kenwebb/README.md

## README.md

      
    Raw
  

              README.md
            
          
    Feinberg - Chemical Reaction Networks 1.1

This gist includes the source code for multiple versions of the same simple mode.
source: Martin Feinberg (1980) Lectures on Chemical Reaction Networks - Lecture 1
http://www.che.eng.ohio-state.edu/~FEINBERG/LecturesOnReactionNetworks/
I've added an additional gist for content related to Systems Biology Markup Language (SBML) at https://gist.github.com/3666649

  
## ReactionNetworkSystem_0_1347056978368_pnml.xml
<?xml version="1.0" encoding="ISO-8859-1"?>
<!-- To view this file, download open-source Vanted from http://vanted.ipk-gatersleben.de/ -->
<!--
Automatically generated by Xholon version 0.8.1, using Xholon2PnmlVanted.java
Fri Sep 07 18:29:38 EDT 2012 1347056978368
model: Petri net - feinberg1
www.primordion.com/Xholon
-->
<pnml xmlns="http://www.informatik.hu-berlin.de/top/pnml/ptNetb">
<net id="Net-One" type="P/T net">
<place id="A">
 <graphics>
  <position x="200" y="10"/>
  <dimension x="25" y="25"/>
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 <name>
  <text>A</text>
  <graphics>
   <offset x="0" y="0"/>
  </graphics>
 </name>
 <initialMarking>
  <text>140</text>
 </initialMarking>
</place>

<place id="B">
 <graphics>
  <position x="200" y="60"/>
  <dimension x="25" y="25"/>
 </graphics>
 <name>
  <text>B</text>
  <graphics>
   <offset x="0" y="0"/>
  </graphics>
 </name>
 <initialMarking>
  <text>180</text>
 </initialMarking>
</place>

<place id="C">
 <graphics>
  <position x="200" y="110"/>
  <dimension x="25" y="25"/>
 </graphics>
 <name>
  <text>C</text>
  <graphics>
   <offset x="0" y="0"/>
  </graphics>
 </name>
 <initialMarking>
  <text>200</text>
 </initialMarking>
</place>

<place id="D">
 <graphics>
  <position x="200" y="160"/>
  <dimension x="25" y="25"/>
 </graphics>
 <name>
  <text>D</text>
  <graphics>
   <offset x="0" y="0"/>
  </graphics>
 </name>
 <initialMarking>
  <text>25</text>
 </initialMarking>
</place>

<place id="E">
 <graphics>
  <position x="200" y="210"/>
  <dimension x="25" y="25"/>
 </graphics>
 <name>
  <text>E</text>
  <graphics>
   <offset x="0" y="0"/>
  </graphics>
 </name>
 <initialMarking>
  <text>80</text>
 </initialMarking>
</place>

<transition id="A_BB">
 <graphics>
  <position x="700" y="260"/>
  <dimension x="25" y="25"/>
 </graphics>
 <name>
  <text>A_BB</text>
  <graphics>
   <offset x="0" y="0"/>
  </graphics>
 </name>
</transition>

<arc id="A_to_A_BB" source="A" target="A_BB">
 <inscription>
  <text>1</text>
 </inscription>
</arc>

<arc id="A_BB_to_B" source="A_BB" target="B">
 <inscription>
  <text>2</text>
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</arc>

<transition id="BB_A">
 <graphics>
  <position x="700" y="310"/>
  <dimension x="25" y="25"/>
 </graphics>
 <name>
  <text>BB_A</text>
  <graphics>
   <offset x="0" y="0"/>
  </graphics>
 </name>
</transition>

<arc id="B_to_BB_A" source="B" target="BB_A">
 <inscription>
  <text>2</text>
 </inscription>
</arc>

<arc id="BB_A_to_A" source="BB_A" target="A">
 <inscription>
  <text>1</text>
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</arc>

<transition id="AC_D">
 <graphics>
  <position x="700" y="360"/>
  <dimension x="25" y="25"/>
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 <name>
  <text>AC_D</text>
  <graphics>
   <offset x="0" y="0"/>
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 </name>
</transition>

<arc id="A_to_AC_D" source="A" target="AC_D">
 <inscription>
  <text>1</text>
 </inscription>
</arc>

<arc id="C_to_AC_D" source="C" target="AC_D">
 <inscription>
  <text>1</text>
 </inscription>
</arc>

<arc id="AC_D_to_D" source="AC_D" target="D">
 <inscription>
  <text>1</text>
 </inscription>
</arc>

<transition id="D_AC">
 <graphics>
  <position x="700" y="410"/>
  <dimension x="25" y="25"/>
 </graphics>
 <name>
  <text>D_AC</text>
  <graphics>
   <offset x="0" y="0"/>
  </graphics>
 </name>
</transition>

<arc id="D_to_D_AC" source="D" target="D_AC">
 <inscription>
  <text>1</text>
 </inscription>
</arc>

<arc id="D_AC_to_A" source="D_AC" target="A">
 <inscription>
  <text>1</text>
 </inscription>
</arc>

<arc id="D_AC_to_C" source="D_AC" target="C">
 <inscription>
  <text>1</text>
 </inscription>
</arc>

<transition id="D_BE">
 <graphics>
  <position x="700" y="460"/>
  <dimension x="25" y="25"/>
 </graphics>
 <name>
  <text>D_BE</text>
  <graphics>
   <offset x="0" y="0"/>
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 </name>
</transition>

<arc id="D_to_D_BE" source="D" target="D_BE">
 <inscription>
  <text>1</text>
 </inscription>
</arc>

<arc id="D_BE_to_B" source="D_BE" target="B">
 <inscription>
  <text>1</text>
 </inscription>
</arc>

<arc id="D_BE_to_E" source="D_BE" target="E">
 <inscription>
  <text>1</text>
 </inscription>
</arc>

<transition id="BE_AC">
 <graphics>
  <position x="700" y="510"/>
  <dimension x="25" y="25"/>
 </graphics>
 <name>
  <text>BE_AC</text>
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   <offset x="0" y="0"/>
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 </name>
</transition>

<arc id="B_to_BE_AC" source="B" target="BE_AC">
 <inscription>
  <text>1</text>
 </inscription>
</arc>

<arc id="E_to_BE_AC" source="E" target="BE_AC">
 <inscription>
  <text>1</text>
 </inscription>
</arc>

<arc id="BE_AC_to_A" source="BE_AC" target="A">
 <inscription>
  <text>1</text>
 </inscription>
</arc>

<arc id="BE_AC_to_C" source="BE_AC" target="C">
 <inscription>
  <text>1</text>
 </inscription>
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</net>
</pnml>

## ReactionNetworkSystem_0_1347382463616vensim.mdl
{UTF-8}
A = INTEG( -A BB 13r +BB A 18r -AC D 23r +D AC 29r +BE AC 41r,140)
	~	things
	~		|

B = INTEG( +2*A BB 13r -2*BB A 18r +D BE 35r -BE AC 41r,180)
	~	things
	~		|

C = INTEG( -AC D 23r +D AC 29r +BE AC 41r,200)
	~	things
	~		|

D = INTEG( +AC D 23r -D AC 29r -D BE 35r,25)
	~	things
	~		|

E = INTEG( +D BE 35r -BE AC 41r,80)
	~	things
	~		|

A BB 13r K = 0.0039
	~	things/s
	~		|

A BB 13r = A BB 13r K * A
	~	things/s
	~		|

BB A 18r K = 0.0038
	~	things/s
	~		|

BB A 18r = BB A 18r K * B^2
	~	things/s
	~		|

AC D 23r K = 0.0037
	~	things/s
	~		|

AC D 23r = AC D 23r K * A * C
	~	things/s
	~		|

D AC 29r K = 0.0036
	~	things/s
	~		|

D AC 29r = D AC 29r K * D
	~	things/s
	~		|

D BE 35r K = 0.0035
	~	things/s
	~		|

D BE 35r = D BE 35r K * D
	~	things/s
	~		|

BE AC 41r K = 0.0034
	~	things/s
	~		|

BE AC 41r = BE AC 41r K * B * E
	~	things/s
	~		|

********************************************************
	.Control
********************************************************~
		Simulation Control Paramaters
	|

FINAL TIME  = 100
	~	s
	~	The final time for the simulation.
	|

INITIAL TIME  = 0
	~	s
	~	The initial time for the simulation.
	|

SAVEPER  = 0.5
	~	s
	~	The frequency with which output is stored.
	|

TIME STEP  = 0.5
	~	s
	~	The time step for the simulation.
	|

\\\---/// Sketch information - do not modify anything except names
V300  Do not put anything below this section - it will be ignored
*View 1
$0-0-0,0,Arial|12||0-0-0|0-0-0|0-0-0|-1--1--1|-1--1--1|144,144,5,0
10,1,A,70,56,35,19,3,131,0,0,0,0,0,0
10,2,B,561,63,33,20,3,131,0,0,0,0,0,0
10,3,C,627,592,37,18,3,131,0,0,0,0,0,0
10,4,D,924,137,33,19,3,131,0,0,0,0,0,0
10,5,E,1134,222,33,18,3,131,0,0,0,0,0,0
11,6,316,309,68,8,9,34,3,0,0,1,0,0,0
10,7,A BB 13r,309,89,62,12,40,3,0,0,0,0,0,0
11,8,156,389,120,8,9,34,3,0,0,1,0,0,0
10,9,BB A 18r,389,141,62,12,40,3,0,0,0,0,0,0
11,10,172,260,470,8,9,34,3,0,0,1,0,0,0
10,11,AC D 23r,260,491,62,12,40,3,0,0,0,0,0,0
11,12,188,790,380,8,9,34,3,0,0,1,0,0,0
10,13,D AC 29r,790,401,62,12,40,3,0,0,0,0,0,0
11,14,204,1039,36,8,9,34,3,0,0,1,0,0,0
10,15,D BE 35r,1039,57,62,12,40,3,0,0,0,0,0,0
11,16,268,1131,480,8,9,34,3,0,0,1,0,0,0
10,17,BE AC 41r,1131,501,62,12,40,3,0,0,0,0,0,0
1,18,7,1,1,0,0,0,0,64,0,-1--1--1,,1|(184,42)|
1,19,11,1,1,0,0,0,0,64,0,-1--1--1,,1|(195,272)|
1,20,9,1,0,0,0,0,0,64,0,-1--1--1,,1|(231,98)|
1,21,17,1,0,0,0,0,0,64,0,-1--1--1,,1|(610,282)|
1,22,13,1,1,0,0,0,0,64,0,-1--1--1,,1|(406,259)|
1,23,7,2,1,0,0,0,0,64,0,-1--1--1,,1|(438,60)|
1,24,9,2,1,0,0,0,0,64,0,-1--1--1,,1|(455,100)|
1,25,17,2,1,0,0,0,0,64,0,-1--1--1,,1|(874,259)|
1,26,15,2,0,0,0,0,0,64,0,-1--1--1,,1|(792,59)|
1,27,11,3,1,0,0,0,0,64,0,-1--1--1,,1|(418,581)|
1,28,17,3,0,0,0,0,0,64,0,-1--1--1,,1|(873,547)|
1,29,13,3,0,0,0,0,0,64,0,-1--1--1,,1|(715,488)|
1,30,11,4,0,0,0,0,0,64,0,-1--1--1,,1|(580,319)|
1,31,13,4,1,0,0,0,0,64,0,-1--1--1,,1|(885,293)|
1,32,15,4,1,0,0,0,0,64,0,-1--1--1,,1|(994,107)|
1,33,17,5,1,0,0,0,0,64,0,-1--1--1,,1|(1103,366)|
1,34,15,5,0,0,0,0,0,64,0,-1--1--1,,1|(1080,130)|
1,35,1,7,1,0,0,0,0,64,0,-1--1--1,,1|(170,57)|
10,36,A BB 13r K,296,-21,77,13,8,2,0,3,-1,0,0,0,128-128-128,0-0-0,|12||128-128-128
1,37,36,7,0,0,0,0,0,64,0,-1--1--1,,1|(301,27)|
1,38,2,9,1,0,0,0,0,64,0,-1--1--1,,1|(488,114)|
10,39,BB A 18r K,574,184,77,13,8,2,0,3,-1,0,0,0,128-128-128,0-0-0,|12||128-128-128
1,40,39,9,0,0,0,0,0,64,0,-1--1--1,,1|(486,163)|
1,41,1,11,1,0,0,0,0,64,0,-1--1--1,,1|(127,281)|
10,42,AC D 23r K,79,566,59,27,8,2,0,3,-1,0,0,0,128-128-128,0-0-0,|12||128-128-128
1,43,42,11,0,0,0,0,0,64,0,-1--1--1,,1|(178,525)|
1,44,3,11,1,0,0,0,0,64,0,-1--1--1,,1|(464,493)|
1,45,4,13,1,0,0,0,0,64,0,-1--1--1,,1|(833,256)|
10,46,D AC 29r K,625,430,59,27,8,2,0,3,-1,0,0,0,128-128-128,0-0-0,|12||128-128-128
1,47,46,13,0,0,0,0,0,64,0,-1--1--1,,1|(699,416)|
1,48,4,15,1,0,0,0,0,64,0,-1--1--1,,1|(970,90)|
10,49,D BE 35r K,1024,185,59,27,8,2,0,3,-1,0,0,0,128-128-128,0-0-0,|12||128-128-128
1,50,49,15,0,0,0,0,0,64,0,-1--1--1,,1|(1031,120)|
1,51,2,17,1,0,0,0,0,64,0,-1--1--1,,1|(828,301)|
10,52,BE AC 41r K,1054,601,67,27,8,2,0,3,-1,0,0,0,128-128-128,0-0-0,|12||128-128-128
1,53,52,17,0,0,0,0,0,64,0,-1--1--1,,1|(1093,549)|
1,54,5,17,1,0,0,0,0,64,0,-1--1--1,,1|(1159,358)|
///---\\\
:GRAPH Kenz_Graph_1
:TITLE
:SCALE
:VAR A|A
:LINE-WIDTH 3
:SCALE
:VAR B|B
:LINE-WIDTH 3
:SCALE
:VAR C|C
:LINE-WIDTH 3
:SCALE
:VAR D|D
:LINE-WIDTH 3
:SCALE
:VAR E|E
:LINE-WIDTH 3
:L<%^E!@
1:Current.vdf
9:Current
23:0
15:0,0,0,0,0,0
19:5,0
27:2,
34:0,
4:Time
5:FINAL TIME
35:Date
36:YYYY-MM-DD
37:2000
38:1
39:1
40:2
41:0
24:0
25:100
26:100

## ReactionNetworkSystem_42_1345649106542_pnml.xml
<?xml version="1.0" encoding="ISO-8859-1"?>
<!-- To view this file, download open-source PIPE from http://pipe2.sourceforge.net/ -->
<!--
Automatically generated by Xholon version 0.8.1, using Xholon2Pnml.java
Wed Aug 22 11:25:06 EDT 2012 1345649106542
model: Feinberg - Chemical Reaction Networks
www.primordion.com/Xholon
-->
<pnml>
<net id="Net-One" type="P/T net">
<token id="Default" enabled="true" red="0" green="0" blue="0"/>

<place id="A">
 <graphics>
  <position x="200.0" y="10.0"/>
 </graphics>
 <name>
  <value>A</value>
  <graphics>
   <offset x="0.0" y="0.0"/>
  </graphics>
 </name>
 <initialMarking>
  <value>Default,140</value>
 </initialMarking>
</place>

<place id="B">
 <graphics>
  <position x="200.0" y="60.0"/>
 </graphics>
 <name>
  <value>B</value>
  <graphics>
   <offset x="0.0" y="0.0"/>
  </graphics>
 </name>
 <initialMarking>
  <value>Default,180</value>
 </initialMarking>
</place>

<place id="C">
 <graphics>
  <position x="200.0" y="110.0"/>
 </graphics>
 <name>
  <value>C</value>
  <graphics>
   <offset x="0.0" y="0.0"/>
  </graphics>
 </name>
 <initialMarking>
  <value>Default,200</value>
 </initialMarking>
</place>

<place id="D">
 <graphics>
  <position x="200.0" y="160.0"/>
 </graphics>
 <name>
  <value>D</value>
  <graphics>
   <offset x="0.0" y="0.0"/>
  </graphics>
 </name>
 <initialMarking>
  <value>Default,25</value>
 </initialMarking>
</place>

<place id="E">
 <graphics>
  <position x="200.0" y="210.0"/>
 </graphics>
 <name>
  <value>E</value>
  <graphics>
   <offset x="0.0" y="0.0"/>
  </graphics>
 </name>
 <initialMarking>
  <value>Default,80</value>
 </initialMarking>
</place>

<transition id="A_BB">
 <graphics>
  <position x="700.0" y="260.0"/>
 </graphics>
 <name>
  <value>A_BB</value>
  <graphics>
   <offset x="0.0" y="0.0"/>
  </graphics>
 </name>
 <rate>
  <value>1.0</value>
 </rate>
</transition>

<arc id="A to A_BB" source="A" target="A_BB">
 <inscription>
  <value>Default,1</value>
 </inscription>
</arc>

<arc id="A_BB to B" source="A_BB" target="B">
 <inscription>
  <value>Default,2</value>
 </inscription>
</arc>

<transition id="BB_A">
 <graphics>
  <position x="700.0" y="310.0"/>
 </graphics>
 <name>
  <value>BB_A</value>
  <graphics>
   <offset x="0.0" y="0.0"/>
  </graphics>
 </name>
 <rate>
  <value>1.0</value>
 </rate>
</transition>

<arc id="B to BB_A" source="B" target="BB_A">
 <inscription>
  <value>Default,2</value>
 </inscription>
</arc>

<arc id="BB_A to A" source="BB_A" target="A">
 <inscription>
  <value>Default,1</value>
 </inscription>
</arc>

<transition id="AC_D">
 <graphics>
  <position x="700.0" y="360.0"/>
 </graphics>
 <name>
  <value>AC_D</value>
  <graphics>
   <offset x="0.0" y="0.0"/>
  </graphics>
 </name>
 <rate>
  <value>1.0</value>
 </rate>
</transition>

<arc id="A to AC_D" source="A" target="AC_D">
 <inscription>
  <value>Default,1</value>
 </inscription>
</arc>

<arc id="C to AC_D" source="C" target="AC_D">
 <inscription>
  <value>Default,1</value>
 </inscription>
</arc>

<arc id="AC_D to D" source="AC_D" target="D">
 <inscription>
  <value>Default,1</value>
 </inscription>
</arc>

<transition id="D_AC">
 <graphics>
  <position x="700.0" y="410.0"/>
 </graphics>
 <name>
  <value>D_AC</value>
  <graphics>
   <offset x="0.0" y="0.0"/>
  </graphics>
 </name>
 <rate>
  <value>1.0</value>
 </rate>
</transition>

<arc id="D to D_AC" source="D" target="D_AC">
 <inscription>
  <value>Default,1</value>
 </inscription>
</arc>

<arc id="D_AC to A" source="D_AC" target="A">
 <inscription>
  <value>Default,1</value>
 </inscription>
</arc>

<arc id="D_AC to C" source="D_AC" target="C">
 <inscription>
  <value>Default,1</value>
 </inscription>
</arc>

<transition id="D_BE">
 <graphics>
  <position x="700.0" y="460.0"/>
 </graphics>
 <name>
  <value>D_BE</value>
  <graphics>
   <offset x="0.0" y="0.0"/>
  </graphics>
 </name>
 <rate>
  <value>1.0</value>
 </rate>
</transition>

<arc id="D to D_BE" source="D" target="D_BE">
 <inscription>
  <value>Default,1</value>
 </inscription>
</arc>

<arc id="D_BE to B" source="D_BE" target="B">
 <inscription>
  <value>Default,1</value>
 </inscription>
</arc>

<arc id="D_BE to E" source="D_BE" target="E">
 <inscription>
  <value>Default,1</value>
 </inscription>
</arc>

<transition id="BE_AC">
 <graphics>
  <position x="700.0" y="510.0"/>
 </graphics>
 <name>
  <value>BE_AC</value>
  <graphics>
   <offset x="0.0" y="0.0"/>
  </graphics>
 </name>
 <rate>
  <value>1.0</value>
 </rate>
</transition>

<arc id="B to BE_AC" source="B" target="BE_AC">
 <inscription>
  <value>Default,1</value>
 </inscription>
</arc>

<arc id="E to BE_AC" source="E" target="BE_AC">
 <inscription>
  <value>Default,1</value>
 </inscription>
</arc>

<arc id="BE_AC to A" source="BE_AC" target="A">
 <inscription>
  <value>Default,1</value>
 </inscription>
</arc>

<arc id="BE_AC to C" source="BE_AC" target="C">
 <inscription>
  <value>Default,1</value>
 </inscription>
</arc>

</net>
</pnml>

## ReactionNetworkSystem_42_1345649357316_mm.xml
<map version="0.9.0">
<!-- To view this file, download free mind mapping software FreeMind from http://freemind.sourceforge.net -->
<!--
Automatically generated by Xholon version 0.8, using Xholon2MindMap.java
Wed Aug 22 11:29:17 EDT 2012 1345649357316
model: Feinberg - Chemical Reaction Networks
www.primordion.com/Xholon
-->
<node CREATED="1345649357316" ID="42" TEXT="ReactionNetworkSystem">
<node CREATED="1345649357316" ID="43" POSITION="right" TEXT="pot:PetriNet">
<node CREATED="1345649357316" ID="45" TEXT="AnalysisPetriNet">
</node>
<node CREATED="1345649357316" ID="46" TEXT="AnalysisCRN">
</node>
<node CREATED="1345649357316" ID="47" TEXT="AnalysisCat">
</node>
<node CREATED="1345649357316" FOLDED="true" ID="48" TEXT="Places">
<node CREATED="1345649357316" ID="49" TEXT="A">
</node>
<node CREATED="1345649357316" ID="50" TEXT="B">
</node>
<node CREATED="1345649357316" ID="51" TEXT="C">
</node>
<node CREATED="1345649357316" ID="52" TEXT="D">
</node>
<node CREATED="1345649357316" ID="53" TEXT="E">
</node>
</node>
<node CREATED="1345649357316" FOLDED="true" ID="55" TEXT="Transitions">
<node CREATED="1345649357316" ID="56" TEXT="A_BB">
<arrowlink COLOR="#B22222" DESTINATION="49" ENDARROW="None" ID="56490" STARTARROW="Default"/>
<arrowlink COLOR="#000080" DESTINATION="50" ENDARROW="Default" ID="56500" STARTARROW="None"/>
</node>
<node CREATED="1345649357316" ID="61" TEXT="BB_A">
<arrowlink COLOR="#B22222" DESTINATION="50" ENDARROW="None" ID="61500" STARTARROW="Default"/>
<arrowlink COLOR="#000080" DESTINATION="49" ENDARROW="Default" ID="61490" STARTARROW="None"/>
</node>
<node CREATED="1345649357316" ID="66" TEXT="AC_D">
<arrowlink COLOR="#B22222" DESTINATION="49" ENDARROW="None" ID="66490" STARTARROW="Default"/>
<arrowlink COLOR="#B22222" DESTINATION="51" ENDARROW="None" ID="66510" STARTARROW="Default"/>
<arrowlink COLOR="#000080" DESTINATION="52" ENDARROW="Default" ID="66520" STARTARROW="None"/>
</node>
<node CREATED="1345649357316" ID="72" TEXT="D_AC">
<arrowlink COLOR="#B22222" DESTINATION="52" ENDARROW="None" ID="72520" STARTARROW="Default"/>
<arrowlink COLOR="#000080" DESTINATION="49" ENDARROW="Default" ID="72490" STARTARROW="None"/>
<arrowlink COLOR="#000080" DESTINATION="51" ENDARROW="Default" ID="72510" STARTARROW="None"/>
</node>
<node CREATED="1345649357316" ID="78" TEXT="D_BE">
<arrowlink COLOR="#B22222" DESTINATION="52" ENDARROW="None" ID="78520" STARTARROW="Default"/>
<arrowlink COLOR="#000080" DESTINATION="50" ENDARROW="Default" ID="78500" STARTARROW="None"/>
<arrowlink COLOR="#000080" DESTINATION="53" ENDARROW="Default" ID="78530" STARTARROW="None"/>
</node>
<node CREATED="1345649357316" ID="84" TEXT="BE_AC">
<arrowlink COLOR="#B22222" DESTINATION="50" ENDARROW="None" ID="84500" STARTARROW="Default"/>
<arrowlink COLOR="#B22222" DESTINATION="53" ENDARROW="None" ID="84530" STARTARROW="Default"/>
<arrowlink COLOR="#000080" DESTINATION="49" ENDARROW="Default" ID="84490" STARTARROW="None"/>
<arrowlink COLOR="#000080" DESTINATION="51" ENDARROW="Default" ID="84510" STARTARROW="None"/>
</node>
</node>
</node>
<node CREATED="1345649357316" ID="91" POSITION="right" TEXT="ConstantlyStirredPot">
<arrowlink COLOR="#000080" DESTINATION="17" ENDARROW="Default" ID="91170" STARTARROW="None"/>
<arrowlink COLOR="#000080" DESTINATION="16" ENDARROW="Default" ID="91161" STARTARROW="None"/>
<arrowlink COLOR="#000080" DESTINATION="43" ENDARROW="Default" ID="91432" STARTARROW="None"/>
</node>
</node>
</map>

## ReactionNetworkSystem_42_1345650135114.html
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
  "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<!-- To view this file, open it in a web browser -->
<!--
Automatically generated by Xholon version 0.8.1, using Xholon2HTModL.java
Wed Aug 22 11:42:15 EDT 2012 1345650135114
model: Feinberg - Chemical Reaction Networks
www.primordion.com/Xholon
-->
<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
<head>
  <title>Feinberg - Chemical Reaction Networks</title>
  <style type="text/css">div {float:left;border:1px solid #1F4F82;padding:1px;margin:1px;background-color:#F0F8FF;font-size:90%} div:after {content: attr(class);}</style>
</head>
<body>
<div class="ReactionNetworkSystem">
<div class="pot:PetriNet">
<div class="QueueTransitions"></div>
<div class="AnalysisPetriNet"></div>
<div class="AnalysisCRN"></div>
<div class="AnalysisCat"></div>
<div class="Places">
<div class="A"></div>
<div class="B"></div>
<div class="C"></div>
<div class="D"></div>
<div class="E"></div>
</div>
<div class="Transitions">
<div class="A_BB">
<div class="InputArcs">
<div class="InputArc"></div>
</div>
<div class="OutputArcs">
<div class="OutputArc"></div>
</div>
</div>
<div class="BB_A">
<div class="InputArcs">
<div class="InputArc"></div>
</div>
<div class="OutputArcs">
<div class="OutputArc"></div>
</div>
</div>
<div class="AC_D">
<div class="InputArcs">
<div class="InputArc"></div>
<div class="InputArc"></div>
</div>
<div class="OutputArcs">
<div class="OutputArc"></div>
</div>
</div>
<div class="D_AC">
<div class="InputArcs">
<div class="InputArc"></div>
</div>
<div class="OutputArcs">
<div class="OutputArc"></div>
<div class="OutputArc"></div>
</div>
</div>
<div class="D_BE">
<div class="InputArcs">
<div class="InputArc"></div>
</div>
<div class="OutputArcs">
<div class="OutputArc"></div>
<div class="OutputArc"></div>
</div>
</div>
<div class="BE_AC">
<div class="InputArcs">
<div class="InputArc"></div>
<div class="InputArc"></div>
</div>
<div class="OutputArcs">
<div class="OutputArc"></div>
<div class="OutputArc"></div>
</div>
</div>
</div>
</div>
<div class="ConstantlyStirredPot"></div>
</div>
</body>
</html>

## ReactionNetworkSystem_42_1345651112552_yuml.txt
[Species]^-[A],
[Reaction]^-[AC_D],
[AC_D]1-inputArcs >1[InputArcs],
[AC_D]1-outputArcs >1[OutputArcs],
[AC_D]1-in >1[InputArc],
[AC_D]1-in >1[InputArc],
[AC_D]1-out >1[OutputArc],
[Reaction]^-[A_BB],
[A_BB]1-inputArcs >1[InputArcs],
[A_BB]1-outputArcs >1[OutputArcs],
[A_BB]1-in >1[InputArc],
[A_BB]1-out >1[OutputArc],
[AnalysisPN]^-[AnalysisCRN],
[AnalysisPN]^-[AnalysisCat],
[PetriNetEntity]^-[AnalysisPN],
[AnalysisPN]^-[AnalysisPetriNet],
[PetriNetEntity]^-[ArcPN],
[ArcPN]1-place >1[A],
[Species]^-[B],
[Reaction]^-[BB_A],
[BB_A]1-inputArcs >1[InputArcs],
[BB_A]1-outputArcs >1[OutputArcs],
[BB_A]1-in >1[InputArc],
[BB_A]1-out >1[OutputArc],
[Reaction]^-[BE_AC],
[BE_AC]1-inputArcs >1[InputArcs],
[BE_AC]1-outputArcs >1[OutputArcs],
[BE_AC]1-in >1[InputArc],
[BE_AC]1-in >1[InputArc],
[BE_AC]1-out >1[OutputArc],
[BE_AC]1-out >1[OutputArc],
[Species]^-[C],
[GridOwner]^-[ConstantlyStirredPot],
[ConstantlyStirredPot]1-xholonHelperService >1[XholonHelperService],
[ConstantlyStirredPot]1-nodeSelectionService >1[NodeSelectionService],
[ConstantlyStirredPot]1-petriNet >1[PetriNet],
[Species]^-[D],
[Reaction]^-[D_AC],
[D_AC]1-inputArcs >1[InputArcs],
[D_AC]1-outputArcs >1[OutputArcs],
[D_AC]1-in >1[InputArc],
[D_AC]1-out >1[OutputArc],
[D_AC]1-out >1[OutputArc],
[Reaction]^-[D_BE],
[D_BE]1-inputArcs >1[InputArcs],
[D_BE]1-outputArcs >1[OutputArcs],
[D_BE]1-in >1[InputArc],
[D_BE]1-out >1[OutputArc],
[D_BE]1-out >1[OutputArc],
[Species]^-[E],
[PetriNetEntity]^-[GridOwner],
[GridOwner]1-xholonHelperService >1[XholonHelperService],
[GridOwner]1-nodeSelectionService >1[NodeSelectionService],
[GridOwner]1-petriNet >1[PetriNet],
[ArcPN]^-[InputArc],
[InputArc]1-place >1[A],
[PetriNetEntity]^-[InputArcs],
[ArcPN]^-[OutputArc],
[OutputArc]1-place >1[B],
[PetriNetEntity]^-[OutputArcs],
[PetriNetEntity]^-[PetriNet],
[XholonMechanism]^-[PetriNetEntity],
[PetriNetEntity]^-[PlacePN],
[PetriNetEntity]^-[Places],
[PetriNetEntity]^-[QueueTransitions],
[QueueTransitions]1-transitionsRoot >1[Transitions],
[QueueTransitions]1-item >1[A_BB],
[QueueTransitions]1-item >1[BB_A],
[QueueTransitions]1-item >1[AC_D],
[QueueTransitions]1-item >1[D_AC],
[QueueTransitions]1-item >1[D_BE],
[QueueTransitions]1-item >1[BE_AC],
[TransitionPN]^-[Reaction],
[Reaction]1-inputArcs >1[InputArcs],
[Reaction]1-outputArcs >1[OutputArcs],
[Reaction]1-in >1[InputArc],
[Reaction]1-out >1[OutputArc],
[ReactionNetworkSystem],
[PlacePN]^-[Species],
[PetriNetEntity]^-[TransitionPN],
[TransitionPN]1-inputArcs >1[InputArcs],
[TransitionPN]1-outputArcs >1[OutputArcs],
[TransitionPN]1-in >1[InputArc],
[TransitionPN]1-out >1[OutputArc],
[PetriNetEntity]^-[Transitions],
[XholonMechanism],

## ReactionNetworkSystem_42_1345651183286.yaml
# Automatically generated by Xholon version 0.8.1
# using Xholon2Yaml.java and YamlStaxWriter.
# Wed Aug 22 11:59:43 EDT 2012 1345651183286
# model: Feinberg - Chemical Reaction Networks
# www.primordion.com/Xholon

%YAML 1.1
---
ReactionNetworkSystem:
  Val: 0.0
  PetriNet:
    roleName: pot
    kineticsType: 1
    p: 1.0
    k: 0.0040
    timeStepMultiplier: 1
    QueueTransitions:
      shouldAct: true
    AnalysisPetriNet:
    AnalysisCRN:
    AnalysisCat:
    Places:
      Val: 0.0
      A:
        token: 140.0
      B:
        token: 180.0
      C:
        token: 200.0
      D:
        token: 25.0
      E:
        token: 80.0
    Transitions:
      Val: 0.0
      A_BB:
        kineticsType: 1
        p: 1.0
        k: 0.0040
        count: 10.0
        InputArcs:
          Val: 0.0
          InputArc:
            connector: ancestor::PetriNet/Places/A
            weight: 1.0
        OutputArcs:
          Val: 0.0
          OutputArc:
            connector: ancestor::PetriNet/Places/B
            weight: 2.0
      BB_A:
        kineticsType: 1
        p: 1.0
        k: 0.0040
        count: 40.0
        InputArcs:
          Val: 0.0
          InputArc:
            connector: ancestor::PetriNet/Places/B
            weight: 2.0
        OutputArcs:
          Val: 0.0
          OutputArc:
            connector: ancestor::PetriNet/Places/A
            weight: 1.0
      AC_D:
        kineticsType: 1
        p: 1.0
        k: 0.0040
        count: 20.0
        InputArcs:
          Val: 0.0
          InputArc:
            connector: ancestor::PetriNet/Places/A
            weight: 1.0
          InputArc:
            connector: ancestor::PetriNet/Places/C
            weight: 1.0
        OutputArcs:
          Val: 0.0
          OutputArc:
            connector: ancestor::PetriNet/Places/D
            weight: 1.0
      D_AC:
        kineticsType: 1
        p: 1.0
        k: 0.0040
        count: 20.0
        InputArcs:
          Val: 0.0
          InputArc:
            connector: ancestor::PetriNet/Places/D
            weight: 1.0
        OutputArcs:
          Val: 0.0
          OutputArc:
            connector: ancestor::PetriNet/Places/A
            weight: 1.0
          OutputArc:
            connector: ancestor::PetriNet/Places/C
            weight: 1.0
      D_BE:
        kineticsType: 1
        p: 1.0
        k: 0.0040
        count: 20.0
        InputArcs:
          Val: 0.0
          InputArc:
            connector: ancestor::PetriNet/Places/D
            weight: 1.0
        OutputArcs:
          Val: 0.0
          OutputArc:
            connector: ancestor::PetriNet/Places/B
            weight: 1.0
          OutputArc:
            connector: ancestor::PetriNet/Places/E
            weight: 1.0
      BE_AC:
        kineticsType: 1
        p: 1.0
        k: 0.0040
        count: 20.0
        InputArcs:
          Val: 0.0
          InputArc:
            connector: ancestor::PetriNet/Places/B
            weight: 1.0
          InputArc:
            connector: ancestor::PetriNet/Places/E
            weight: 1.0
        OutputArcs:
          Val: 0.0
          OutputArc:
            connector: ancestor::PetriNet/Places/A
            weight: 1.0
          OutputArc:
            connector: ancestor::PetriNet/Places/C
            weight: 1.0
  ConstantlyStirredPot:
    rows: 50
    cols: 50
    gridCellColor: 32
    tokenFactor: 1.0
...

## xholonWorkbook.xml
<?xml version="1.0" encoding="UTF-8"?>
<!--Xholon Workbook http://www.primordion.com/Xholon/wb/ (C) Ken Webb Fri Aug 24 2012 11:20:48 GMT-0400 (EDT)-->
<XholonWorkbook>

<Notes><![CDATA[
Xholon
------
Title: Feinberg - Chemical Reaction Networks 1.1
Description:
Url: http://www.che.eng.ohio-state.edu/~FEINBERG/LecturesOnReactionNetworks/
InternalName:
YoutubeId:
Keywords:

My Notes
--------
source: Martin Feinberg (1980) Lectures on Chemical Reaction Networks - Lecture 1
http://www.che.eng.ohio-state.edu/~FEINBERG/LecturesOnReactionNetworks/

Chemical Reaction Networks are essentially the same as Petri nets.

How to run the Java app that's included on this Xholon Workbook page::
 (1) Click the "Save locally" button at the top of this page.
     This will assemble the contents of the workbook into a separate web browser page.
     Position the cursor in the new page and do "Select All" (Ctrl-A).

 (2) Click the second "Launch" button further down on this page (http://www.primordion.com/Xholon/jnlp/Chameleon_0.jnlp).
     This will start the Chameleon Java application. It's called Chameleon because if can be changed into anything else.
     Select "File --> Open".

 (3) Drag the contents of the workbook into the Chameleon app.
     Just click on the selected text in the new browser window, and drag it anywhere within the Chameleon window.

 (4) Click the "Refresh" button in the Chameleon window.
     Explore the model to confirm that it has the same structure that's specified on this page.
     Click the "Start" button to start the simulation.
     Use the "Pause" and "Step" buttons to pause, unpause, and single-step the simulation.

 (5) Expand the View node, and click the xYChart node to display a line chart.

By default, the kinetics type is 1 "Basic place/transition net kinetics".

Feinberg also discusses the model as a collection of molecules moving around in a stirred pot. To run the simulation as species and reaction nodes moving around in a ConstantlyStirredPot (Grid), change the following before running the app::
  Change PetriNet kineticsType="1" to kineticsType="3".
  Change QueueTransitions shouldAct="true" to shouldAct="false".
To change these and other aspects of the model, scroll down to the ReactionNetworkSystem editor on this page, and start typing.

You can also change most attributes of nodes in the model once the simulation is loaded and running.

]]></Notes>

<script implName="lang:python:inline:"><![CDATA[

]]></script>

<script implName="lang:javascript:inline:"><![CDATA[

]]></script>

<_-.XholonClass>
  <ReactionNetworkSystem/>

  <ConstantlyStirredPot superClass="GridOwner"/>

  <Reaction superClass="TransitionPN">
    <A_BB/>
    <BB_A/>
    <AC_D/>
    <D_AC/>
    <D_BE/>
    <BE_AC/>
  </Reaction>

  <Species superClass="PlacePN">
    <A/>
    <B/>
    <C/>
    <D/>
    <E/>
  </Species>

</_-.XholonClass>

<xholonClassDetails>
  <ConstantlyStirredPot>
    <port name="petriNet" connector="#xpointer(ancestor::ReactionNetworkSystem/PetriNet)"/>
  </ConstantlyStirredPot>
</xholonClassDetails>

<ReactionNetworkSystem xmlns:xi="http://www.w3.org/2001/XInclude">
  <!-- kineticsType
  1 = Basic place/transition net kinetics (default)
  2 = Mass action kinetics
  3 = Grid
  -->
  <PetriNet roleName="pot" kineticsType="1">
    <QueueTransitions shouldAct="true"/>
    <AnalysisPetriNet/>
    <AnalysisCRN/>
    <AnalysisCat/>

    <Places>
      <A token="140"/>
      <B token="180"/>
      <C token="200"/>
      <D token="25"/>
      <E token="80"/>
      <Plot mode="new"/>
    </Places>

    <Transitions>

      <A_BB count="10">
        <InputArcs>
          <InputArc weight="1" connector="ancestor::PetriNet/Places/A"/>
        </InputArcs>
        <OutputArcs>
          <OutputArc weight="2" connector="ancestor::PetriNet/Places/B"/>
        </OutputArcs>
      </A_BB>

      <BB_A count="40">
        <InputArcs>
          <InputArc weight="2" connector="ancestor::PetriNet/Places/B"/>
        </InputArcs>
        <OutputArcs>
          <OutputArc weight="1" connector="ancestor::PetriNet/Places/A"/>
        </OutputArcs>
      </BB_A>

      <AC_D count="20">
        <InputArcs>
          <InputArc weight="1" connector="ancestor::PetriNet/Places/A"/>
          <InputArc weight="1" connector="ancestor::PetriNet/Places/C"/>
        </InputArcs>
        <OutputArcs>
          <OutputArc weight="1" connector="ancestor::PetriNet/Places/D"/>
        </OutputArcs>
      </AC_D>

      <D_AC count="20">
        <InputArcs>
          <InputArc weight="1" connector="ancestor::PetriNet/Places/D"/>
        </InputArcs>
        <OutputArcs>
          <OutputArc weight="1" connector="ancestor::PetriNet/Places/A"/>
          <OutputArc weight="1" connector="ancestor::PetriNet/Places/C"/>
        </OutputArcs>
      </D_AC>

      <D_BE count="20">
        <InputArcs>
          <InputArc weight="1" connector="ancestor::PetriNet/Places/D"/>
        </InputArcs>
        <OutputArcs>
          <OutputArc weight="1" connector="ancestor::PetriNet/Places/B"/>
          <OutputArc weight="1" connector="ancestor::PetriNet/Places/E"/>
        </OutputArcs>
      </D_BE>

      <BE_AC count="20">
        <InputArcs>
          <InputArc weight="1" connector="ancestor::PetriNet/Places/B"/>
          <InputArc weight="1" connector="ancestor::PetriNet/Places/E"/>
        </InputArcs>
        <OutputArcs>
          <OutputArc weight="1" connector="ancestor::PetriNet/Places/A"/>
          <OutputArc weight="1" connector="ancestor::PetriNet/Places/C"/>
        </OutputArcs>
      </BE_AC>

    </Transitions>
  </PetriNet>

  <!-- grid owner -->
  <!--<ConstantlyStirredPot rows="80" cols="120" gridCellColor="000030" shouldPlacesMove="true"/>-->
  <ConstantlyStirredPot rows="50" cols="50" gridCellColor="000020" shouldPlacesMove="true"/>
  <!--<ConstantlyStirredPot rows="20" cols="20" gridCellColor="000020" shouldPlacesMove="true"/>-->

  <!-- Variations of the same network, as found in the Feinberg lectures. -->
  <!--
  <xi:include href="https://raw.github.com/gist/3377668/crn_2_31_csh.xml"/>
  -->

</ReactionNetworkSystem>

<Blockbehavior implName="lang:python:inline:"><![CDATA[

]]></Blockbehavior>

<Blockbehavior implName="lang:javascript:inline:"><![CDATA[

]]></Blockbehavior>

<Blockbehavior implName="lang:webEditionjs:inline:"><![CDATA[

]]></Blockbehavior>

<Blockbehavior implName="lang:bsh:inline:"><![CDATA[

]]></Blockbehavior>

<Blockbehavior implName="lang:jruby:inline:"><![CDATA[

]]></Blockbehavior>

<Blockbehavior implName="lang:groovy:inline:"><![CDATA[

]]></Blockbehavior>

<SvgClient><Attribute_String roleName="svgUri"><![CDATA[data:image/svg+xml,
<svg width="100" height="50" xmlns="http://www.w3.org/2000/svg">
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    <title>Feinberg - Chemical Reaction Networks</title>
    <rect id="ReactionNetworkSystem" fill="#98FB98" height="50" width="50" x="25" y="0"/>
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</XholonWorkbook>
	<?xml version="1.0" encoding="ISO-8859-1"?>
	<!-- To view this file, download open-source Vanted from http://vanted.ipk-gatersleben.de/ -->
	<!--
	Automatically generated by Xholon version 0.8.1, using Xholon2PnmlVanted.java
	Fri Sep 07 18:29:38 EDT 2012 1347056978368
	model: Petri net - feinberg1
	www.primordion.com/Xholon
	-->
	<pnml xmlns="http://www.informatik.hu-berlin.de/top/pnml/ptNetb">
	<net id="Net-One" type="P/T net">
	<place id="A">
	<graphics>
	<position x="200" y="10"/>
	<dimension x="25" y="25"/>
	</graphics>
	<name>
	<text>A</text>
	<graphics>
	<offset x="0" y="0"/>
	</graphics>
	</name>
	<initialMarking>
	<text>140</text>
	</initialMarking>
	</place>

	<place id="B">
	<graphics>
	<position x="200" y="60"/>
	<dimension x="25" y="25"/>
	</graphics>
	<name>
	<text>B</text>
	<graphics>
	<offset x="0" y="0"/>
	</graphics>
	</name>
	<initialMarking>
	<text>180</text>
	</initialMarking>
	</place>

	<place id="C">
	<graphics>
	<position x="200" y="110"/>
	<dimension x="25" y="25"/>
	</graphics>
	<name>
	<text>C</text>
	<graphics>
	<offset x="0" y="0"/>
	</graphics>
	</name>
	<initialMarking>
	<text>200</text>
	</initialMarking>
	</place>

	<place id="D">
	<graphics>
	<position x="200" y="160"/>
	<dimension x="25" y="25"/>
	</graphics>
	<name>
	<text>D</text>
	<graphics>
	<offset x="0" y="0"/>
	</graphics>
	</name>
	<initialMarking>
	<text>25</text>
	</initialMarking>
	</place>

	<place id="E">
	<graphics>
	<position x="200" y="210"/>
	<dimension x="25" y="25"/>
	</graphics>
	<name>
	<text>E</text>
	<graphics>
	<offset x="0" y="0"/>
	</graphics>
	</name>
	<initialMarking>
	<text>80</text>
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	<transition id="A_BB">
	<graphics>
	<position x="700" y="260"/>
	<dimension x="25" y="25"/>
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	<name>
	<text>A_BB</text>
	<graphics>
	<offset x="0" y="0"/>
	</graphics>
	</name>
	</transition>

	<arc id="A_to_A_BB" source="A" target="A_BB">
	<inscription>
	<text>1</text>
	</inscription>
	</arc>

	<arc id="A_BB_to_B" source="A_BB" target="B">
	<inscription>
	<text>2</text>
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	<transition id="BB_A">
	<graphics>
	<position x="700" y="310"/>
	<dimension x="25" y="25"/>
	</graphics>
	<name>
	<text>BB_A</text>
	<graphics>
	<offset x="0" y="0"/>
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	</transition>

	<arc id="B_to_BB_A" source="B" target="BB_A">
	<inscription>
	<text>2</text>
	</inscription>
	</arc>

	<arc id="BB_A_to_A" source="BB_A" target="A">
	<inscription>
	<text>1</text>
	</inscription>
	</arc>

	<transition id="AC_D">
	<graphics>
	<position x="700" y="360"/>
	<dimension x="25" y="25"/>
	</graphics>
	<name>
	<text>AC_D</text>
	<graphics>
	<offset x="0" y="0"/>
	</graphics>
	</name>
	</transition>

	<arc id="A_to_AC_D" source="A" target="AC_D">
	<inscription>
	<text>1</text>
	</inscription>
	</arc>

	<arc id="C_to_AC_D" source="C" target="AC_D">
	<inscription>
	<text>1</text>
	</inscription>
	</arc>

	<arc id="AC_D_to_D" source="AC_D" target="D">
	<inscription>
	<text>1</text>
	</inscription>
	</arc>

	<transition id="D_AC">
	<graphics>
	<position x="700" y="410"/>
	<dimension x="25" y="25"/>
	</graphics>
	<name>
	<text>D_AC</text>
	<graphics>
	<offset x="0" y="0"/>
	</graphics>
	</name>
	</transition>

	<arc id="D_to_D_AC" source="D" target="D_AC">
	<inscription>
	<text>1</text>
	</inscription>
	</arc>

	<arc id="D_AC_to_A" source="D_AC" target="A">
	<inscription>
	<text>1</text>
	</inscription>
	</arc>

	<arc id="D_AC_to_C" source="D_AC" target="C">
	<inscription>
	<text>1</text>
	</inscription>
	</arc>

	<transition id="D_BE">
	<graphics>
	<position x="700" y="460"/>
	<dimension x="25" y="25"/>
	</graphics>
	<name>
	<text>D_BE</text>
	<graphics>
	<offset x="0" y="0"/>
	</graphics>
	</name>
	</transition>

	<arc id="D_to_D_BE" source="D" target="D_BE">
	<inscription>
	<text>1</text>
	</inscription>
	</arc>

	<arc id="D_BE_to_B" source="D_BE" target="B">
	<inscription>
	<text>1</text>
	</inscription>
	</arc>

	<arc id="D_BE_to_E" source="D_BE" target="E">
	<inscription>
	<text>1</text>
	</inscription>
	</arc>

	<transition id="BE_AC">
	<graphics>
	<position x="700" y="510"/>
	<dimension x="25" y="25"/>
	</graphics>
	<name>
	<text>BE_AC</text>
	<graphics>
	<offset x="0" y="0"/>
	</graphics>
	</name>
	</transition>

	<arc id="B_to_BE_AC" source="B" target="BE_AC">
	<inscription>
	<text>1</text>
	</inscription>
	</arc>

	<arc id="E_to_BE_AC" source="E" target="BE_AC">
	<inscription>
	<text>1</text>
	</inscription>
	</arc>

	<arc id="BE_AC_to_A" source="BE_AC" target="A">
	<inscription>
	<text>1</text>
	</inscription>
	</arc>

	<arc id="BE_AC_to_C" source="BE_AC" target="C">
	<inscription>
	<text>1</text>
	</inscription>
	</arc>

	</net>
	</pnml>
	{UTF-8}
	A = INTEG( -A BB 13r +BB A 18r -AC D 23r +D AC 29r +BE AC 41r,140)
	~ things
	~ \|

	B = INTEG( +2A BB 13r -2BB A 18r +D BE 35r -BE AC 41r,180)
	~ things
	~ \|

	C = INTEG( -AC D 23r +D AC 29r +BE AC 41r,200)
	~ things
	~ \|

	D = INTEG( +AC D 23r -D AC 29r -D BE 35r,25)
	~ things
	~ \|

	E = INTEG( +D BE 35r -BE AC 41r,80)
	~ things
	~ \|

	A BB 13r K = 0.0039
	~ things/s
	~ \|

	A BB 13r = A BB 13r K * A
	~ things/s
	~ \|

	BB A 18r K = 0.0038
	~ things/s
	~ \|

	BB A 18r = BB A 18r K * B^2
	~ things/s
	~ \|

	AC D 23r K = 0.0037
	~ things/s
	~ \|

	AC D 23r = AC D 23r K * A * C
	~ things/s
	~ \|

	D AC 29r K = 0.0036
	~ things/s
	~ \|

	D AC 29r = D AC 29r K * D
	~ things/s
	~ \|

	D BE 35r K = 0.0035
	~ things/s
	~ \|

	D BE 35r = D BE 35r K * D
	~ things/s
	~ \|

	BE AC 41r K = 0.0034
	~ things/s
	~ \|

	BE AC 41r = BE AC 41r K * B * E
	~ things/s
	~ \|

	********************************************************
	.Control
	********************************************************~
	Simulation Control Paramaters
	\|

	FINAL TIME = 100
	~ s
	~ The final time for the simulation.
	\|

	INITIAL TIME = 0
	~ s
	~ The initial time for the simulation.
	\|

	SAVEPER = 0.5
	~ s
	~ The frequency with which output is stored.
	\|

	TIME STEP = 0.5
	~ s
	~ The time step for the simulation.
	\|

	\\\---/// Sketch information - do not modify anything except names
	V300 Do not put anything below this section - it will be ignored
	*View 1
	$0-0-0,0,Arial\|12\|\|0-0-0\|0-0-0\|0-0-0\|-1--1--1\|-1--1--1\|144,144,5,0
	10,1,A,70,56,35,19,3,131,0,0,0,0,0,0
	10,2,B,561,63,33,20,3,131,0,0,0,0,0,0
	10,3,C,627,592,37,18,3,131,0,0,0,0,0,0
	10,4,D,924,137,33,19,3,131,0,0,0,0,0,0
	10,5,E,1134,222,33,18,3,131,0,0,0,0,0,0
	11,6,316,309,68,8,9,34,3,0,0,1,0,0,0
	10,7,A BB 13r,309,89,62,12,40,3,0,0,0,0,0,0
	11,8,156,389,120,8,9,34,3,0,0,1,0,0,0
	10,9,BB A 18r,389,141,62,12,40,3,0,0,0,0,0,0
	11,10,172,260,470,8,9,34,3,0,0,1,0,0,0
	10,11,AC D 23r,260,491,62,12,40,3,0,0,0,0,0,0
	11,12,188,790,380,8,9,34,3,0,0,1,0,0,0
	10,13,D AC 29r,790,401,62,12,40,3,0,0,0,0,0,0
	11,14,204,1039,36,8,9,34,3,0,0,1,0,0,0
	10,15,D BE 35r,1039,57,62,12,40,3,0,0,0,0,0,0
	11,16,268,1131,480,8,9,34,3,0,0,1,0,0,0
	10,17,BE AC 41r,1131,501,62,12,40,3,0,0,0,0,0,0
	1,18,7,1,1,0,0,0,0,64,0,-1--1--1,,1\|(184,42)\|
	1,19,11,1,1,0,0,0,0,64,0,-1--1--1,,1\|(195,272)\|
	1,20,9,1,0,0,0,0,0,64,0,-1--1--1,,1\|(231,98)\|
	1,21,17,1,0,0,0,0,0,64,0,-1--1--1,,1\|(610,282)\|
	1,22,13,1,1,0,0,0,0,64,0,-1--1--1,,1\|(406,259)\|
	1,23,7,2,1,0,0,0,0,64,0,-1--1--1,,1\|(438,60)\|
	1,24,9,2,1,0,0,0,0,64,0,-1--1--1,,1\|(455,100)\|
	1,25,17,2,1,0,0,0,0,64,0,-1--1--1,,1\|(874,259)\|
	1,26,15,2,0,0,0,0,0,64,0,-1--1--1,,1\|(792,59)\|
	1,27,11,3,1,0,0,0,0,64,0,-1--1--1,,1\|(418,581)\|
	1,28,17,3,0,0,0,0,0,64,0,-1--1--1,,1\|(873,547)\|
	1,29,13,3,0,0,0,0,0,64,0,-1--1--1,,1\|(715,488)\|
	1,30,11,4,0,0,0,0,0,64,0,-1--1--1,,1\|(580,319)\|
	1,31,13,4,1,0,0,0,0,64,0,-1--1--1,,1\|(885,293)\|
	1,32,15,4,1,0,0,0,0,64,0,-1--1--1,,1\|(994,107)\|
	1,33,17,5,1,0,0,0,0,64,0,-1--1--1,,1\|(1103,366)\|
	1,34,15,5,0,0,0,0,0,64,0,-1--1--1,,1\|(1080,130)\|
	1,35,1,7,1,0,0,0,0,64,0,-1--1--1,,1\|(170,57)\|
	10,36,A BB 13r K,296,-21,77,13,8,2,0,3,-1,0,0,0,128-128-128,0-0-0,\|12\|\|128-128-128
	1,37,36,7,0,0,0,0,0,64,0,-1--1--1,,1\|(301,27)\|
	1,38,2,9,1,0,0,0,0,64,0,-1--1--1,,1\|(488,114)\|
	10,39,BB A 18r K,574,184,77,13,8,2,0,3,-1,0,0,0,128-128-128,0-0-0,\|12\|\|128-128-128
	1,40,39,9,0,0,0,0,0,64,0,-1--1--1,,1\|(486,163)\|
	1,41,1,11,1,0,0,0,0,64,0,-1--1--1,,1\|(127,281)\|
	10,42,AC D 23r K,79,566,59,27,8,2,0,3,-1,0,0,0,128-128-128,0-0-0,\|12\|\|128-128-128
	1,43,42,11,0,0,0,0,0,64,0,-1--1--1,,1\|(178,525)\|
	1,44,3,11,1,0,0,0,0,64,0,-1--1--1,,1\|(464,493)\|
	1,45,4,13,1,0,0,0,0,64,0,-1--1--1,,1\|(833,256)\|
	10,46,D AC 29r K,625,430,59,27,8,2,0,3,-1,0,0,0,128-128-128,0-0-0,\|12\|\|128-128-128
	1,47,46,13,0,0,0,0,0,64,0,-1--1--1,,1\|(699,416)\|
	1,48,4,15,1,0,0,0,0,64,0,-1--1--1,,1\|(970,90)\|
	10,49,D BE 35r K,1024,185,59,27,8,2,0,3,-1,0,0,0,128-128-128,0-0-0,\|12\|\|128-128-128
	1,50,49,15,0,0,0,0,0,64,0,-1--1--1,,1\|(1031,120)\|
	1,51,2,17,1,0,0,0,0,64,0,-1--1--1,,1\|(828,301)\|
	10,52,BE AC 41r K,1054,601,67,27,8,2,0,3,-1,0,0,0,128-128-128,0-0-0,\|12\|\|128-128-128
	1,53,52,17,0,0,0,0,0,64,0,-1--1--1,,1\|(1093,549)\|
	1,54,5,17,1,0,0,0,0,64,0,-1--1--1,,1\|(1159,358)\|
	///---\\\
	:GRAPH Kenz_Graph_1
	:TITLE
	:SCALE
	:VAR A\|A
	:LINE-WIDTH 3
	:SCALE
	:VAR B\|B
	:LINE-WIDTH 3
	:SCALE
	:VAR C\|C
	:LINE-WIDTH 3
	:SCALE
	:VAR D\|D
	:LINE-WIDTH 3
	:SCALE
	:VAR E\|E
	:LINE-WIDTH 3
	:L<%^E!@
	1:Current.vdf
	9:Current
	23:0
	15:0,0,0,0,0,0
	19:5,0
	27:2,
	34:0,
	4:Time
	5:FINAL TIME
	35:Date
	36:YYYY-MM-DD
	37:2000
	38:1
	39:1
	40:2
	41:0
	24:0
	25:100
	26:100
	<map version="0.9.0">
	<!-- To view this file, download free mind mapping software FreeMind from http://freemind.sourceforge.net -->
	<!--
	Automatically generated by Xholon version 0.8, using Xholon2MindMap.java
	Wed Aug 22 11:29:17 EDT 2012 1345649357316
	model: Feinberg - Chemical Reaction Networks
	www.primordion.com/Xholon
	-->
	<node CREATED="1345649357316" ID="42" TEXT="ReactionNetworkSystem">
	<node CREATED="1345649357316" ID="43" POSITION="right" TEXT="pot:PetriNet">
	<node CREATED="1345649357316" ID="45" TEXT="AnalysisPetriNet">
	</node>
	<node CREATED="1345649357316" ID="46" TEXT="AnalysisCRN">
	</node>
	<node CREATED="1345649357316" ID="47" TEXT="AnalysisCat">
	</node>
	<node CREATED="1345649357316" FOLDED="true" ID="48" TEXT="Places">
	<node CREATED="1345649357316" ID="49" TEXT="A">
	</node>
	<node CREATED="1345649357316" ID="50" TEXT="B">
	</node>
	<node CREATED="1345649357316" ID="51" TEXT="C">
	</node>
	<node CREATED="1345649357316" ID="52" TEXT="D">
	</node>
	<node CREATED="1345649357316" ID="53" TEXT="E">
	</node>
	</node>
	<node CREATED="1345649357316" FOLDED="true" ID="55" TEXT="Transitions">
	<node CREATED="1345649357316" ID="56" TEXT="A_BB">
	<arrowlink COLOR="#B22222" DESTINATION="49" ENDARROW="None" ID="56490" STARTARROW="Default"/>
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	</node>
	<node CREATED="1345649357316" ID="61" TEXT="BB_A">
	<arrowlink COLOR="#B22222" DESTINATION="50" ENDARROW="None" ID="61500" STARTARROW="Default"/>
	<arrowlink COLOR="#000080" DESTINATION="49" ENDARROW="Default" ID="61490" STARTARROW="None"/>
	</node>
	<node CREATED="1345649357316" ID="66" TEXT="AC_D">
	<arrowlink COLOR="#B22222" DESTINATION="49" ENDARROW="None" ID="66490" STARTARROW="Default"/>
	<arrowlink COLOR="#B22222" DESTINATION="51" ENDARROW="None" ID="66510" STARTARROW="Default"/>
	<arrowlink COLOR="#000080" DESTINATION="52" ENDARROW="Default" ID="66520" STARTARROW="None"/>
	</node>
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	<arrowlink COLOR="#000080" DESTINATION="51" ENDARROW="Default" ID="72510" STARTARROW="None"/>
	</node>
	<node CREATED="1345649357316" ID="78" TEXT="D_BE">
	<arrowlink COLOR="#B22222" DESTINATION="52" ENDARROW="None" ID="78520" STARTARROW="Default"/>
	<arrowlink COLOR="#000080" DESTINATION="50" ENDARROW="Default" ID="78500" STARTARROW="None"/>
	<arrowlink COLOR="#000080" DESTINATION="53" ENDARROW="Default" ID="78530" STARTARROW="None"/>
	</node>
	<node CREATED="1345649357316" ID="84" TEXT="BE_AC">
	<arrowlink COLOR="#B22222" DESTINATION="50" ENDARROW="None" ID="84500" STARTARROW="Default"/>
	<arrowlink COLOR="#B22222" DESTINATION="53" ENDARROW="None" ID="84530" STARTARROW="Default"/>
	<arrowlink COLOR="#000080" DESTINATION="49" ENDARROW="Default" ID="84490" STARTARROW="None"/>
	<arrowlink COLOR="#000080" DESTINATION="51" ENDARROW="Default" ID="84510" STARTARROW="None"/>
	</node>
	</node>
	</node>
	<node CREATED="1345649357316" ID="91" POSITION="right" TEXT="ConstantlyStirredPot">
	<arrowlink COLOR="#000080" DESTINATION="17" ENDARROW="Default" ID="91170" STARTARROW="None"/>
	<arrowlink COLOR="#000080" DESTINATION="16" ENDARROW="Default" ID="91161" STARTARROW="None"/>
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	</node>
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	</map>
	<?xml version="1.0" encoding="UTF-8"?>
	<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
	"http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
	<!-- To view this file, open it in a web browser -->
	<!--
	Automatically generated by Xholon version 0.8.1, using Xholon2HTModL.java
	Wed Aug 22 11:42:15 EDT 2012 1345650135114
	model: Feinberg - Chemical Reaction Networks
	www.primordion.com/Xholon
	-->
	<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
	<head>
	<title>Feinberg - Chemical Reaction Networks</title>
	<style type="text/css">div {float:left;border:1px solid #1F4F82;padding:1px;margin:1px;background-color:#F0F8FF;font-size:90%} div:after {content: attr(class);}</style>
	</head>
	<body>
	<div class="ReactionNetworkSystem">
	<div class="pot:PetriNet">
	<div class="QueueTransitions"></div>
	<div class="AnalysisPetriNet"></div>
	<div class="AnalysisCRN"></div>
	<div class="AnalysisCat"></div>
	<div class="Places">
	<div class="A"></div>
	<div class="B"></div>
	<div class="C"></div>
	<div class="D"></div>
	<div class="E"></div>
	</div>
	<div class="Transitions">
	<div class="A_BB">
	<div class="InputArcs">
	<div class="InputArc"></div>
	</div>
	<div class="OutputArcs">
	<div class="OutputArc"></div>
	</div>
	</div>
	<div class="BB_A">
	<div class="InputArcs">
	<div class="InputArc"></div>
	</div>
	<div class="OutputArcs">
	<div class="OutputArc"></div>
	</div>
	</div>
	<div class="AC_D">
	<div class="InputArcs">
	<div class="InputArc"></div>
	<div class="InputArc"></div>
	</div>
	<div class="OutputArcs">
	<div class="OutputArc"></div>
	</div>
	</div>
	<div class="D_AC">
	<div class="InputArcs">
	<div class="InputArc"></div>
	</div>
	<div class="OutputArcs">
	<div class="OutputArc"></div>
	<div class="OutputArc"></div>
	</div>
	</div>
	<div class="D_BE">
	<div class="InputArcs">
	<div class="InputArc"></div>
	</div>
	<div class="OutputArcs">
	<div class="OutputArc"></div>
	<div class="OutputArc"></div>
	</div>
	</div>
	<div class="BE_AC">
	<div class="InputArcs">
	<div class="InputArc"></div>
	<div class="InputArc"></div>
	</div>
	<div class="OutputArcs">
	<div class="OutputArc"></div>
	<div class="OutputArc"></div>
	</div>
	</div>
	</div>
	</div>
	<div class="ConstantlyStirredPot"></div>
	</div>
	</body>
	</html>
	[Species]^-[A],
	[Reaction]^-[AC_D],
	[AC_D]1-inputArcs >1[InputArcs],
	[AC_D]1-outputArcs >1[OutputArcs],
	[AC_D]1-in >1[InputArc],
	[AC_D]1-in >1[InputArc],
	[AC_D]1-out >1[OutputArc],
	[Reaction]^-[A_BB],
	[A_BB]1-inputArcs >1[InputArcs],
	[A_BB]1-outputArcs >1[OutputArcs],
	[A_BB]1-in >1[InputArc],
	[A_BB]1-out >1[OutputArc],
	[AnalysisPN]^-[AnalysisCRN],
	[AnalysisPN]^-[AnalysisCat],
	[PetriNetEntity]^-[AnalysisPN],
	[AnalysisPN]^-[AnalysisPetriNet],
	[PetriNetEntity]^-[ArcPN],
	[ArcPN]1-place >1[A],
	[Species]^-[B],
	[Reaction]^-[BB_A],
	[BB_A]1-inputArcs >1[InputArcs],
	[BB_A]1-outputArcs >1[OutputArcs],
	[BB_A]1-in >1[InputArc],
	[BB_A]1-out >1[OutputArc],
	[Reaction]^-[BE_AC],
	[BE_AC]1-inputArcs >1[InputArcs],
	[BE_AC]1-outputArcs >1[OutputArcs],
	[BE_AC]1-in >1[InputArc],
	[BE_AC]1-in >1[InputArc],
	[BE_AC]1-out >1[OutputArc],
	[BE_AC]1-out >1[OutputArc],
	[Species]^-[C],
	[GridOwner]^-[ConstantlyStirredPot],
	[ConstantlyStirredPot]1-xholonHelperService >1[XholonHelperService],
	[ConstantlyStirredPot]1-nodeSelectionService >1[NodeSelectionService],
	[ConstantlyStirredPot]1-petriNet >1[PetriNet],
	[Species]^-[D],
	[Reaction]^-[D_AC],
	[D_AC]1-inputArcs >1[InputArcs],
	[D_AC]1-outputArcs >1[OutputArcs],
	[D_AC]1-in >1[InputArc],
	[D_AC]1-out >1[OutputArc],
	[D_AC]1-out >1[OutputArc],
	[Reaction]^-[D_BE],
	[D_BE]1-inputArcs >1[InputArcs],
	[D_BE]1-outputArcs >1[OutputArcs],
	[D_BE]1-in >1[InputArc],
	[D_BE]1-out >1[OutputArc],
	[D_BE]1-out >1[OutputArc],
	[Species]^-[E],
	[PetriNetEntity]^-[GridOwner],
	[GridOwner]1-xholonHelperService >1[XholonHelperService],
	[GridOwner]1-nodeSelectionService >1[NodeSelectionService],
	[GridOwner]1-petriNet >1[PetriNet],
	[ArcPN]^-[InputArc],
	[InputArc]1-place >1[A],
	[PetriNetEntity]^-[InputArcs],
	[ArcPN]^-[OutputArc],
	[OutputArc]1-place >1[B],
	[PetriNetEntity]^-[OutputArcs],
	[PetriNetEntity]^-[PetriNet],
	[XholonMechanism]^-[PetriNetEntity],
	[PetriNetEntity]^-[PlacePN],
	[PetriNetEntity]^-[Places],
	[PetriNetEntity]^-[QueueTransitions],
	[QueueTransitions]1-transitionsRoot >1[Transitions],
	[QueueTransitions]1-item >1[A_BB],
	[QueueTransitions]1-item >1[BB_A],
	[QueueTransitions]1-item >1[AC_D],
	[QueueTransitions]1-item >1[D_AC],
	[QueueTransitions]1-item >1[D_BE],
	[QueueTransitions]1-item >1[BE_AC],
	[TransitionPN]^-[Reaction],
	[Reaction]1-inputArcs >1[InputArcs],
	[Reaction]1-outputArcs >1[OutputArcs],
	[Reaction]1-in >1[InputArc],
	[Reaction]1-out >1[OutputArc],
	[ReactionNetworkSystem],
	[PlacePN]^-[Species],
	[PetriNetEntity]^-[TransitionPN],
	[TransitionPN]1-inputArcs >1[InputArcs],
	[TransitionPN]1-outputArcs >1[OutputArcs],
	[TransitionPN]1-in >1[InputArc],
	[TransitionPN]1-out >1[OutputArc],
	[PetriNetEntity]^-[Transitions],
	[XholonMechanism],
	# Automatically generated by Xholon version 0.8.1
	# using Xholon2Yaml.java and YamlStaxWriter.
	# Wed Aug 22 11:59:43 EDT 2012 1345651183286
	# model: Feinberg - Chemical Reaction Networks
	# www.primordion.com/Xholon

	%YAML 1.1
	---
	ReactionNetworkSystem:
	Val: 0.0
	PetriNet:
	roleName: pot
	kineticsType: 1
	p: 1.0
	k: 0.0040
	timeStepMultiplier: 1
	QueueTransitions:
	shouldAct: true
	AnalysisPetriNet:
	AnalysisCRN:
	AnalysisCat:
	Places:
	Val: 0.0
	A:
	token: 140.0
	B:
	token: 180.0
	C:
	token: 200.0
	D:
	token: 25.0
	E:
	token: 80.0
	Transitions:
	Val: 0.0
	A_BB:
	kineticsType: 1
	p: 1.0
	k: 0.0040
	count: 10.0
	InputArcs:
	Val: 0.0
	InputArc:
	connector: ancestor::PetriNet/Places/A
	weight: 1.0
	OutputArcs:
	Val: 0.0
	OutputArc:
	connector: ancestor::PetriNet/Places/B
	weight: 2.0
	BB_A:
	kineticsType: 1
	p: 1.0
	k: 0.0040
	count: 40.0
	InputArcs:
	Val: 0.0
	InputArc:
	connector: ancestor::PetriNet/Places/B
	weight: 2.0
	OutputArcs:
	Val: 0.0
	OutputArc:
	connector: ancestor::PetriNet/Places/A
	weight: 1.0
	AC_D:
	kineticsType: 1
	p: 1.0
	k: 0.0040
	count: 20.0
	InputArcs:
	Val: 0.0
	InputArc:
	connector: ancestor::PetriNet/Places/A
	weight: 1.0
	InputArc:
	connector: ancestor::PetriNet/Places/C
	weight: 1.0
	OutputArcs:
	Val: 0.0
	OutputArc:
	connector: ancestor::PetriNet/Places/D
	weight: 1.0
	D_AC:
	kineticsType: 1
	p: 1.0
	k: 0.0040
	count: 20.0
	InputArcs:
	Val: 0.0
	InputArc:
	connector: ancestor::PetriNet/Places/D
	weight: 1.0
	OutputArcs:
	Val: 0.0
	OutputArc:
	connector: ancestor::PetriNet/Places/A
	weight: 1.0
	OutputArc:
	connector: ancestor::PetriNet/Places/C
	weight: 1.0
	D_BE:
	kineticsType: 1
	p: 1.0
	k: 0.0040
	count: 20.0
	InputArcs:
	Val: 0.0
	InputArc:
	connector: ancestor::PetriNet/Places/D
	weight: 1.0
	OutputArcs:
	Val: 0.0
	OutputArc:
	connector: ancestor::PetriNet/Places/B
	weight: 1.0
	OutputArc:
	connector: ancestor::PetriNet/Places/E
	weight: 1.0
	BE_AC:
	kineticsType: 1
	p: 1.0
	k: 0.0040
	count: 20.0
	InputArcs:
	Val: 0.0
	InputArc:
	connector: ancestor::PetriNet/Places/B
	weight: 1.0
	InputArc:
	connector: ancestor::PetriNet/Places/E
	weight: 1.0
	OutputArcs:
	Val: 0.0
	OutputArc:
	connector: ancestor::PetriNet/Places/A
	weight: 1.0
	OutputArc:
	connector: ancestor::PetriNet/Places/C
	weight: 1.0
	ConstantlyStirredPot:
	rows: 50
	cols: 50
	gridCellColor: 32
	tokenFactor: 1.0
	...
	<?xml version="1.0" encoding="UTF-8"?>
	<!--Xholon Workbook http://www.primordion.com/Xholon/wb/ (C) Ken Webb Fri Aug 24 2012 11:20:48 GMT-0400 (EDT)-->
	<XholonWorkbook>

	<Notes><![CDATA[
	Xholon
	------
	Title: Feinberg - Chemical Reaction Networks 1.1
	Description:
	Url: http://www.che.eng.ohio-state.edu/~FEINBERG/LecturesOnReactionNetworks/
	InternalName:
	YoutubeId:
	Keywords:

	My Notes
	--------
	source: Martin Feinberg (1980) Lectures on Chemical Reaction Networks - Lecture 1
	http://www.che.eng.ohio-state.edu/~FEINBERG/LecturesOnReactionNetworks/

	Chemical Reaction Networks are essentially the same as Petri nets.

	How to run the Java app that's included on this Xholon Workbook page::
	(1) Click the "Save locally" button at the top of this page.
	This will assemble the contents of the workbook into a separate web browser page.
	Position the cursor in the new page and do "Select All" (Ctrl-A).

	(2) Click the second "Launch" button further down on this page (http://www.primordion.com/Xholon/jnlp/Chameleon_0.jnlp).
	This will start the Chameleon Java application. It's called Chameleon because if can be changed into anything else.
	Select "File --> Open".

	(3) Drag the contents of the workbook into the Chameleon app.
	Just click on the selected text in the new browser window, and drag it anywhere within the Chameleon window.

	(4) Click the "Refresh" button in the Chameleon window.
	Explore the model to confirm that it has the same structure that's specified on this page.
	Click the "Start" button to start the simulation.
	Use the "Pause" and "Step" buttons to pause, unpause, and single-step the simulation.

	(5) Expand the View node, and click the xYChart node to display a line chart.

	By default, the kinetics type is 1 "Basic place/transition net kinetics".

	Feinberg also discusses the model as a collection of molecules moving around in a stirred pot. To run the simulation as species and reaction nodes moving around in a ConstantlyStirredPot (Grid), change the following before running the app::
	Change PetriNet kineticsType="1" to kineticsType="3".
	Change QueueTransitions shouldAct="true" to shouldAct="false".
	To change these and other aspects of the model, scroll down to the ReactionNetworkSystem editor on this page, and start typing.

	You can also change most attributes of nodes in the model once the simulation is loaded and running.

	]]></Notes>

	<script implName="lang:python:inline:"><![CDATA[

	]]></script>

	<script implName="lang:javascript:inline:"><![CDATA[

	]]></script>

	<_-.XholonClass>
	<ReactionNetworkSystem/>

	<ConstantlyStirredPot superClass="GridOwner"/>

	<Reaction superClass="TransitionPN">
	<A_BB/>
	<BB_A/>
	<AC_D/>
	<D_AC/>
	<D_BE/>
	<BE_AC/>
	</Reaction>

	<Species superClass="PlacePN">
	<A/>
	<B/>
	<C/>
	<D/>
	<E/>
	</Species>

	</_-.XholonClass>

	<xholonClassDetails>
	<ConstantlyStirredPot>
	<port name="petriNet" connector="#xpointer(ancestor::ReactionNetworkSystem/PetriNet)"/>
	</ConstantlyStirredPot>
	</xholonClassDetails>

	<ReactionNetworkSystem xmlns:xi="http://www.w3.org/2001/XInclude">
	<!-- kineticsType
	1 = Basic place/transition net kinetics (default)
	2 = Mass action kinetics
	3 = Grid
	-->
	<PetriNet roleName="pot" kineticsType="1">
	<QueueTransitions shouldAct="true"/>
	<AnalysisPetriNet/>
	<AnalysisCRN/>
	<AnalysisCat/>

	<Places>
	<A token="140"/>
	<B token="180"/>
	<C token="200"/>
	<D token="25"/>
	<E token="80"/>
	<Plot mode="new"/>
	</Places>

	<Transitions>

	<A_BB count="10">
	<InputArcs>
	<InputArc weight="1" connector="ancestor::PetriNet/Places/A"/>
	</InputArcs>
	<OutputArcs>
	<OutputArc weight="2" connector="ancestor::PetriNet/Places/B"/>
	</OutputArcs>
	</A_BB>

	<BB_A count="40">
	<InputArcs>
	<InputArc weight="2" connector="ancestor::PetriNet/Places/B"/>
	</InputArcs>
	<OutputArcs>
	<OutputArc weight="1" connector="ancestor::PetriNet/Places/A"/>
	</OutputArcs>
	</BB_A>

	<AC_D count="20">
	<InputArcs>
	<InputArc weight="1" connector="ancestor::PetriNet/Places/A"/>
	<InputArc weight="1" connector="ancestor::PetriNet/Places/C"/>
	</InputArcs>
	<OutputArcs>
	<OutputArc weight="1" connector="ancestor::PetriNet/Places/D"/>
	</OutputArcs>
	</AC_D>

	<D_AC count="20">
	<InputArcs>
	<InputArc weight="1" connector="ancestor::PetriNet/Places/D"/>
	</InputArcs>
	<OutputArcs>
	<OutputArc weight="1" connector="ancestor::PetriNet/Places/A"/>
	<OutputArc weight="1" connector="ancestor::PetriNet/Places/C"/>
	</OutputArcs>
	</D_AC>

	<D_BE count="20">
	<InputArcs>
	<InputArc weight="1" connector="ancestor::PetriNet/Places/D"/>
	</InputArcs>
	<OutputArcs>
	<OutputArc weight="1" connector="ancestor::PetriNet/Places/B"/>
	<OutputArc weight="1" connector="ancestor::PetriNet/Places/E"/>
	</OutputArcs>
	</D_BE>

	<BE_AC count="20">
	<InputArcs>
	<InputArc weight="1" connector="ancestor::PetriNet/Places/B"/>
	<InputArc weight="1" connector="ancestor::PetriNet/Places/E"/>
	</InputArcs>
	<OutputArcs>
	<OutputArc weight="1" connector="ancestor::PetriNet/Places/A"/>
	<OutputArc weight="1" connector="ancestor::PetriNet/Places/C"/>
	</OutputArcs>
	</BE_AC>

	</Transitions>
	</PetriNet>

	<!-- grid owner -->
	<!--<ConstantlyStirredPot rows="80" cols="120" gridCellColor="000030" shouldPlacesMove="true"/>-->
	<ConstantlyStirredPot rows="50" cols="50" gridCellColor="000020" shouldPlacesMove="true"/>
	<!--<ConstantlyStirredPot rows="20" cols="20" gridCellColor="000020" shouldPlacesMove="true"/>-->

	<!-- Variations of the same network, as found in the Feinberg lectures. -->
	<!--
	<xi:include href="https://raw.github.com/gist/3377668/crn_2_31_csh.xml"/>
	-->

	</ReactionNetworkSystem>

	<Blockbehavior implName="lang:python:inline:"><![CDATA[

	]]></Blockbehavior>

	<Blockbehavior implName="lang:javascript:inline:"><![CDATA[

	]]></Blockbehavior>

	<Blockbehavior implName="lang:webEditionjs:inline:"><![CDATA[

	]]></Blockbehavior>

	<Blockbehavior implName="lang:bsh:inline:"><![CDATA[

	]]></Blockbehavior>

	<Blockbehavior implName="lang:jruby:inline:"><![CDATA[

	]]></Blockbehavior>

	<Blockbehavior implName="lang:groovy:inline:"><![CDATA[

	]]></Blockbehavior>

	<SvgClient><Attribute_String roleName="svgUri"><![CDATA[data:image/svg+xml,
	<svg width="100" height="50" xmlns="http://www.w3.org/2000/svg">
	<g>
	<title>Feinberg - Chemical Reaction Networks</title>
	<rect id="ReactionNetworkSystem" fill="#98FB98" height="50" width="50" x="25" y="0"/>
	</g>
	</svg>
	]]></Attribute_String><Attribute_String roleName="setup">${MODELNAME_DEFAULT},${SVGURI_DEFAULT}</Attribute_String></SvgClient>

	</XholonWorkbook>