cameo medium pfba

Synopsis: Simulate a model after adding media change(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-medium-pfba [option]

where [option] can be

• model: Model acceptable by Cameo (see http://cameo.bio/02-import-models.html).
• change: String to define medium change(s). Each change is defined as <compound ID>:<new value>. For example, EX_o2_e,0 will represent anaerobic condition. Multiple changes 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-medium-pfba \
    --model=iAF1260 \
    --change=EX_o2_e,0;EX_glc__D_e,5.0 \
    --result_type=objective

Working example:

D:\Dropbox\MyProjects\astoolkit>python astools.py cameo-medium-pfba --model=iAF1260 --change=EX_o2_e,0;EX_glc__D_e,5.0 --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: iAF1260
Process medium change(s) ...
Compound EX_o2_e found
... Change: 18.5 --> 0.0
Compound EX_glc__D_e found
... Change: 8.0 --> 5.0
Run parsimonious flux balance analysis on model iAF1260
Objective value = 214.4651630305937