Team:UTDallas/Modelling

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=An Elementary Model=
 
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We used Matlab and SimBiology for modeling. Lets begin with an easy model where Gene A is promoting Gene B. [[Image:a_b_promoter.png|center]]
 
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Its easier to model using the SimBiology desktop than the command interface. In Matlab command interface type "simbiology" to open the SimBiology desktop. Open a new project from file menu. Click next to go to the next step in the new window. In step 2 you can name the model. In step 3, select simulation model.
 
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Now from the Project Explorer which is in the left panel, expand SimBiology Model. Go to Diagram View. Here we can draw the network. From the block library browser drag a species, rename it as Gene_A. Drag another one and name it as Gene_B.
 
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[[Image:A_b_diag.png|650px|center]]
 
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Drag more and name them as mRNA_A, prA, prA_geneB_complex, mRNA_B, prB. We need them because From Gene A mRNA will be produced, from that protein A which will interact with Gene B and make a complex. After that the complex will produce mRNA which will subsequently produce protein B. mRNA and protein degrades with time so there will be degradation rection for them in the model. Lets drag some reaction block from the block browser and name them as degr_mRNA_A, degr_pr_A, degr_mRNA_B, degr_pr_B. Now from the reaction block towards the mRNAs and proteins we connect them. Configure them for mass-kinatic reaction. We also add other reaction blocks to complete the modeling. Then simulate it.
 
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=====Parameters=====
 
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[[Image:A_b_param.png|650px|center]]
 
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=====Reactions=====
 
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[[Image:A_b_react.png|650px|center]]
 
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=====Simulation=====
 
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[[Image:A_b_sim.png|650px|center]]
 
=References=
=References=

Latest revision as of 15:55, 5 August 2010



References

  • Baronas, Romas, Ivanauskas, Feliksas, Kulys, Juozas, Mathematical Modeling of Biosensors An Introduction for Chemists and Mathematicians, Springer Series on Chemical Sensors and Biosensors, Vol. 9, 2010, Springer.
  • J. D. Murray, Mathematical Biology I: An Introduction, 2002, Springer.
  • [http://www.mathworks.es/matlabcentral/fileexchange/20420| SimBiology Tutorial Webiner]

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