FASIMU: Flux-balance Analysis based SIMUlations

Features of the flux optimization in FASIMU

The following is just a selection, for full reference, please see the manual.
The main call for a single flux optimization is "compute-FBA" and it has the following options:
-F <fluxmin-type>
type of the fluxmin computation
backward and forward flux weighted equally
backward flux weighted with equilibrium constant
backward flux weighted with equilibrium constant, quadratically adjusted
backward flux weighted with equilibrium constant, adjusted Scott Holzhütter method (Holzhütter & Holzhütter, 2004)
flux weigthed upon enzyme costs
flux weigthed upon enzyme costs, backward flux additionally weighted with equilibrium constant
-m <rea-names> ...
Minimization of these reactions (several rea names may follow)
-b <rea-names> ...
Maximization of these reactions (several rea names may follow)
-f [<type> [<weight>]]
use fitness maximization instead of fixing targetfluxes, default type 3, default weight 1e5
unadjusted type
linearly adjusted type
fully adjusted type (quadratic)
Computationally very easy normalized linear type, but the value of the targetflux will be restricted to the same sign as the target value
linear type. Not normalized.
linear type. Normalized.
maximum norm, Not normalized.
maximum norm, Normalized.
each component is divided by the (squared for 0-2) absolute value of targetflux. Ensures that each targetflux has the same relative impact. If the targetflux is zero, its impact is considered to be 1.
Options for expression:
--xs [<lower threshold> [<upper threshold> [<significant flux> [<weight>]]]]
Shlomi-type expression match
<lower threshold>
lower threshold on the expression level, default 0.5
<upper threshold>
upper threshold on the expression level, default = lower threshold
<significant flux>
threshold on significant flux, default 1
weight relative to other cost factors, default 1e3
-xg [<threshold> [<weight>]]
GIMME expression match (PMID:18483554)
threshold on the expression level, default 0.5
weight relative to other cost factors, default 1e3
Options for thermodynamic realizability (TR) constraint:
use TR criterion, default type
-T [A-Ea-e]r?
use TR with type identifier
-k <number>
potential tolerance maximum
-K <number>
penalty multiplicator for potential tolerance
-s [<weight>]
use soft bounds, set penalty weight (default 1)
-w [<weight>]
use set points, to be found in concentration ranges, default weight 1e-5
concentration range if no file concentration-ranges is available
Program control options:
prepare only 'problem.lp', do not compute
-t <seconds>
timeout in seconds, finish (single flux computation), default 300, 0 means unlimited time
-CPLEXnodes <nodes>
abolish computation number of nodes, default 5000, 0 means unlimited number of modes
-CPLEXemph <1..4>
MIP emphasis setting to be tried out in critcal size models
-CPLEXline "<cplex-parameter-line>"
Give this line to CPLEX
check the results with another optimizer run
print documentation files

More options are controlled by the following files:

fixes the flux of one reaction to a linear combination of other fluxes
expression data
cost of specific enzymes, to be used in conjunction with -F e or -F E
list of reactions having no weight
list of reactions excluded from TR criterion
Range of concentration values for a concentration class, given as: lower hard bound, lower soft bound, set point, upper soft bound, upper hard bound
Assigns a metabolite to a concentration range