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Team:TU Delft/Modeling
From 2010.igem.org
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| + | {{Team:TU_Delft/frame_check}} | ||
__NOTOC__ | __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. | 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. | ||
| - | ==Modeling== | + | ===Modeling=== |
''introduction to modeling'' | ''introduction to modeling'' | ||
Some stuff about what we modeled and why | Some stuff about what we modeled and why | ||
| - | ===Metabolic Flux Analysis=== | + | ====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. | 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. | ||
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Find out more [[Team:TU_Delft/Modeling/MFA|here]] | Find out more [[Team:TU_Delft/Modeling/MFA|here]] | ||
| - | ===Hydrocarbon regulated expression system=== | + | ====Hydrocarbon regulated expression system==== |
''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. | ''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. | ||
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Find out more [[Team:TU_Delft/Modeling/HC_regulation|here]] | Find out more [[Team:TU_Delft/Modeling/HC_regulation|here]] | ||
| - | ==Interaction mapping== | + | ===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. | 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]] | More info [[Team:TU_Delft/Modeling/interaction-mapping|here]] | ||
| - | ==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 out [[Team:TU_Delft/Modeling/wiki-tips-tricks|here]] | 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]] | ||
Revision as of 12:27, 28 September 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. More information on these projects can be found here.
Modeling
introduction to modeling Some stuff about what we modeled and why
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.
Find out more here
Hydrocarbon regulated expression system
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.
Find out more here
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 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 here
