Team:Newcastle/Modelling

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__NOTOC__
= Computational Modelling =
= Computational Modelling =
[[Image:Team Newcastle iGem 2009 08-07-09 no 7.JPG|300px|center]]
[[Image:Team Newcastle iGem 2009 08-07-09 no 7.JPG|300px|center]]
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== Sub-projects ==
 
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===Stochastic Switch===
 
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Here are the matlab files for our stochastic switch model, and below are some graphs which the model produced.
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The modelling in our 2009 iGEM project, BacMan, can be split into a number of sections - the [[Team:Newcastle/Modelling/Stochastic|Stochastic Switch]], [[Team:Newcastle/Modelling/Degradation|Degradation system]], [[Team:Newcastle/Modelling/MetalIntake|Metal Intake]], [[Team:Newcastle/SporulationTuning#Modelling|Sporulation Tuning]] and [[Team:Newcastle/Modelling/Population|Population Simulation]]. We are particularly proud of our Population Simulation Model as it combines distributed computing, agent based and cellular models.
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*[[Image:Newcastle Metalcontainerruntime.m]]
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*[[Image:Newcastle Metalcontainer initial values.m]]
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*[[Image:Newcastle Metalcontainer.m]]
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For computational modelling, we are using a number of technologies, including [[Team:Newcastle/Java|Java]], [[Team:Newcastle/Matlab|Matlab]], [[Team:Newcastle/Amazon EC2|Amazon EC2]], [[Team:Newcastle/Microbase|Microbase]], [[Team:Newcastle/SBML|SBML]] and [[Team:Newcastle/CellML|CellML]].
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[[Image:NewcastleStochastic Model1.PNG|450px]]
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== Sub-projects ==
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[[Image:NewcastleStochastic Model2.PNG|500px]]
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=== Stochastic Switch ===
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[[Image:NewcastleStochastic Model3.PNG|500px]]
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: '' See [[Team:Newcastle/Modelling/Stochastic|Stochastic Switch Model]]''
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[[Image:NewcastleStochastic Model4.PNG|500px]]
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We have modelled our stochastic switch.
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[[Image:NewcastleStochastic Model5.PNG|500px]]
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=== Population modelling ===
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We also designed an inducible protein degradation system for our switch.
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: '' See [[Team:Newcastle/Modelling/Degradation|Degradation Model]]''
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=== Population Modelling ===
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: '' See [[Team:Newcastle/Modelling/Population|Population Simulation]]''
One of the models which we are producing is one concerning the population numbers of our bacteria. It looks at how our additions to the DNA may affect the growth of the bacterial population.
One of the models which we are producing is one concerning the population numbers of our bacteria. It looks at how our additions to the DNA may affect the growth of the bacterial population.
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This model is currently being implemented in the Java programming language, and connects to other models which we have written in CellML. Due to the design of the program, the team has enlisted the help of some very powerful computers.
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=== Sporulation Tuning ===
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: '' See [[Team:Newcastle/Modelling/KinAExpression|KinA Expression Model]]''
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The KinA Expression model describes how KinA is expressed.
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<br>
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: '' See [[Team:Newcastle/Modelling/SporulationTuning|Sporulation Tuning Model]]''
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Building on the KinA Expression model, the phosphorelay is implented into our model, using the expression of KinA to induce sporulation.
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<br>
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: '' See [[Team:Newcastle/Modelling/SinOperon|Sin Operon Model]]''
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The Sin Operon model is used to repress sporulation, in view of making our model more realistic.
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<br>
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=== Metal Intake ===
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: '' See [[Team:Newcastle/Modelling/MetalIntake|Metal Intake Model]]''
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Another of our models looks at metal intake. Specifically this looks at Cadmium transport throughout our bacteria.
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Latest revision as of 20:58, 21 October 2009

Computational Modelling

Team Newcastle iGem 2009 08-07-09 no 7.JPG


The modelling in our 2009 iGEM project, BacMan, can be split into a number of sections - the Stochastic Switch, Degradation system, Metal Intake, Sporulation Tuning and Population Simulation. We are particularly proud of our Population Simulation Model as it combines distributed computing, agent based and cellular models.

For computational modelling, we are using a number of technologies, including Java, Matlab, Amazon EC2, Microbase, SBML and CellML.

Sub-projects

Stochastic Switch

See Stochastic Switch Model

We have modelled our stochastic switch.

We also designed an inducible protein degradation system for our switch.

See Degradation Model

Population Modelling

See Population Simulation

One of the models which we are producing is one concerning the population numbers of our bacteria. It looks at how our additions to the DNA may affect the growth of the bacterial population.

Sporulation Tuning

See KinA Expression Model

The KinA Expression model describes how KinA is expressed.

See Sporulation Tuning Model

Building on the KinA Expression model, the phosphorelay is implented into our model, using the expression of KinA to induce sporulation.

See Sin Operon Model

The Sin Operon model is used to repress sporulation, in view of making our model more realistic.

Metal Intake

See Metal Intake Model

Another of our models looks at metal intake. Specifically this looks at Cadmium transport throughout our bacteria.



News

Events

Social Net

  • Newcastle iGEM Twitter
  • [http://www.facebook.com/home.php#/group.php?gid=131709337641 Newcastle on Facebook]
  • [http://www.youtube.com/user/newcastle2009igem Newcastle Youtube Channel]
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