Team:Newcastle/modelling

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Modelling

In order to understand the behaviour of our parts, we computationally modelled them by encoding biochemical networks in [http://sbml.org SBML] and simulating them using [http://www.copasi.org COPASI].

Calcium carbonate

For more details, please see Calcium carbonate precipitation via urease expression.

Flux balance analysis

In order to inform our calcium carbonate part design, we performed flux balance analysis to identify pathways which indirectly lead to urea hydrolysis.

Newcastle Arginine and Ornithine Degradation.png

Taken from [http://seed-viewer.theseed.org/seedviewer.cgi?page=Subsystems&subsystem=Arginine_and_Ornithine_Degradation&organism=224308.1 SEED]


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Biochemical network in SBML

We wrote a computational model of our calcium carbonate system in SBML and simulated it in COPASI. The graph below shows that carbonate increases over time, as desired.

ModelrocFsr1.png

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Filamentous cells

For more details, please see Filamentous cells.

Biochemical network in SBML

We wrote a computational model of our filamentous cell system in SBML and simulated it in COPASI. The graph below shows that FtsZ ring formation is low when yneA is overexpressed.

Newcastle ModelFilamentous.png

Visualisation of the model's biochemical network in CellDesigner:

Newcastle CellDesigner Filamentous.png

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