Team:TU Delft/Modeling

From 2010.igem.org

(Difference between revisions)

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).

@@ Line 1: / Line 1: @@
-=In Silico=
+{{Team:TU_Delft/frame_check}}
-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.
+__NOTOC__
+==In Silico==
+[[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
-*MFA
+===Continue reading===
-[[Team:TU_Delft/Modeling/MFA|Metabolic Flux Analysis]]
+*[[Team:TU_Delft/Modeling/MFA|Metabolic Flux Analysis]]
+**[[Team:TU_Delft/Modeling/MFA/explanation|MFA explained]]
-*Hydrocarbon regulated expression system
+**[[Team:TU_Delft/Modeling/MFA/additional_pathways|Additional Pathways]]
-[[Team:TU_Delft/Modeling/HC_regulation|Hydrocarbon regulated expression system]]
+**[[Team:TU_Delft/Modeling/MFA/results|Detailed MFA Results]]
+*[[Team:TU_Delft/Modeling/HC_regulation|Hydrocarbon regulated expression system]]
-==Interaction mapping==
+**[[Team:TU_Delft/Modeling/HC_regulation/Sensitivity|Sensitivity analysis of the expression system]]
-A team member of ours, Jelmer, designed a cool software tool which allows ... ... ... (''insert text here'')
+*[[Team:TU_Delft/Modeling/Protein-production-model|Protein production model]]
-More info [[Team:TU_Delft/Modeling/software-tool|here]]
+*[[Team:TU_Delft/Modeling/pcaif-model|pCaiF CRP sensing model]]
+*[[Team:TU_Delft/Modeling/interaction-mapping|Homolog Interation Mapping (HIM)]]
+*[[Team:TU_Delft/Software/part-search|Part search server and iPhone app]]
-==Wiki Tips & Tricks==
+*[[Team:TU_Delft/Modeling/wiki-tips-tricks|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 our [[Team:TU_Delft/Modeling/wiki-tips-tricks|here]]