# 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
- 0
- backward and forward flux weighted equally
- 1
- backward flux weighted with equilibrium constant
- 2
- backward flux weighted with equilibrium constant, quadratically adjusted
- s
- backward flux weighted with equilibrium constant, adjusted Scott Holzhütter method (Holzhütter & Holzhütter, 2004)
- e
- flux weigthed upon enzyme costs
- E
- 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
- 0
- unadjusted type
- 1
- linearly adjusted type
- 2
- fully adjusted type (quadratic)
- 3
- Computationally very easy normalized linear type, but the value of the targetflux will be restricted to the same sign as the target value
- 4
- linear type. Not normalized.
- 5
- linear type. Normalized.
- 6
- maximum norm, Not normalized.
- 7
- maximum norm, Normalized.
- Normalization:
- 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>
- weight relative to other cost factors, default 1e3
- -xg [<threshold> [<weight>]]
- GIMME expression match (PMID:18483554)
- <threshold>
- threshold on the expression level, default 0.5
- <weight>
- weight relative to other cost factors, default 1e3

**Options for thermodynamic realizability (TR) constraint:**

**Program control options:**

### More options are controlled by the following files:

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