Difference between revisions of "Team:RHIT"
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| + | <div class="container"> | ||
| + | <a href="https://2018.igem.org/Team:RHIT/KineticsModel"> | ||
| + | <img src = "https://static.igem.org/mediawiki/2018/0/0d/T--RHIT--Pebble_Logo.jpg" class="image"> | ||
| + | <div class="overlay"> | ||
| + | <div class="text"> Kinetics Model </div> | ||
| + | </div></div> | ||
| + | </a> | ||
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| + | </div> | ||
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| + | <div class="column full_size"> | ||
| + | <h3>Metabolism Model </h3> | ||
| + | <p>The last modeled portion of the project used the Flux Balance Analysis tool to predict the growth rate of the E. coli cells on the sole carbon source of PET. The original matrix and parameters where downloaded from the CoBRA toolbox iJO1366 model [ ]. The model was then expanded to include this new pathway and genes and then the system was optimized for biomass growth and the objective value was proportional to the growth rate of the bacteria. | ||
| + | FBA uses a stochastic matrix of the all the metabolisms’ chemical reactions and optimizes these various equations to produce a unit of biomass, which is inferred as another metabolite of the system. The general form of the model is:<br/ > | ||
| + | <center> | ||
| + | max { v_g: S v=O} <br /> | ||
| + | s.t. L≤v≤U and v≠0 <br /> | ||
| + | </center> | ||
| + | <p>The variable column V are fluxes, which are bounded by the upper and lower bounds of U and L. The S matrix is a matrix of stoichiometric coefficients for the metabolites in the reactions. A flux is best described as the number of times the reaction must run forwards or backwards for the entire system to meet the homogenous assumption that the rates of the metabolites changing are zero. The dimensions of the matrix is MxN, where M is number of metabolites and N is number of reactions in the metabolism. The maximized flux, vg, is the flux for the biomass growth equation. | ||
| + | </p> | ||
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| + | <div class="column third_size"> | ||
| + | <img src="https://static.igem.org/mediawiki/2018/6/68/T--RHIT--FluxModel.png" > | ||
| + | </div> | ||
| + | |||
| + | <div class="column two_thirds_size"> | ||
| + | <p>For the fake chemical reaction: 2 [A] ↔ [B] + 3 [C] | ||
| + | The reaction is input into the matrix so that metabolite A loses 2 units, while metabolites B and C gain 1 and 3 units respectively. | ||
| + | The dotted column shows the biomass growth reaction with it producing 1 unit of biomass. All the reactions have some bounds on the flux values so that the system will return a real number. <br /><br /><br /><br /> | ||
| + | </p> | ||
| + | </div> | ||
| + | |||
Revision as of 15:02, 25 June 2018
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Metabolism Model
The last modeled portion of the project used the Flux Balance Analysis tool to predict the growth rate of the E. coli cells on the sole carbon source of PET. The original matrix and parameters where downloaded from the CoBRA toolbox iJO1366 model [ ]. The model was then expanded to include this new pathway and genes and then the system was optimized for biomass growth and the objective value was proportional to the growth rate of the bacteria.
FBA uses a stochastic matrix of the all the metabolisms’ chemical reactions and optimizes these various equations to produce a unit of biomass, which is inferred as another metabolite of the system. The general form of the model is:
s.t. L≤v≤U and v≠0
The variable column V are fluxes, which are bounded by the upper and lower bounds of U and L. The S matrix is a matrix of stoichiometric coefficients for the metabolites in the reactions. A flux is best described as the number of times the reaction must run forwards or backwards for the entire system to meet the homogenous assumption that the rates of the metabolites changing are zero. The dimensions of the matrix is MxN, where M is number of metabolites and N is number of reactions in the metabolism. The maximized flux, vg, is the flux for the biomass growth equation.
For the fake chemical reaction: 2 [A] ↔ [B] + 3 [C]
The reaction is input into the matrix so that metabolite A loses 2 units, while metabolites B and C gain 1 and 3 units respectively.
The dotted column shows the biomass growth reaction with it producing 1 unit of biomass. All the reactions have some bounds on the flux values so that the system will return a real number.
Project Abstract
We can put a general project description on this first page
Obviously we can replace these with better pictures, I just thought the picture links were kinda cool too
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Uploading pictures and files
You must upload any pictures and files to the iGEM 2018 server. Remember to keep all your pictures and files within your team's namespace or at least include your team's name in the file name.
When you upload, set the "Destination Filename" to
T--YourOfficialTeamName--NameOfFile.jpg
. (If you don't do this, someone else might upload a different file with the same "Destination Filename", and your file would be erased!)Wiki template information
We have created these wiki template pages to help you get started and to help you think about how your team will be evaluated. You can find a list of all the pages tied to awards here at the Pages for awards link. You must edit these pages to be evaluated for medals and awards, but ultimately the design, layout, style and all other elements of your team wiki is up to you!
Editing your wiki
On this page you can document your project, introduce your team members, document your progress and share your iGEM experience with the rest of the world!
Use WikiTools - Edit in the black menu bar to edit this page
Tips
This wiki will be your team’s first interaction with the rest of the world, so here are a few tips to help you get started:
- State your accomplishments! Tell people what you have achieved from the start.
- Be clear about what you are doing and how you plan to do this.
- You have a global audience! Consider the different backgrounds that your users come from.
- Make sure information is easy to find; nothing should be more than 3 clicks away.
- Avoid using very small fonts and low contrast colors; information should be easy to read.
- Start documenting your project as early as possible; don’t leave anything to the last minute before the Wiki Freeze. For a complete list of deadlines visit the iGEM 2018 calendar
- Have lots of fun!
Inspiration
You can also view other team wikis for inspiration! Here are some examples:
Before you start
Please read the following pages