Team:TU Delft/Modeling

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Latest revision as of 19:49, 27 October 2010

In Silico

Seeing as our team consists of a number of members who know their way around computers, quite some in silico work has been perfomed. Before adding DNA to a microorganism, we designed the theoretical system to find out whether a system is viable or not. Metabolic flux analyses were calculated to find the co-factor balance. In addition we made a model of the hydrocarbon regulated expression system to simulate this regulation mechanism. Additionally a model was made on the pCaiF promoter which was fitted to the experimental data.

To give some clues about how our BioBricks are working in their new E. coli proteome, we developed an application that maps interactions from native proteomes to E.coli proteome. This is not all we did with a computer. As you might have noticed, we had some fun designing our wiki, want to know how we did it? You can find out here. Last but not least, a part search server and iPhone app was developed, that allows to browse parts based on category (Search by category is not available at the partsregistry itself).

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+{{Team:TU_Delft/frame_check}}
 __NOTOC__
-=In Silico=
+==In Silico==
-Seeing as our team consists of a number of members who know their way around computers, quite some in silico work has been perfomed. More information on these projects can be found here.
+[[Image:TUDelft_2010_SiliconWithFrame.png|right]]
+Seeing as our team consists of a number of members who know their way around computers, quite some in silico work has
+been perfomed. Before adding DNA to a microorganism, we designed the theoretical system to find out whether a system is viable or not. [[Team:TU_Delft/Modeling/MFA|Metabolic flux analyses]] were calculated to find the co-factor balance. In addition we made a model of the [[Team:TU_Delft/Modeling/HC_regulation|hydrocarbon regulated expression system]] to simulate this regulation mechanism. Additionally a model was made on the [[Team:TU_Delft/Modeling/pcaif-model|pCaiF promoter]] which was fitted to the experimental data.
-==Modeling==
+To give some clues about how our BioBricks are working in their new ''E. coli'' proteome, we developed an [[Team:TU_Delft/Modeling/interaction-mapping|application]] that maps interactions from native proteomes to ''E.coli'' proteome.
-''introduction to modeling''
+This is not all we did with a computer. As you might have noticed, we had some fun designing our wiki, want to know how we did it? You can find out [[Team:TU_Delft/Modeling/wiki-tips-tricks|here]]. Last but not least, a [[Team:TU_Delft/Software/part-search|part search server and iPhone app]] was developed, that allows to browse parts based on category (Search by category is not available at the partsregistry itself).
-Some stuff about what we modeled and why
-===Metabolic Flux Analysis===
+===Continue reading===
+*[[Team:TU_Delft/Modeling/MFA|Metabolic Flux Analysis]]
-A metabolic flux analysis is an analysis to calculate the theoretical maximal yields for a proposed system of pathways in a micro-organism. With this analysis it is also possible to find whether a system is not viable because of a co-factor imbalance. Lastly, several product pathways were introduced to ''E. coli'' with hydrocarbon degradation to see what maximal theoretical yields on hydrocarbons are.
+**[[Team:TU_Delft/Modeling/MFA/explanation|MFA explained]]
+**[[Team:TU_Delft/Modeling/MFA/additional_pathways|Additional Pathways]]
-Find out more [[Team:TU_Delft/Modeling/MFA|here]]
+**[[Team:TU_Delft/Modeling/MFA/results|Detailed MFA Results]]
+*[[Team:TU_Delft/Modeling/HC_regulation|Hydrocarbon regulated expression system]]
-===Hydrocarbon regulated expression system===
+**[[Team:TU_Delft/Modeling/HC_regulation/Sensitivity|Sensitivity analysis of the expression system]]
+*[[Team:TU_Delft/Modeling/Protein-production-model|Protein production model]]
-''P. putida'' has a regulation system that controls the expression of its hydrocarbon degradation pathway. This involves the protein crc, a global regulator. This regulator however is not present in ''E. coli'' and so a substitute was used. In our ''E. coli'' a crp dependent promoter was added to the gene. crp is a global regulator for ''E. coli''. crc works on the mRNA and crp works on a promoter in the DNA. This simulation explores the difference between these two regulation mechanisms.
+*[[Team:TU_Delft/Modeling/pcaif-model|pCaiF CRP sensing model]]
+*[[Team:TU_Delft/Modeling/interaction-mapping|Homolog Interation Mapping (HIM)]]
-Find out more [[Team:TU_Delft/Modeling/HC_regulation|here]]
+*[[Team:TU_Delft/Software/part-search|Part search server and iPhone app]]
+*[[Team:TU_Delft/Modeling/wiki-tips-tricks|Wiki Tips & Tricks]]
-==Interaction mapping==
-To give some clues about how our biobricks are working in their new E. coli proteome, an application has been developed that maps interactions from the native proteomes to the E. coli proteome.
-More info [[Team:TU_Delft/Modeling/interaction-mapping|here]]
-==Wiki Tips & Tricks==
-As you might have noticed, we had some fun designing our wiki, want to know how we did it? You can find out [[Team:TU_Delft/Modeling/wiki-tips-tricks|here]]