any examples to get EFVs?
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Hao Luo
Oct 17, 2019, 5:20:56 PM10/17/19
to CellNetAnalyzer User Forum
Are there any examples to set bounds and get EFVs? I can't get the references EFVs numbers.
ref : ECC2 model, ATPM >3.15,glcuo<10, o2up<5 and get 904,599 EFVs.
Steffen Klamt
Oct 18, 2019, 4:02:34 AM10/18/19
to CellNetAnalyzer User Forum
There are two ways to compute EFVs with flux bounds.
1) Write the flux bounds into the text boxes of the respective reactions.
For example: ">= 3.15" (with space between >= and 3.15; and NOT "> 3.15" as you did)
2) Set the bounds via min/max rates in the reaction properties and tick then
the box "Use flux bounds to calculate elementary flux vectors" in the dialog box
appearing when starting the computation of EFMs/EFVs.
Note: you will then be requested to set a threshold for flux bounds beyond
which you consider a flux bound to be infinity. For example, in the ECC2 model
all unknown flux bounds have been set to 1000. A correct threshold would then
be, e.g. 500.
Does this help?
1) Write the flux bounds into the text boxes of the respective reactions.
For example: ">= 3.15" (with space between >= and 3.15; and NOT "> 3.15" as you did)
2) Set the bounds via min/max rates in the reaction properties and tick then
the box "Use flux bounds to calculate elementary flux vectors" in the dialog box
appearing when starting the computation of EFMs/EFVs.
Note: you will then be requested to set a threshold for flux bounds beyond
which you consider a flux bound to be infinity. For example, in the ECC2 model
all unknown flux bounds have been set to 1000. A correct threshold would then
be, e.g. 500.
Does this help?
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