Team:Newcastle/modelling

From 2010.igem.org

(Difference between revisions)
(Modelling)
(Calcium carbonate)
Line 13: Line 13:
==Calcium carbonate==
==Calcium carbonate==
-
We
+
For more details, please see the [[Team:Newcastle/Urease|Calcium carbonate precipitation via urease expression]].
 +
 
===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.  
-
 
-
 
[[Image:ModelrocFsr1.png|400px]]
[[Image:ModelrocFsr1.png|400px]]

Revision as of 20:27, 25 October 2010

iGEM Homepage Newcastle University BacillaFilla Homepage Image Map

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 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.

ModelrocFsr1.png

Downloads:

Newcastle University logo.png    Newcastle cbcb logo.pngNewcastle Biomedicine logo.gif    Team Newcastle CEG logo.gif
Newcastle iww logo.jpg  UNIPV Pavia Logo.gif  Newcastle BBSRC.gif    Newcastle Genevision logo.png Newcastle WelcomeTrust.jpg
FaceBook Icon