo-mutant-fba \
    --model=iJO1366 \
    --mutation=NNAM,100,0;RBFK,0,0 \
    --result_type=objective

Working example:

D:\Dropbox\MyProjects\astoolkit>python astools.py cameo-mutant-fba --model=iJO1366 --mutation=NNAM,100,0;RBFK,0,0 --result_type=objective
C:\Users\mauri\.conda\envs\py37\lib\site-packages\cameo\visualization\plotting\__init__.py:52 UserWarning: Cannot import any plotting library. Please install one of 'plotly', 'bokeh' or 'ggplot' if you want to use any plotting function.

This operation uses Cameo (https://github.com/biosustain/cameo). If you used it in your study, please cite: Cardoso, J.G., Jensen, K., Lieven, C., Lærke Hansen, A.S., Galkina, S., Beber, M., Ozdemir, E., Herrgård, M.J., Redestig, H. and Sonnenschein, N., 2018. Cameo: a Python library for computer aided metabolic engineering and optimization of cell factories. ACS synthetic biology, 7(4), pp.1163-1166.


Load model: iJO1366
Process mutation(s) ...
Metabolite NNAM found
... Upper Bound: 1000.0 --> 100
... Lower Bound: 0.0 --> 0
Metabolite RBFK found
... Upper Bound: 1000.0 --> 0
... Lower Bound: 0.0 --> 0
Run flux balance analysis on model iJO1366
Objective value = 22.995000000000005