Team:USTC Software/demo

From 2010.igem.org

(Difference between revisions)
(→the XML)
 
(87 intermediate revisions not shown)
Line 1: Line 1:
{{Team:USTC_Software/Header}}
{{Team:USTC_Software/Header}}
-
 
+
{| cellpadding="15" cellspacing="0"
-
Using C-N Model we can model systems with great complexity
+
|-
-
==The simplest example with only E.coli cell==
+
!|<font size="5">[[Team:USTC_Software/Transfer%20function%20of%20Part:BBa_F2620|pLux-LuxR repression system]]</font>
-
 
+
!|<font size="5">[[Team:USTC_Software/Toggle-Switch|Toggle-Switch]]</font>
-
===introduction===
+
|-
-
As the simplest example, a model of a flask with only E.coli cells inside will be shown. Only one reaction will be considered: the replication of E.coli. However, it is not trivial. '''MoDeL''' enables users to add such an auto-catalytic replication reaction easily and conveniently. The minimal database used for this model could be download here.
+
|valign="top"|[[Image:USTCs luxr gfp assembly.PNG|400px|thumb|center]]
-
 
+
|valign="top"|[[Image:USTCs Toggle assembly.PNG|400px|thumb|center]]
-
===database construction===
+
|-
-
We only provide key points regarded with construction of this minimal database. To add the auto-catalytic reaction in the Reaction container, a species with only part E.coli is required. It has the simplest '''Chain-Node''' model format: only one chain with one part and no trees. The auto-catalytic reaction has one modifier and one product and they are both referred to E.coli defined in Species container. Since they are compartment-type species (species representing a compartment), attribute '''itself''' of '''compartmentLabel''' node in modifiers and products definitions should be set the same with label of the compartment they represent in the compartments definition. It ensures that the product and the modifier are the same, avoiding wrong mismatch of the product which is different with the modifier. Since number of E.coli cells will reach a stable level in a long time course, we use <math>k_{g}(1-C_{E.coli}/C_{max})C_{E.coli}V_{Flask}</math> as the reaction rate, where <math>k_{g}</math> is the growth rate of E.coli, <math>V_{Flask}</math>  represents the size of E.coli, and <math>C_{E.coli}</math> and <math>
+
!|<font size="5">[[Team:USTC_Software/Repressilator|Repressilator]]</font>
-
C_{max}</math> are concentration of E.coli and its max concentration in the flask, respectively. The negative sign in the rate equation indicates self-repression of E.coli cells.
+
|-
-
 
+
|valign="top"|[[Image:USTCs Oscillator assembling.PNG|400px|thumb|center]]
-
===modelling and simulation===
+
|}
-
[[Image:Ustcs Graph1.png|400px|thumb|right|Figure 1: Replication of E.coli cell]]
+
-
Model written in '''SBML''' format is available here. The dynamic curve of E.coli replication is plotted by time course simulation:
+
-
 
+
-
===the XML===
+
-
 
+
-
<pre>
+
-
<?xml version="1.0" encoding="UTF-8"?>
+
-
<sbml xmlns="http://www.sbml.org/sbml/level2/version4" level="2" version="4">
+
-
  <model id="iGameModel">
+
-
<listOfUnitDefinitions>
+
-
  <unitDefinition id="per_second">
+
-
<listOfUnits>
+
-
  <unit kind="second" exponent="-1"/>
+
-
</listOfUnits>
+
-
  </unitDefinition>
+
-
  <unitDefinition id="mole_per_litre">
+
-
<listOfUnits>
+
-
  <unit kind="mole"/>
+
-
  <unit kind="litre" exponent="-1"/>
+
-
</listOfUnits>
+
-
  </unitDefinition>
+
-
</listOfUnitDefinitions>
+
-
<listOfCompartments>
+
-
  <compartment id="Flask" size="0.4"/>
+
-
  <compartment id="E_coli" size="1e-14" outside="Flask"/>
+
-
</listOfCompartments>
+
-
<listOfSpecies>
+
-
  <species id="sPecIes0" compartment="Flask" initialConcentration="1e-20" substanceUnits="mole"/>
+
-
</listOfSpecies>
+
-
<listOfReactions>
+
-
  <reaction id="rEactIon0" name="reproduction of Ecoli" reversible="false" fast="false">
+
-
<listOfProducts>
+
-
  <speciesReference species="sPecIes0"/>
+
-
</listOfProducts>
+
-
<listOfModifiers>
+
-
  <modifierSpeciesReference species="sPecIes0"/>
+
-
</listOfModifiers>
+
-
<kineticLaw>
+
-
  <math xmlns="http://www.w3.org/1998/Math/MathML">
+
-
<apply>
+
-
  <times/>
+
-
  <ci> kgrowth </ci>
+
-
  <apply>
+
-
<minus/>
+
-
<cn type="integer"> 1 </cn>
+
-
<apply>
+
-
  <divide/>
+
-
  <ci> sPecIes0 </ci>
+
-
  <ci> maxc </ci>
+
-
</apply>
+
-
  </apply>
+
-
  <ci> sPecIes0 </ci>
+
-
  <ci> Flask </ci>
+
-
</apply>
+
-
  </math>
+
-
  <listOfParameters>
+
-
<parameter id="kgrowth" name="growth rate" value="0.0005766" units="per_second"/>
+
-
<parameter id="maxc" name="max concentration" value="1.66e-12" units="mole_per_litre"/>
+
-
  </listOfParameters>
+
-
</kineticLaw>
+
-
  </reaction>
+
-
</listOfReactions>
+
-
  </model>
+
-
</sbml>
+
-
</pre>
+
-
 
+
-
 
+
-
 
+
-
 
+
-
 
+
-
 
+
-
 
+
-
=========================================
+
-
 
+
-
==Basic example with pLac-LacI repression system==
+
-
 
+
-
===introduction===
+
-
'''MoDeL''' provides poweful supports for description of interactions between two species. No interactions exist in the previous example. In this example, we will construct a plasmid backbone with promoter, rbs, coding sequence and terminator inserted and transform it into E.coli. LacI repressor are produced after two steps of transcription and translation. It binds with itself to form a dimer and then a tetramer, which could bind with promoter LacI on the plasmid to repress the process of transcription. Besides, replication of E.coli cells, degradation of proteins and mRNAs, as well as dilution due to replication of cells, are also considered.
+
-
 
+
-
==Demo of oscillator==
+
-
==Demo with reverse parts(Demo of toggle switch)==
+
-
==Demo with environmental conditions==
+
-
==Demo with substituent transfers==
+
-
==Demo with multi-compartment reactions==
+
-
==Demo with complex binding product==
+

Latest revision as of 05:37, 28 November 2010

pLux-LuxR repression system Toggle-Switch
USTCs luxr gfp assembly.PNG
USTCs Toggle assembly.PNG
Repressilator
USTCs Oscillator assembling.PNG
Retrieved from "http://2010.igem.org/Team:USTC_Software/demo"