cameo mutant pfba

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

pFBA reference: Lewis, N.E., Hixson, K.K., Conrad, T.M., Lerman, J.A., Charusanti, P., Polpitiya, A.D., Adkins, J.N., Schramm, G., Purvine, S.O., Lopez‐Ferrer, D. and Weitz, K.K., 2010. Omic data from evolved E. coli are consistent with computed optimal growth from genome‐scale models. Molecular Systems Biology, 6(1):390. http://www.ncbi.nlm.nih.gov/pubmed/20664636

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

Working example:

D:\Dropbox\MyProjects\astoolkit>python astools.py cameo-mutant-pfba --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 parsimonious flux balance analysis on model iJO1366
Objective value = 20.910638297872342