IGEM:Stanford/2009/Project Homeostasis/Modeling

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Project Goals
III. Modeling Goal: To model and optimize the kinetics of these devices.
 * Inflammation Device: optimize both parts of the device—input and output—for sensitivity and function
 * Immunosuppression Device: optimize both parts of the device—input and output—for sensitivity and function
 * Population dynamics: analyze the conditions to switch between Th17 and Tregs.


 * [[Media:ModelingPlan.jpg| Image of Modeling Plan Created by Mary and Leon]]

Modeling

 * Current code
 * trp.m
 * IDO.m


 * Diff EQs
 * Monte Carlo
 * Dynamic Simulation
 * Process Control


 * Previous work
 * Check out this simple bistablity model

Anti-Inflammation Device

 * Our Models for the Anti-Inflammation Device

Anti-Immunosuppression Device

 * Our Models for the Anti-Immunosuppression Device

Results and Findings

 * The Results from our Models

Important Notes

 * People help us update the database! Thanks!
 * Hey team, if there are any questions post them here. -Chris
 * Hey Modeling, it would be good to define what you are trying to model and why you are trying to model it. Inputs and outputs would be nice too.

Computational Support

 * Test and Teach new programs
 * APE
 * GeneDesigner
 * Vector NTI
 * Clothos
 * Serial Cloner
 * Geneious


 * Modeling software
 * SimBiology
 * MATLAB
 * Dizzy
 * SynBioSS
 * System biology Workbench


 * Fun Stuff
 * FoldIt
 * Pymol

Stuff to Calculate

 * B-carotene
 * SS-levels
 * Retinal
 * SS levels
 * RA
 * SS levels

Comments

 * Please suggest what information will be useful to calculate.

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:
 * http://spreadsheets.google.com/ccc?key=t85tDECACdEU3IFccCAZWMg
 * Week Four: Creating Simple Models
 * Discussed role of the modeling team.
 * Week four was spent creating some simple models. Our first task

Helpful Links

 * http://www.brenda-enzymes.org
 * 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/

Papers

 * Book of Systems Biology
 * Paper on Bacteria migration. Kinda need theory a bit complex.


 * 1) Brandman-2005 pmid=16239477
 * 2) Il6-2005 pmid=2788034