Team:Alberta/Project/Modeling

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<P>Constraint Based Flux Analysis is a mathematical way of representing biological system information and allows for easy manipulation of this data.  It is based on a stoichiometric matrix of reactions which correspond to individual enzymatic or transport reactions which have been characterized inside of the organism.  In other words, it computationally represents each reaction using a linear array of numbers (see Figure 1).  
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<P>Constraint Based Flux Analysis is a mathematical way of representing biological system information and allows for easy manipulation of this data.  It is based on a stoichiometric matrix of reactions which correspond to individual enzymatic or transport reactions which have been characterized inside of the organism.  In other words, it computationally represents each reaction using a linear array of numbers (see Figure 1). </P>
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The flux can be defined as the amount of substrate moving to product for each individual reaction.  The model assumes that the system is at steady state therefore, the overall flux is zero since each product becomes a substrate of another reaction.  All substrates entering the system will have the same amount leaving the system.  The products leaving the system can be removed by changing the boundary condition of the compound (that is making it unavailable to the system) or by using it to produce growth of the organism.  A master growth equation determines which products are required for the cell to grow and this represented in units of DW/unit time.  Systems Biology Markup Language (SBML) and the Cobra Toolbox (both produced from System’s Biology Research Group) allows for flux analysis to be performed in the MatLab program.  
The flux can be defined as the amount of substrate moving to product for each individual reaction.  The model assumes that the system is at steady state therefore, the overall flux is zero since each product becomes a substrate of another reaction.  All substrates entering the system will have the same amount leaving the system.  The products leaving the system can be removed by changing the boundary condition of the compound (that is making it unavailable to the system) or by using it to produce growth of the organism.  A master growth equation determines which products are required for the cell to grow and this represented in units of DW/unit time.  Systems Biology Markup Language (SBML) and the Cobra Toolbox (both produced from System’s Biology Research Group) allows for flux analysis to be performed in the MatLab program.  
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Revision as of 05:30, 15 September 2009

University of Alberta - BioBytes










































































































Modeling

Metabolic modeling allows for computational analysis of entire genomes which would be impossible to accomplish any other way. The various sources and methods used to collect data has allowed for an unique gene list which has the best possible chance of producing a minimal genome. This has been produced through a series of multiple gene deletions and media change in silico experiments. The MatLab protocols demonstrated in the modeling section can be used to identify any organism’s essential genes provided a model is available.

Constraint Based Flux Analysis – Cobra Toolbox and SBML

Constraint Based Flux Analysis is a mathematical way of representing biological system information and allows for easy manipulation of this data. It is based on a stoichiometric matrix of reactions which correspond to individual enzymatic or transport reactions which have been characterized inside of the organism. In other words, it computationally represents each reaction using a linear array of numbers (see Figure 1).

The flux can be defined as the amount of substrate moving to product for each individual reaction. The model assumes that the system is at steady state therefore, the overall flux is zero since each product becomes a substrate of another reaction. All substrates entering the system will have the same amount leaving the system. The products leaving the system can be removed by changing the boundary condition of the compound (that is making it unavailable to the system) or by using it to produce growth of the organism. A master growth equation determines which products are required for the cell to grow and this represented in units of DW/unit time. Systems Biology Markup Language (SBML) and the Cobra Toolbox (both produced from System’s Biology Research Group) allows for flux analysis to be performed in the MatLab program.

Constraint Based Flux Analysis – Cobra Toolbox and SBML

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