View source for Score based FBC table builder (analysis)

;Analysis title
:[[File:Differential-algebraic-equations-Score-based-FBC-table-builder-icon.png]] Score based FBC table builder
;Provider
:[[Institute of Systems Biology]]
;Class
:{{Class|biouml.plugins.fbc.table.ScoreBasedFbcTableBuilder}}
;Plugin
:[[Biouml.plugins.fbc (plugin)|biouml.plugins.fbc (Flux Balance)]]

==== Description ====
This analysis constructs FBC data table using data about enzymes (reaction modifiers) from the specified tables.

==== Parameters: ====

* '''Diagram''' – Path to diagram
* '''Enzymes table''' – Path to table with enzymes
* '''Max column''' – Name of the column with values for flux upper bound
* '''Normalize bounds''' – Shows if bounds should be normalized
* '''Score column''' – Name of the column with score from table with enzymes
* '''Is score correlation''' (expert) – Shows if enzymes score is correlation
* '''Objective function table''' – Table with objective function values
* '''Objective column''' – Name of the column with values of objective function
* '''Output table''' – Path to output table with FBA data table

==== Method description: ====

This analysis constructs FBC data table for '''Flux Balance Constraint''' analysis. Such table contains information about fluxes (reactions): lower and upper bound, objective function coefficients. Unlike '''Building Flux Balance DataTable''' analysis, this one constructs FBC data table using data about enzymes (reaction modifiers) from the specified tables. So if one want to use, e.g., enzymes expression or other data about enzymes as in <nowiki>[</nowiki>1<nowiki>]</nowiki>, <nowiki>[</nowiki>2<nowiki>]</nowiki>, this analysis is recommended.

'''Upper bound'''

Upper bound of reaction is constructed in a following way. If '''Enzymes table''' or '''Max column''' is not specified <nowiki>'</nowiki>1.0<nowiki>'</nowiki> is selected as upper bound. Else we select values from '''Max column''' for all enzymes which are reaction modifiers and choose the smallest in absolute value. If no enzymes were found, then the smallest absolute value from '''Max column''' will be used.

'''Lower bound'''

Lower bound will be <nowiki>'</nowiki>-upperBound<nowiki>'</nowiki> for reversible reaction and <nowiki>'</nowiki>0.0<nowiki>'</nowiki> for irreversible.

'''Objective function coefficient'''

Three different ways can be used to obtain objective function coefficient. For this purpose 4 parameters are used: '''Enzymes table''', '''Score column''', '''Objective function table''' and '''Objective column''', and must be specified at least one: '''Objective function table''' or ('''Enzymes table''' and '''Score column''').

# '''Objective function table''' is not specified. In this case '''Enzymes table''' and '''Score column''' must be specified. Coefficient is evaluated in the same way as upper bound, but will be selected the max value from '''Score column''' for all enzymes which are reaction modifiers.
# '''Enzymes table''' or '''Score column''' is not specified. For all reactions, which name is in IDs of '''Objective function table''' table, coefficient will be equal value from '''Objective column''' (if this parameter is specified) and <nowiki>'</nowiki>1.0<nowiki>'</nowiki> (if not). And <nowiki>'</nowiki>0.0<nowiki>'</nowiki> for others.
# '''Objective function table''', '''Enzymes table''' and '''Score column''' are specified. In this case coefficient will be equal to multiplication of the values obtained by items 1. and 2.

'''References:'''
# Caroline Colijn, Aaron Brandes, Jeremy Zucker, Desmond S. Lun, Brian Weiner, Maha R. Farhat, Tan-Yun Cheng, D. Branch Moody, Megan Murray, James E. Galagan. ''"Interpreting Expression Data with Metabolic Flux Models: Predicting Mycobacterium tuberculosis Mycolic Acid Production."'' PLoS Comput Biol. 2009 August; 5(8): e1000489. doi: [http://dx.doi.org/10.1371/journal.pcbi.1000489 10.1371/journal.pcbi.1000489]
# Rasmus Agren, Sergio Bordel, Adil Mardinoglu, Natapol Pornputtapong, Intawat Nookaew, Jens Nielsen. ''"Reconstruction of Genome-Scale Active Metabolic Networks for 69 Human Cell Types and 16 Cancer Types Using INIT."'' PLoS Comput Biol. 2012 May; 8(5): e1002518. doi: [http://dx.doi.org/10.1371/journal.pcbi.1002518 10.1371/journal.pcbi.1002518]

[[Category:Analyses]]
[[Category:Differential algebraic equations (analyses group)]]
[[Category:ISB analyses]]
[[Category:Autogenerated pages]]