Flux balance analysis

From BioUML platform
Jump to: navigation, search

Constraint-based flux balance analysis (FBA) is a mathematical approach that enables to provide a holistic view of the cellular metabolism in pro- and eukaryotes and predict flux distribution in a global (on a genome-scale level) metabolic network both under a range of environmental conditions and genetic perturbations. The maximization of the biomass equation is typically used as an objective function of the model for FBA.


Contents

FBA via Diagram

If the Type-diagram-icon.png diagram contains fluxes properties written as fbc extension of the SBML "FBC table" tab can be used. Advantage of this tab usage is lack of necessity in creation table with data about fluxes: it will be created automatically using Type-diagram-icon.png diagram.

FBA via Analysis tab

FBA can be also conducted via the Flux Balance Constraint analysis in the BioUML. Firstly, move to Analysis tab in the Tree Area by a single click with the right mouse button on the corresponding tab.

FBC data table creation

To start the analysis via the tab it is required to create the table with flux balance constraint data. It can be created via Building Flux Balance Data Table analysis. It is worth noting that the Building Flux Balance Data Table analysis and "FBC table" tab work only with SBML L3v1 Type-diagram-icon.png diagrams with special fbc package. Thus, if the Type-diagram-icon.png diagram does not satisfy these conditions it should be transformed before using this analysis. For example, if the Type-diagram-icon.png diagram does not use fbc package but contains all necessary information about fluxes, it should be preprocessed by Recon transformer firstly.

FBA viaAnalysis Fig1.png

Figure 1. View of Building Flux Balance Data Table analysis. Double-click of the left mouse button the analysis icon (marked red) opens the analysis settings in the Work Space (marked red). It is necessary to specify a path to the diagram, output path for the table and values of lower and upper bounds in mmol*gDCW-1*h-1.


One click of the left mouse button on the Run will launch the analysis. The resulting Flux Balance Data Table for FBA will be automatically opened in the Work Space as an output of the analysis.

FBA viaAnalysis Fig2.png

Figure 2. Resulting Flux Balance Data Table for iMK1321 model. The objective function of the model is marked red.


FBC analysis usage

To start work with the Flux Balance Constraint analysis one needs a Type-diagram-icon.png diagram and a special table with data about its fluxes (names, bounds, objective function coefficients, etc.). To open the analysis settings in the Work Space double-click of the left mouse button the analysis icon (marked red).

FBA viaAnalysis Fig3.png

Figure 3. Flux Balance Constraint<b> analysis in the BioUML.</span>


Analysis enables to select path to the Type-diagram-icon.png diagram, to the data table and to the table with output results. Also it has an expert mode where user can select type of the objective function, solver type (GLPK, Apache simplex solver and Gurobi solver are available) and some solver's properties.

FBA viaAnalysis Fig4.png

Figure 4. Solver type selection in the FBC analysis.


One click of the left mouse button on the <b>Run</b> will launch the analysis. The outcome of the FBA will be automatically opened in the <b>Work Space
as an output table of the analysis.

FBA viaAnalysis Fig5.png

Figure 5. Resulting "FBC table" tab usage for iMK1321 model. The objective function's value of the model is marked red. </font size="3">

Personal tools
Namespaces

Variants
Actions
BioUML platform
Community
Modelling
Analysis & Workflows
Collaborative research
Development
Virtual biology
Wiki
Toolbox