IGEM:Stanford/2009/Notebook/Marys iGEM Notebook

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0 MODELING SUMMARY!

 * [[Media:Final_Modeling_Report.key‎| LEON'S SUPER DUPER KEYNOTE]]

Project Goals

 * To model and optimize the kinetics of these devices.
 * Population dynamics: analyze the conditions to switch between Th17 and Tregs.
 * [[Media:ModelingPlan.jpg| Image of Modeling Plan Created by Mary and Leon]]

Device I: Anti-Inflammatory Device
Summary


 * The IPP-->B-carotene-->RA model(2009/08/05)
 * Paremeters for the IPP-->B-carotene model(2009/08/04)


 * The NO-->SoxS-SoxR model
 * Parameters to be found!: Approximate rate of NO activating SoxR. Probably Suzie is looking for that right now. Thanks Suzie^^

Device II: Anti Immunosuppression Device
A Model ignoring cooperativity in the wild type trp system A Model considering cooperativity in the wild type trp system Important things to find out for the new trp model The Trp Operon Regulatory Mechanisim Model

Logo Design
Sketch I & II

3 Our Progress and Future Plans

 * Week One and Two: Gaining Background Information
 * During the first two weeks, Leon primarily read books on biological systems and enzyme kinetics. More specifically, he read portions of a Physical Chemistry textbook by Raymond Chang and Chapters in An Introduction to Systems Biology by Uri Alon and Process Dynamics and Control by Dale Seborg, Thomas Edgar, and Duncan Mellichamp. Mary, who arrived in the middle of the second week, spent the majority of her time learning about the project by reading papers that had been read by the other team members.
 * Week Three: Data Gathering
 * The beginning of the week was spent creating a block diagram of all the reactions that take place within our system. The block model illustrates all of the important reactions we hope to model over the course of the summer. Note that the block model does not come close to completely describing our system (such a model can be found somewhere else in our wiki (insert place). Instead, this is a minimalist model and contains only the most crucial components of our system. Much time was spent discussing with the team regarding which components should be included in the model and many drafts of the model were analyzed before deciding on the model presented here:
 * upload picture of model
 * After devising a model, Mary and Leon then worked with Chris to come up with a table of important values which we would need to create mathematical models of our system. We then spent the remainder of the week filling out this table. The table is presented as a Google Doc and can be found at:
 * Crucial data spreadsheet
 * Week Four: Creating Simple Models
 * Discussed role of the modeling team.
 * Week four was spent creating some simple models. Our first task

4 Helpful Links

 * Fun Programs
 * http://www.brenda-enzymes.org
 * E.coli Statistics
 * http://sabio.villa-bosch.de
 * http://en.wikipedia.org/wiki/Category:Bioinformatics_databases
 * http://www.bindingdb.org/bind/index.jsp
 * Bionumbers
 * BioModels
 * SBML
 * http://www.ncbi.nlm.nih.gov/pubmed/19001483
 * http://www.yeastgenome.org/help/proteinProperties.html
 * http://ecocyc.org/
 * http://www.wikipathways.org/index.php/WikiPathways
 * http://www.reactome.org/cgi-bin/frontpage?DB=gk_current
 * http://www.genome.jp/kegg/

Comments

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