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Team:Newcastle/modelling
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==Calcium carbonate== | ==Calcium carbonate== | ||
| - | + | For more details, please see the [[Team:Newcastle/Urease|Calcium carbonate precipitation via urease expression]]. | |
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===Flux balance analysis=== | ===Flux balance analysis=== | ||
| - | + | In order to inform our part design, [[Team:Newcastle/Urease#Flux_balance_analysis|we performed flux balance analysis]] to identify pathways which indirectly lead to urea hydrolysis. | |
===Biochemical network in SBML=== | ===Biochemical network in SBML=== | ||
We wrote a computational model of our [[Team:Newcastle/Urease|calcium carbonate system]] in SBML and simulated it in COPASI. The graph below shows that carbonate increases over time, as desired. | We wrote a computational model of our [[Team:Newcastle/Urease|calcium carbonate system]] in SBML and simulated it in COPASI. The graph below shows that carbonate increases over time, as desired. | ||
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[[Image:ModelrocFsr1.png|400px]] | [[Image:ModelrocFsr1.png|400px]] | ||
Revision as of 20:27, 25 October 2010
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Contents |
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 the Calcium carbonate precipitation via urease expression.
Flux balance analysis
In order to inform our part design, we performed flux balance analysis to identify pathways which indirectly lead to urea hydrolysis.
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.
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