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Team:Newcastle/Modelling
From 2009.igem.org
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[[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]] | ||
| - | For computational modelling, we are using a number of technologies, including [[Team:Newcastle/Java|Java]], [[Team:Newcastle/Matlab|Matlab]], SBML and [[Team:Newcastle/CellML|CellML]]. | + | |
| + | 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. | ||
| + | |||
| + | 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]]. | ||
== Sub-projects == | == Sub-projects == | ||
| - | ===Stochastic Switch=== | + | === Stochastic Switch === |
| - | :'' See [[Team:Newcastle/Modelling/Stochastic]]'' | + | : '' See [[Team:Newcastle/Modelling/Stochastic|Stochastic Switch Model]]'' |
| - | We | + | We have modelled our stochastic switch. |
| - | We also designed an | + | We also designed an inducible protein degradation system for our switch. |
| - | :'' See [[Team:Newcastle/Modelling/Degradation]]'' | + | : '' See [[Team:Newcastle/Modelling/Degradation|Degradation Model]]'' |
| - | === Population | + | === Population Modelling === |
| - | :'' See [[Team:Newcastle/Modelling/Population]]'' | + | : '' 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. | ||
| - | === Sporulation | + | === Sporulation Tuning === |
| - | < | + | : '' See [[Team:Newcastle/Modelling/KinAExpression|KinA Expression Model]]'' |
| - | :'' See [[Team:Newcastle/ | + | The KinA Expression model describes how KinA is expressed. |
| - | + | <br> | |
| - | + | : '' See [[Team:Newcastle/Modelling/SporulationTuning|Sporulation Tuning Model]]'' | |
| + | Building on the KinA Expression model, the phosphorelay is implented into our model, using the expression of KinA to induce sporulation. | ||
| + | <br> | ||
| + | : '' See [[Team:Newcastle/Modelling/SinOperon|Sin Operon Model]]'' | ||
| + | The Sin Operon model is used to repress sporulation, in view of making our model more realistic. | ||
| + | <br> | ||
| - | === Metal | + | === Metal Intake === |
| - | :'' See [[Team:Newcastle/Modelling/MetalIntake]]'' | + | : '' See [[Team:Newcastle/Modelling/MetalIntake|Metal Intake Model]]'' |
| - | Another of our models looks at metal intake. | + | Another of our models looks at metal intake. Specifically this looks at Cadmium transport throughout our bacteria. |
{{:Team:Newcastle/Footer}} | {{:Team:Newcastle/Footer}} | ||
{{:Team:Newcastle/Right}} | {{:Team:Newcastle/Right}} | ||
Latest revision as of 20:58, 21 October 2009
Project
Sub-projects
Wet Lab
Meetings
Planning
Links
Computational Modelling
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
We have modelled our stochastic switch.
We also designed an inducible protein degradation system for our switch.
Population Modelling
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
The KinA Expression model describes how KinA is expressed.
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
Another of our models looks at metal intake. Specifically this looks at Cadmium transport throughout our bacteria.
News
Events
- 20 – 21 June 2009 - Europe workshop (London)
- 23 – 24 June 2009 - UK iGEM meetup (Edinburgh)
- 23 October Practice Presentation (Newcastle)
- 23 October T-shirts are ready
- 27 October Practice Presentation (Sunderland)
- 27 October Poster is ready
- 30 October – 2 November 2009 - Jamboree (Boston)
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]
