Team:Newcastle/modelling

From 2010.igem.org

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==Calcium carbonate==
==Calcium carbonate==
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For more details, please see the [[Team:Newcastle/Urease|Calcium carbonate precipitation via urease expression]].
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For more details, please see [[Team:Newcastle/Urease|Calcium carbonate precipitation via urease expression]].
===Flux balance analysis===
===Flux balance analysis===
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*[[Media:Newcastle_urease.mod.txt|SBML-shorthand]]
*[[Media:Newcastle_urease.mod.txt|SBML-shorthand]]
*[[Media:Newcastle_urease.xml.txt|SBML]]
*[[Media:Newcastle_urease.xml.txt|SBML]]
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==Filamentous cells==
==Filamentous cells==
{{Team:Newcastle/footer}}
{{Team:Newcastle/footer}}

Revision as of 23:38, 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].


Diagram ver 0 Diagram ver 1 Model

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]


Downloads:


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

Downloads:

Filamentous cells

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