[med-svn] [libroadrunner] 04/08: Fix line endings after removing .gitattributes
Andreas Tille
tille at debian.org
Wed Feb 1 12:39:26 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository libroadrunner.
commit 80dd66d3ed55837a2e722d6ea6ba5f9431c6ae76
Author: Andreas Tille <tille at debian.org>
Date: Wed Feb 1 13:24:21 2017 +0100
Fix line endings after removing .gitattributes
---
cmake/FindNumPy.cmake | 202 +--
data/simpleNoise-MissingData.dat | 620 +++----
data/simpleNoise.dat | 620 +++----
data/simpleNoiseWeights.dat | 620 +++----
examples/CMakeLists.txt | 62 +-
examples/create_uuid/main.cpp | 42 +-
examples/events/feedback.xml | 942 +++++------
examples/load_model_dll/CMakeLists.txt | 98 +-
examples/load_model_dll/Readme.txt | 2 +-
examples/load_model_dll/main.cpp | 84 +-
examples/one_rr/CMakeLists.txt | 98 +-
examples/one_rr/Readme.txt | 8 +-
examples/one_rr/main.cpp | 94 +-
examples/two_rrs/CMakeLists.txt | 98 +-
examples/two_rrs/Readme.txt | 2 +-
examples/two_rrs/main.cpp | 98 +-
models/BorisEJB.xml | 1858 ++++++++++-----------
models/CMakeLists.txt | 48 +-
models/MinimizationTest_A.xml | 146 +-
models/bug.xml | 904 +++++-----
models/sbml_test_0001.xml | 70 +-
models/simple.xml | 106 +-
models/squareWaveModel.xml | 138 +-
models/ss_SimpleConservedCycle.xml | 122 +-
models/ss_TurnOnConservationAnalysis.xml | 122 +-
models/ss_threeSpecies.xml | 216 +--
models/ss_threestep.xml | 216 +--
models/test_models/CMakeLists.txt | 34 +-
models/test_models/TestModel_1.xml | 324 ++--
models/test_models/reference_data/CMakeLists.txt | 26 +-
models/test_models/reference_data/TestModel_1.dat | 190 +--
rr_support/CMakeLists.txt | 32 +-
rr_support/bcc.cfg | 14 +-
rr_support/rrSupport.c | 88 +-
source/llvm_testing/run_cpp_tests.bat | 36 +-
source/testing/CMakeLists.txt | 244 +--
source/testing/run_cpp_tests.bat | 36 +-
source/testing/run_cpp_tests.sh | 40 +-
38 files changed, 4350 insertions(+), 4350 deletions(-)
diff --git a/cmake/FindNumPy.cmake b/cmake/FindNumPy.cmake
index a353673..6feeb73 100644
--- a/cmake/FindNumPy.cmake
+++ b/cmake/FindNumPy.cmake
@@ -1,101 +1,101 @@
-# - Find the NumPy libraries
-# This module finds if NumPy is installed, and sets the following variables
-# indicating where it is.
-#
-# TODO: Update to provide the libraries and paths for linking npymath lib.
-#
-# NUMPY_FOUND - was NumPy found
-# NUMPY_VERSION - the version of NumPy found as a string
-# NUMPY_VERSION_MAJOR - the major version number of NumPy
-# NUMPY_VERSION_MINOR - the minor version number of NumPy
-# NUMPY_VERSION_PATCH - the patch version number of NumPy
-# NUMPY_VERSION_DECIMAL - e.g. version 1.6.1 is 10601
-# NUMPY_INCLUDE_DIRS - path to the NumPy include files
-
-#============================================================================
-# Copyright 2012 Continuum Analytics, Inc.
-#
-# MIT License
-#
-# Permission is hereby granted, free of charge, to any person obtaining
-# a copy of this software and associated documentation files
-# (the "Software"), to deal in the Software without restriction, including
-# without limitation the rights to use, copy, modify, merge, publish,
-# distribute, sublicense, and/or sell copies of the Software, and to permit
-# persons to whom the Software is furnished to do so, subject to
-# the following conditions:
-#
-# The above copyright notice and this permission notice shall be included
-# in all copies or substantial portions of the Software.
-#
-# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
-# OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
-# THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR
-# OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE,
-# ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
-# OTHER DEALINGS IN THE SOFTWARE.
-#
-#============================================================================
-
-# Finding NumPy involves calling the Python interpreter
-if(NumPy_FIND_REQUIRED)
- find_package(PythonInterp REQUIRED)
-else()
- find_package(PythonInterp)
-endif()
-
-if(NOT PYTHONINTERP_FOUND)
- set(NUMPY_FOUND FALSE)
- return()
-endif()
-
-execute_process(COMMAND "${PYTHON_EXECUTABLE}" "-c"
- "import numpy as n; print(n.__version__); print(n.get_include());"
- RESULT_VARIABLE _NUMPY_SEARCH_SUCCESS
- OUTPUT_VARIABLE _NUMPY_VALUES_OUTPUT
- ERROR_VARIABLE _NUMPY_ERROR_VALUE
- OUTPUT_STRIP_TRAILING_WHITESPACE)
-
-if(NOT _NUMPY_SEARCH_SUCCESS MATCHES 0)
- if(NumPy_FIND_REQUIRED)
- message(FATAL_ERROR
- "NumPy import failure:\n${_NUMPY_ERROR_VALUE}")
- endif()
- set(NUMPY_FOUND FALSE)
- return()
-endif()
-
-# Convert the process output into a list
-string(REGEX REPLACE ";" "\\\\;" _NUMPY_VALUES ${_NUMPY_VALUES_OUTPUT})
-string(REGEX REPLACE "\n" ";" _NUMPY_VALUES ${_NUMPY_VALUES})
-list(GET _NUMPY_VALUES 0 NUMPY_VERSION)
-list(GET _NUMPY_VALUES 1 NUMPY_INCLUDE_DIRS)
-
-string(REGEX MATCH "^[0-9]+\\.[0-9]+\\.[0-9]+" _VER_CHECK "${NUMPY_VERSION}")
-if("${_VER_CHECK}" STREQUAL "")
- # The output from Python was unexpected. Raise an error always
- # here, because we found NumPy, but it appears to be corrupted somehow.
- message(FATAL_ERROR
- "Requested version and include path from NumPy, got instead:\n${_NUMPY_VALUES_OUTPUT}\n")
- return()
-endif()
-
-# Make sure all directory separators are '/'
-string(REGEX REPLACE "\\\\" "/" NUMPY_INCLUDE_DIRS ${NUMPY_INCLUDE_DIRS})
-
-# Get the major and minor version numbers
-string(REGEX REPLACE "\\." ";" _NUMPY_VERSION_LIST ${NUMPY_VERSION})
-list(GET _NUMPY_VERSION_LIST 0 NUMPY_VERSION_MAJOR)
-list(GET _NUMPY_VERSION_LIST 1 NUMPY_VERSION_MINOR)
-list(GET _NUMPY_VERSION_LIST 2 NUMPY_VERSION_PATCH)
-string(REGEX MATCH "[0-9]*" NUMPY_VERSION_PATCH ${NUMPY_VERSION_PATCH})
-math(EXPR NUMPY_VERSION_DECIMAL
- "(${NUMPY_VERSION_MAJOR} * 10000) + (${NUMPY_VERSION_MINOR} * 100) + ${NUMPY_VERSION_PATCH}")
-
-find_package_message(NUMPY
- "Found NumPy: version \"${NUMPY_VERSION}\" ${NUMPY_INCLUDE_DIRS}"
- "${NUMPY_INCLUDE_DIRS}${NUMPY_VERSION}")
-
-set(NUMPY_FOUND TRUE)
-
+# - Find the NumPy libraries
+# This module finds if NumPy is installed, and sets the following variables
+# indicating where it is.
+#
+# TODO: Update to provide the libraries and paths for linking npymath lib.
+#
+# NUMPY_FOUND - was NumPy found
+# NUMPY_VERSION - the version of NumPy found as a string
+# NUMPY_VERSION_MAJOR - the major version number of NumPy
+# NUMPY_VERSION_MINOR - the minor version number of NumPy
+# NUMPY_VERSION_PATCH - the patch version number of NumPy
+# NUMPY_VERSION_DECIMAL - e.g. version 1.6.1 is 10601
+# NUMPY_INCLUDE_DIRS - path to the NumPy include files
+
+#============================================================================
+# Copyright 2012 Continuum Analytics, Inc.
+#
+# MIT License
+#
+# Permission is hereby granted, free of charge, to any person obtaining
+# a copy of this software and associated documentation files
+# (the "Software"), to deal in the Software without restriction, including
+# without limitation the rights to use, copy, modify, merge, publish,
+# distribute, sublicense, and/or sell copies of the Software, and to permit
+# persons to whom the Software is furnished to do so, subject to
+# the following conditions:
+#
+# The above copyright notice and this permission notice shall be included
+# in all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
+# OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+# THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR
+# OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE,
+# ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+# OTHER DEALINGS IN THE SOFTWARE.
+#
+#============================================================================
+
+# Finding NumPy involves calling the Python interpreter
+if(NumPy_FIND_REQUIRED)
+ find_package(PythonInterp REQUIRED)
+else()
+ find_package(PythonInterp)
+endif()
+
+if(NOT PYTHONINTERP_FOUND)
+ set(NUMPY_FOUND FALSE)
+ return()
+endif()
+
+execute_process(COMMAND "${PYTHON_EXECUTABLE}" "-c"
+ "import numpy as n; print(n.__version__); print(n.get_include());"
+ RESULT_VARIABLE _NUMPY_SEARCH_SUCCESS
+ OUTPUT_VARIABLE _NUMPY_VALUES_OUTPUT
+ ERROR_VARIABLE _NUMPY_ERROR_VALUE
+ OUTPUT_STRIP_TRAILING_WHITESPACE)
+
+if(NOT _NUMPY_SEARCH_SUCCESS MATCHES 0)
+ if(NumPy_FIND_REQUIRED)
+ message(FATAL_ERROR
+ "NumPy import failure:\n${_NUMPY_ERROR_VALUE}")
+ endif()
+ set(NUMPY_FOUND FALSE)
+ return()
+endif()
+
+# Convert the process output into a list
+string(REGEX REPLACE ";" "\\\\;" _NUMPY_VALUES ${_NUMPY_VALUES_OUTPUT})
+string(REGEX REPLACE "\n" ";" _NUMPY_VALUES ${_NUMPY_VALUES})
+list(GET _NUMPY_VALUES 0 NUMPY_VERSION)
+list(GET _NUMPY_VALUES 1 NUMPY_INCLUDE_DIRS)
+
+string(REGEX MATCH "^[0-9]+\\.[0-9]+\\.[0-9]+" _VER_CHECK "${NUMPY_VERSION}")
+if("${_VER_CHECK}" STREQUAL "")
+ # The output from Python was unexpected. Raise an error always
+ # here, because we found NumPy, but it appears to be corrupted somehow.
+ message(FATAL_ERROR
+ "Requested version and include path from NumPy, got instead:\n${_NUMPY_VALUES_OUTPUT}\n")
+ return()
+endif()
+
+# Make sure all directory separators are '/'
+string(REGEX REPLACE "\\\\" "/" NUMPY_INCLUDE_DIRS ${NUMPY_INCLUDE_DIRS})
+
+# Get the major and minor version numbers
+string(REGEX REPLACE "\\." ";" _NUMPY_VERSION_LIST ${NUMPY_VERSION})
+list(GET _NUMPY_VERSION_LIST 0 NUMPY_VERSION_MAJOR)
+list(GET _NUMPY_VERSION_LIST 1 NUMPY_VERSION_MINOR)
+list(GET _NUMPY_VERSION_LIST 2 NUMPY_VERSION_PATCH)
+string(REGEX MATCH "[0-9]*" NUMPY_VERSION_PATCH ${NUMPY_VERSION_PATCH})
+math(EXPR NUMPY_VERSION_DECIMAL
+ "(${NUMPY_VERSION_MAJOR} * 10000) + (${NUMPY_VERSION_MINOR} * 100) + ${NUMPY_VERSION_PATCH}")
+
+find_package_message(NUMPY
+ "Found NumPy: version \"${NUMPY_VERSION}\" ${NUMPY_INCLUDE_DIRS}"
+ "${NUMPY_INCLUDE_DIRS}${NUMPY_VERSION}")
+
+set(NUMPY_FOUND TRUE)
+
diff --git a/data/simpleNoise-MissingData.dat b/data/simpleNoise-MissingData.dat
index 839ffb8..00efdb6 100644
--- a/data/simpleNoise-MissingData.dat
+++ b/data/simpleNoise-MissingData.dat
@@ -1,310 +1,310 @@
-[INFO]
-ROAD_RUNNER_VERSION=0.5
-CREATOR=rrWinC-0.1
-NUMBER_OF_COLS=2
-NUMBER_OF_ROWS=150
-COLUMN_HEADERS=time,S1
-
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index 9c134c8..8cdd98d 100644
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diff --git a/data/simpleNoiseWeights.dat b/data/simpleNoiseWeights.dat
index b162696..39954b3 100644
--- a/data/simpleNoiseWeights.dat
+++ b/data/simpleNoiseWeights.dat
@@ -1,310 +1,310 @@
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+150,1
diff --git a/examples/CMakeLists.txt b/examples/CMakeLists.txt
index 416c332..e015444 100644
--- a/examples/CMakeLists.txt
+++ b/examples/CMakeLists.txt
@@ -1,31 +1,31 @@
-cmake_minimum_required(VERSION 2.8)
-PROJECT(rrExamples)
-set(RR_INCLUDE_ROOT "../source")
-
-# rr Includes
-include_directories(${RR_INCLUDE_ROOT})
-include_directories(${THIRD_PARTY_INSTALL_FOLDER}/include)
-include_directories(${THIRD_PARTY_INSTALL_FOLDER}/include/sbml)
-include_directories(${THIRD_PARTY_INSTALL_FOLDER}/include/cvode)
-
-if(${MSVC})
-endif(${MSVC})
-
-set(examples
-one_rr
-#load_model_dll
-)
-
-foreach(example ${examples})
- #add_subdirectory(${example})
-
- FILE (GLOB hdrs ${example}/*.h)
- install (FILES ${hdrs} DESTINATION Examples/${example} COMPONENT example_files)
- FILE (GLOB src ${example}/*.cpp)
- install (FILES ${src} DESTINATION Examples/${example} COMPONENT example_files)
- install (FILES ${example}/Readme.txt DESTINATION Examples/${example} COMPONENT example_files)
- install (FILES ${example}/CMakeLists.txt DESTINATION Examples/${example} COMPONENT example_files)
-endforeach(example)
-
-install (FILES Readme.txt DESTINATION Examples COMPONENT info)
-install (FILES CMakeLists.txt DESTINATION Examples COMPONENT example_files)
+cmake_minimum_required(VERSION 2.8)
+PROJECT(rrExamples)
+set(RR_INCLUDE_ROOT "../source")
+
+# rr Includes
+include_directories(${RR_INCLUDE_ROOT})
+include_directories(${THIRD_PARTY_INSTALL_FOLDER}/include)
+include_directories(${THIRD_PARTY_INSTALL_FOLDER}/include/sbml)
+include_directories(${THIRD_PARTY_INSTALL_FOLDER}/include/cvode)
+
+if(${MSVC})
+endif(${MSVC})
+
+set(examples
+one_rr
+#load_model_dll
+)
+
+foreach(example ${examples})
+ #add_subdirectory(${example})
+
+ FILE (GLOB hdrs ${example}/*.h)
+ install (FILES ${hdrs} DESTINATION Examples/${example} COMPONENT example_files)
+ FILE (GLOB src ${example}/*.cpp)
+ install (FILES ${src} DESTINATION Examples/${example} COMPONENT example_files)
+ install (FILES ${example}/Readme.txt DESTINATION Examples/${example} COMPONENT example_files)
+ install (FILES ${example}/CMakeLists.txt DESTINATION Examples/${example} COMPONENT example_files)
+endforeach(example)
+
+install (FILES Readme.txt DESTINATION Examples COMPONENT info)
+install (FILES CMakeLists.txt DESTINATION Examples COMPONENT example_files)
diff --git a/examples/create_uuid/main.cpp b/examples/create_uuid/main.cpp
index d101e49..c997d9a 100644
--- a/examples/create_uuid/main.cpp
+++ b/examples/create_uuid/main.cpp
@@ -1,22 +1,22 @@
-#pragma hdrstop
-#pragma argsused
-
-#include <iostream>
-#include "Poco/UUIDGenerator.h"
-#include "Poco/UUIDGenerator.h"
-
-using Poco::UUID;
-using Poco::UUIDGenerator;
-
-int main()
-{
- UUIDGenerator& generator = UUIDGenerator::defaultGenerator();
- UUID uuid2(generator.createRandom());
- UUID uuid3(generator.createRandom());
- std::cout << uuid2.toString() << std::endl;
- std::cout << uuid3.toString() << std::endl;
- return 0;
-}
-
-
+#pragma hdrstop
+#pragma argsused
+
+#include <iostream>
+#include "Poco/UUIDGenerator.h"
+#include "Poco/UUIDGenerator.h"
+
+using Poco::UUID;
+using Poco::UUIDGenerator;
+
+int main()
+{
+ UUIDGenerator& generator = UUIDGenerator::defaultGenerator();
+ UUID uuid2(generator.createRandom());
+ UUID uuid3(generator.createRandom());
+ std::cout << uuid2.toString() << std::endl;
+ std::cout << uuid3.toString() << std::endl;
+ return 0;
+}
+
+
#pragma comment(lib, "poco_foundation-static.lib")
\ No newline at end of file
diff --git a/examples/events/feedback.xml b/examples/events/feedback.xml
index 7b8f423..0a80e71 100644
--- a/examples/events/feedback.xml
+++ b/examples/events/feedback.xml
@@ -1,471 +1,471 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<sbml xmlns="http://www.sbml.org/sbml/level2" xmlns:jd2="http://www.sys-bio.org/sbml/jd2" level="2" version="1">
- <model id="feedback" name="Feedback">
- <annotation>
- <jd2:JDesignerLayout xmlns:jd2="http://www.sys-bio.org/sbml/jd2" version="2.0" MajorVersion="2" MinorVersion="3" BuildVersion="45">
- <jd2:header>
- <jd2:VersionHeader JDesignerVersion="1.0"/>
- <jd2:ModelHeader ModelTitle="Feedback"/>
- <jd2:TimeCourseDetails timeStart="0" timeEnd="25" numberOfPoints="200"/>
- </jd2:header>
- <jd2:JDGraphicsHeader BackGroundColor="FFFFFFEF"/>
- <jd2:listOfCompartments>
- <jd2:compartment id="compartment" size="1" visible="false">
- <jd2:boundingBox x="0" y="0" w="0" h="0"/>
- <jd2:membraneStyle thickness="12" color="FF00A5FF"/>
- <jd2:interiorStyle color="FFEEEEFF"/>
- <jd2:text value="compartment" visible="true">
- <jd2:position rx="-31" ry="-16"/>
- <jd2:font fontName="Arial" fontSize="8" fontColor="FF000000"/>
- </jd2:text>
- </jd2:compartment>
- </jd2:listOfCompartments>
- <jd2:listOfSpecies>
- <jd2:species id="S1" boundaryCondition="false" compartment="compartment" initialConcentration="0">
- <jd2:positionLocked value="false"/>
- <jd2:boundingBox x="138" y="104"/>
- <jd2:displayValue visible="false">
- <jd2:position rx="0" ry="0"/>
- <jd2:font fontName="Arial" fontSize="8" fontColor="FF000000"/>
- </jd2:displayValue>
- <jd2:text value="S1" visible="true">
- <jd2:position rx="4" ry="6"/>
- <jd2:font fontName="Arial" fontSize="8" fontColor="FF000000"/>
- </jd2:text>
- <jd2:complex id="DefaultMolecule" w="24" h="24" boundarySpeciesStyle="bsBox" boundaryStyleColor="FF0000FF" captionPosition="npCenter" aliasBoundaryColor="FFFF0000" aliasBoundaryThickness="3">
- <jd2:subunit shape="suRoundSquare">
- <jd2:boundingBox rx="0" ry="0" w="24" h="24"/>
- <jd2:text value="S1" visible="false">
- <jd2:position rx="6" ry="5"/>
- <jd2:font fontName="Arial" fontSize="8" fontColor="FF000000"/>
- </jd2:text>
- <jd2:color scheme="gtHorizLinear" startColor="FFCCFFFF" endColor="FFFFFFFF"/>
- <jd2:edgeStyle color="FF969696" thickness="1" stroke="dsSolid"/>
- </jd2:subunit>
- </jd2:complex>
- </jd2:species>
- <jd2:species id="S2" boundaryCondition="false" compartment="compartment" initialConcentration="0">
- <jd2:positionLocked value="false"/>
- <jd2:boundingBox x="234" y="143"/>
- <jd2:displayValue visible="false">
- <jd2:position rx="0" ry="0"/>
- <jd2:font fontName="Arial" fontSize="8" fontColor="FF000000"/>
- </jd2:displayValue>
- <jd2:text value="S2" visible="true">
- <jd2:position rx="4" ry="6"/>
- <jd2:font fontName="Arial" fontSize="8" fontColor="FF000000"/>
- </jd2:text>
- <jd2:complex id="DefaultMolecule" w="24" h="24" boundarySpeciesStyle="bsBox" boundaryStyleColor="FF0000FF" captionPosition="npCenter" aliasBoundaryColor="FFFF0000" aliasBoundaryThickness="3">
- <jd2:subunit shape="suRoundSquare">
- <jd2:boundingBox rx="0" ry="0" w="24" h="24"/>
- <jd2:text value="S1" visible="false">
- <jd2:position rx="6" ry="5"/>
- <jd2:font fontName="Arial" fontSize="8" fontColor="FF000000"/>
- </jd2:text>
- <jd2:color scheme="gtHorizLinear" startColor="FFCCFFFF" endColor="FFFFFFFF"/>
- <jd2:edgeStyle color="FF969696" thickness="1" stroke="dsSolid"/>
- </jd2:subunit>
- </jd2:complex>
- </jd2:species>
- <jd2:species id="S3" boundaryCondition="false" compartment="compartment" initialConcentration="0">
- <jd2:positionLocked value="false"/>
- <jd2:boundingBox x="318" y="178"/>
- <jd2:displayValue visible="false">
- <jd2:position rx="0" ry="0"/>
- <jd2:font fontName="Arial" fontSize="8" fontColor="FF000000"/>
- </jd2:displayValue>
- <jd2:text value="S3" visible="true">
- <jd2:position rx="4" ry="6"/>
- <jd2:font fontName="Arial" fontSize="8" fontColor="FF000000"/>
- </jd2:text>
- <jd2:complex id="DefaultMolecule" w="24" h="24" boundarySpeciesStyle="bsBox" boundaryStyleColor="FF0000FF" captionPosition="npCenter" aliasBoundaryColor="FFFF0000" aliasBoundaryThickness="3">
- <jd2:subunit shape="suRoundSquare">
- <jd2:boundingBox rx="0" ry="0" w="24" h="24"/>
- <jd2:text value="S1" visible="false">
- <jd2:position rx="6" ry="5"/>
- <jd2:font fontName="Arial" fontSize="8" fontColor="FF000000"/>
- </jd2:text>
- <jd2:color scheme="gtHorizLinear" startColor="FFCCFFFF" endColor="FFFFFFFF"/>
- <jd2:edgeStyle color="FF969696" thickness="1" stroke="dsSolid"/>
- </jd2:subunit>
- </jd2:complex>
- </jd2:species>
- <jd2:species id="S4" boundaryCondition="false" compartment="compartment" initialConcentration="0">
- <jd2:positionLocked value="false"/>
- <jd2:boundingBox x="411" y="212"/>
- <jd2:displayValue visible="false">
- <jd2:position rx="0" ry="0"/>
- <jd2:font fontName="Arial" fontSize="8" fontColor="FF000000"/>
- </jd2:displayValue>
- <jd2:text value="S4" visible="true">
- <jd2:position rx="4" ry="6"/>
- <jd2:font fontName="Arial" fontSize="8" fontColor="FF000000"/>
- </jd2:text>
- <jd2:complex id="DefaultMolecule" w="24" h="24" boundarySpeciesStyle="bsBox" boundaryStyleColor="FF0000FF" captionPosition="npCenter" aliasBoundaryColor="FFFF0000" aliasBoundaryThickness="3">
- <jd2:subunit shape="suRoundSquare">
- <jd2:boundingBox rx="0" ry="0" w="24" h="24"/>
- <jd2:text value="S1" visible="false">
- <jd2:position rx="6" ry="5"/>
- <jd2:font fontName="Arial" fontSize="8" fontColor="FF000000"/>
- </jd2:text>
- <jd2:color scheme="gtHorizLinear" startColor="FFCCFFFF" endColor="FFFFFFFF"/>
- <jd2:edgeStyle color="FF969696" thickness="1" stroke="dsSolid"/>
- </jd2:subunit>
- </jd2:complex>
- </jd2:species>
- <jd2:species id="X0" boundaryCondition="true" compartment="compartment" initialConcentration="10">
- <jd2:positionLocked value="false"/>
- <jd2:boundingBox x="33" y="60"/>
- <jd2:displayValue visible="false">
- <jd2:position rx="0" ry="0"/>
- <jd2:font fontName="Arial" fontSize="8" fontColor="FF000000"/>
- </jd2:displayValue>
- <jd2:text value="X0" visible="true">
- <jd2:position rx="4" ry="6"/>
- <jd2:font fontName="Arial" fontSize="8" fontColor="FF000000"/>
- </jd2:text>
- <jd2:complex id="DefaultMolecule" w="24" h="24" boundarySpeciesStyle="bsBox" boundaryStyleColor="FF0000FF" captionPosition="npCenter" aliasBoundaryColor="FFFF0000" aliasBoundaryThickness="3">
- <jd2:subunit shape="suRoundSquare">
- <jd2:boundingBox rx="0" ry="0" w="24" h="24"/>
- <jd2:text value="S1" visible="false">
- <jd2:position rx="6" ry="5"/>
- <jd2:font fontName="Arial" fontSize="8" fontColor="FF000000"/>
- </jd2:text>
- <jd2:color scheme="gtHorizLinear" startColor="FFCCFFFF" endColor="FFFFFFFF"/>
- <jd2:edgeStyle color="FF969696" thickness="1" stroke="dsSolid"/>
- </jd2:subunit>
- </jd2:complex>
- </jd2:species>
- <jd2:species id="X1" boundaryCondition="true" compartment="compartment" initialConcentration="0">
- <jd2:positionLocked value="false"/>
- <jd2:boundingBox x="415" y="292"/>
- <jd2:displayValue visible="false">
- <jd2:position rx="0" ry="0"/>
- <jd2:font fontName="Arial" fontSize="8" fontColor="FF000000"/>
- </jd2:displayValue>
- <jd2:text value="X1" visible="true">
- <jd2:position rx="4" ry="6"/>
- <jd2:font fontName="Arial" fontSize="8" fontColor="FF000000"/>
- </jd2:text>
- <jd2:complex id="DefaultMolecule" w="24" h="24" boundarySpeciesStyle="bsBox" boundaryStyleColor="FF0000FF" captionPosition="npCenter" aliasBoundaryColor="FFFF0000" aliasBoundaryThickness="3">
- <jd2:subunit shape="suRoundSquare">
- <jd2:boundingBox rx="0" ry="0" w="24" h="24"/>
- <jd2:text value="S1" visible="false">
- <jd2:position rx="6" ry="5"/>
- <jd2:font fontName="Arial" fontSize="8" fontColor="FF000000"/>
- </jd2:text>
- <jd2:color scheme="gtHorizLinear" startColor="FFCCFFFF" endColor="FFFFFFFF"/>
- <jd2:edgeStyle color="FF969696" thickness="1" stroke="dsSolid"/>
- </jd2:subunit>
- </jd2:complex>
- </jd2:species>
- </jd2:listOfSpecies>
- <jd2:listOfReactions>
- <jd2:reaction id="J0" reversible="false">
- <jd2:listOfReactants>
- <jd2:speciesReference species="X0" stoichiometry="1"/>
- </jd2:listOfReactants>
- <jd2:listOfProducts>
- <jd2:speciesReference species="S1" stoichiometry="1"/>
- </jd2:listOfProducts>
- <jd2:listOfModifierEdges>
- <jd2:modifierEdge>
- <jd2:speciesReference species="S4"/>
- <jd2:destinationReaction name="J0" regulatorType="rtNegative" relativePosition="0.415929203539823" destinationArcId="0" destinationLineSegmentId="0"/>
- <jd2:display lineThickness="2" lineColor="FF0000FF" lineDashStyle="dsSolid" negativeMarkerStyle="rmBar">
- <jd2:lineType type="ltSegmentedLine">
- <jd2:pt x="423" y="224" type="modifier" speciesRef="S4"/>
- <jd2:pt x="353" y="243"/>
- <jd2:pt x="69" y="127"/>
- <jd2:pt x="84" y="101"/>
- </jd2:lineType>
- </jd2:display>
- </jd2:modifierEdge>
- </jd2:listOfModifierEdges>
- <jd2:kineticLaw type="explicit">
- <jd2:rateEquation value="J0_VM1*(X0-S1/J0_Keq1)/(1+X0+S1+pow(S4,J0_h))"/>
- </jd2:kineticLaw>
- <jd2:display arrowStyle="ar1" arrowFillColor="FF000000" lineColor="FF838464" lineThickness="2">
- <jd2:lineType type="ltLine">
- <jd2:edge>
- <jd2:pt x="45" y="72" type="substrate" speciesRef="X0"/>
- <jd2:pt x="150" y="116" type="product" speciesRef="S1"/>
- </jd2:edge>
- </jd2:lineType>
- </jd2:display>
- </jd2:reaction>
- <jd2:reaction id="J1" reversible="false">
- <jd2:listOfReactants>
- <jd2:speciesReference species="S1" stoichiometry="1"/>
- </jd2:listOfReactants>
- <jd2:listOfProducts>
- <jd2:speciesReference species="S2" stoichiometry="1"/>
- </jd2:listOfProducts>
- <jd2:listOfModifierEdges/>
- <jd2:kineticLaw type="explicit">
- <jd2:rateEquation value="(10*S1-2*S2)/(1+S1+S2)"/>
- </jd2:kineticLaw>
- <jd2:display arrowStyle="ar1" arrowFillColor="FF000000" lineColor="FF838464" lineThickness="2">
- <jd2:lineType type="ltLine">
- <jd2:edge>
- <jd2:pt x="150" y="116" type="substrate" speciesRef="S1"/>
- <jd2:pt x="246" y="155" type="product" speciesRef="S2"/>
- </jd2:edge>
- </jd2:lineType>
- </jd2:display>
- </jd2:reaction>
- <jd2:reaction id="J2" reversible="false">
- <jd2:listOfReactants>
- <jd2:speciesReference species="S2" stoichiometry="1"/>
- </jd2:listOfReactants>
- <jd2:listOfProducts>
- <jd2:speciesReference species="S3" stoichiometry="1"/>
- </jd2:listOfProducts>
- <jd2:listOfModifierEdges/>
- <jd2:kineticLaw type="explicit">
- <jd2:rateEquation value="(10*S2-2*S3)/(1+S2+S3)"/>
- </jd2:kineticLaw>
- <jd2:display arrowStyle="ar1" arrowFillColor="FF000000" lineColor="FF838464" lineThickness="2">
- <jd2:lineType type="ltLine">
- <jd2:edge>
- <jd2:pt x="246" y="155" type="substrate" speciesRef="S2"/>
- <jd2:pt x="330" y="190" type="product" speciesRef="S3"/>
- </jd2:edge>
- </jd2:lineType>
- </jd2:display>
- </jd2:reaction>
- <jd2:reaction id="J3" reversible="false">
- <jd2:listOfReactants>
- <jd2:speciesReference species="S3" stoichiometry="1"/>
- </jd2:listOfReactants>
- <jd2:listOfProducts>
- <jd2:speciesReference species="S4" stoichiometry="1"/>
- </jd2:listOfProducts>
- <jd2:listOfModifierEdges/>
- <jd2:kineticLaw type="explicit">
- <jd2:rateEquation value="(10*S3-2*S4)/(1+S3+S4)"/>
- </jd2:kineticLaw>
- <jd2:display arrowStyle="ar1" arrowFillColor="FF000000" lineColor="FF838464" lineThickness="2">
- <jd2:lineType type="ltLine">
- <jd2:edge>
- <jd2:pt x="330" y="190" type="substrate" speciesRef="S3"/>
- <jd2:pt x="423" y="224" type="product" speciesRef="S4"/>
- </jd2:edge>
- </jd2:lineType>
- </jd2:display>
- </jd2:reaction>
- <jd2:reaction id="J4" reversible="false">
- <jd2:listOfReactants>
- <jd2:speciesReference species="S4" stoichiometry="1"/>
- </jd2:listOfReactants>
- <jd2:listOfProducts>
- <jd2:speciesReference species="X1" stoichiometry="1"/>
- </jd2:listOfProducts>
- <jd2:listOfModifierEdges/>
- <jd2:kineticLaw type="explicit">
- <jd2:rateEquation value="J4_V4*S4/(J4_KS4+S4)"/>
- </jd2:kineticLaw>
- <jd2:display arrowStyle="ar1" arrowFillColor="FF000000" lineColor="FF838464" lineThickness="2">
- <jd2:lineType type="ltLine">
- <jd2:edge>
- <jd2:pt x="423" y="224" type="substrate" speciesRef="S4"/>
- <jd2:pt x="427" y="304" type="product" speciesRef="X1"/>
- </jd2:edge>
- </jd2:lineType>
- </jd2:display>
- </jd2:reaction>
- </jd2:listOfReactions>
- </jd2:JDesignerLayout>
- </annotation>
- <listOfCompartments>
- <compartment id="compartment" size="1"/>
- </listOfCompartments>
- <listOfSpecies>
- <species id="S1" compartment="compartment" initialConcentration="0"/>
- <species id="S2" compartment="compartment" initialConcentration="0"/>
- <species id="S3" compartment="compartment" initialConcentration="0"/>
- <species id="S4" compartment="compartment" initialConcentration="0"/>
- <species id="X0" compartment="compartment" initialConcentration="10" boundaryCondition="true"/>
- <species id="X1" compartment="compartment" initialConcentration="0" boundaryCondition="true"/>
- </listOfSpecies>
- <listOfParameters>
- <parameter id="J0_VM1" value="10"/>
- <parameter id="J0_Keq1" value="10"/>
- <parameter id="J0_h" value="10"/>
- <parameter id="J4_V4" value="2.5"/>
- <parameter id="J4_KS4" value="0.5"/>
- </listOfParameters>
- <listOfReactions>
- <reaction id="J0" reversible="false">
- <listOfReactants>
- <speciesReference species="X0"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="S1"/>
- </listOfProducts>
- <listOfModifiers>
- <modifierSpeciesReference species="S4"/>
- <modifierSpeciesReference species="S4"/>
- </listOfModifiers>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <apply>
- <divide/>
- <apply>
- <times/>
- <ci> J0_VM1 </ci>
- <apply>
- <minus/>
- <ci> X0 </ci>
- <apply>
- <divide/>
- <ci> S1 </ci>
- <ci> J0_Keq1 </ci>
- </apply>
- </apply>
- </apply>
- <apply>
- <plus/>
- <cn type="integer"> 1 </cn>
- <ci> X0 </ci>
- <ci> S1 </ci>
- <apply>
- <power/>
- <ci> S4 </ci>
- <ci> J0_h </ci>
- </apply>
- </apply>
- </apply>
- </math>
- </kineticLaw>
- </reaction>
- <reaction id="J1" reversible="false">
- <listOfReactants>
- <speciesReference species="S1"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="S2"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <apply>
- <divide/>
- <apply>
- <minus/>
- <apply>
- <times/>
- <cn type="integer"> 10 </cn>
- <ci> S1 </ci>
- </apply>
- <apply>
- <times/>
- <cn type="integer"> 2 </cn>
- <ci> S2 </ci>
- </apply>
- </apply>
- <apply>
- <plus/>
- <cn type="integer"> 1 </cn>
- <ci> S1 </ci>
- <ci> S2 </ci>
- </apply>
- </apply>
- </math>
- </kineticLaw>
- </reaction>
- <reaction id="J2" reversible="false">
- <listOfReactants>
- <speciesReference species="S2"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="S3"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <apply>
- <divide/>
- <apply>
- <minus/>
- <apply>
- <times/>
- <cn type="integer"> 10 </cn>
- <ci> S2 </ci>
- </apply>
- <apply>
- <times/>
- <cn type="integer"> 2 </cn>
- <ci> S3 </ci>
- </apply>
- </apply>
- <apply>
- <plus/>
- <cn type="integer"> 1 </cn>
- <ci> S2 </ci>
- <ci> S3 </ci>
- </apply>
- </apply>
- </math>
- </kineticLaw>
- </reaction>
- <reaction id="J3" reversible="false">
- <listOfReactants>
- <speciesReference species="S3"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="S4"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <apply>
- <divide/>
- <apply>
- <minus/>
- <apply>
- <times/>
- <cn type="integer"> 10 </cn>
- <ci> S3 </ci>
- </apply>
- <apply>
- <times/>
- <cn type="integer"> 2 </cn>
- <ci> S4 </ci>
- </apply>
- </apply>
- <apply>
- <plus/>
- <cn type="integer"> 1 </cn>
- <ci> S3 </ci>
- <ci> S4 </ci>
- </apply>
- </apply>
- </math>
- </kineticLaw>
- </reaction>
- <reaction id="J4" reversible="false">
- <listOfReactants>
- <speciesReference species="S4"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="X1"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <apply>
- <divide/>
- <apply>
- <times/>
- <ci> J4_V4 </ci>
- <ci> S4 </ci>
- </apply>
- <apply>
- <plus/>
- <ci> J4_KS4 </ci>
- <ci> S4 </ci>
- </apply>
- </apply>
- </math>
- </kineticLaw>
- </reaction>
- </listOfReactions>
- </model>
-</sbml>
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level2" xmlns:jd2="http://www.sys-bio.org/sbml/jd2" level="2" version="1">
+ <model id="feedback" name="Feedback">
+ <annotation>
+ <jd2:JDesignerLayout xmlns:jd2="http://www.sys-bio.org/sbml/jd2" version="2.0" MajorVersion="2" MinorVersion="3" BuildVersion="45">
+ <jd2:header>
+ <jd2:VersionHeader JDesignerVersion="1.0"/>
+ <jd2:ModelHeader ModelTitle="Feedback"/>
+ <jd2:TimeCourseDetails timeStart="0" timeEnd="25" numberOfPoints="200"/>
+ </jd2:header>
+ <jd2:JDGraphicsHeader BackGroundColor="FFFFFFEF"/>
+ <jd2:listOfCompartments>
+ <jd2:compartment id="compartment" size="1" visible="false">
+ <jd2:boundingBox x="0" y="0" w="0" h="0"/>
+ <jd2:membraneStyle thickness="12" color="FF00A5FF"/>
+ <jd2:interiorStyle color="FFEEEEFF"/>
+ <jd2:text value="compartment" visible="true">
+ <jd2:position rx="-31" ry="-16"/>
+ <jd2:font fontName="Arial" fontSize="8" fontColor="FF000000"/>
+ </jd2:text>
+ </jd2:compartment>
+ </jd2:listOfCompartments>
+ <jd2:listOfSpecies>
+ <jd2:species id="S1" boundaryCondition="false" compartment="compartment" initialConcentration="0">
+ <jd2:positionLocked value="false"/>
+ <jd2:boundingBox x="138" y="104"/>
+ <jd2:displayValue visible="false">
+ <jd2:position rx="0" ry="0"/>
+ <jd2:font fontName="Arial" fontSize="8" fontColor="FF000000"/>
+ </jd2:displayValue>
+ <jd2:text value="S1" visible="true">
+ <jd2:position rx="4" ry="6"/>
+ <jd2:font fontName="Arial" fontSize="8" fontColor="FF000000"/>
+ </jd2:text>
+ <jd2:complex id="DefaultMolecule" w="24" h="24" boundarySpeciesStyle="bsBox" boundaryStyleColor="FF0000FF" captionPosition="npCenter" aliasBoundaryColor="FFFF0000" aliasBoundaryThickness="3">
+ <jd2:subunit shape="suRoundSquare">
+ <jd2:boundingBox rx="0" ry="0" w="24" h="24"/>
+ <jd2:text value="S1" visible="false">
+ <jd2:position rx="6" ry="5"/>
+ <jd2:font fontName="Arial" fontSize="8" fontColor="FF000000"/>
+ </jd2:text>
+ <jd2:color scheme="gtHorizLinear" startColor="FFCCFFFF" endColor="FFFFFFFF"/>
+ <jd2:edgeStyle color="FF969696" thickness="1" stroke="dsSolid"/>
+ </jd2:subunit>
+ </jd2:complex>
+ </jd2:species>
+ <jd2:species id="S2" boundaryCondition="false" compartment="compartment" initialConcentration="0">
+ <jd2:positionLocked value="false"/>
+ <jd2:boundingBox x="234" y="143"/>
+ <jd2:displayValue visible="false">
+ <jd2:position rx="0" ry="0"/>
+ <jd2:font fontName="Arial" fontSize="8" fontColor="FF000000"/>
+ </jd2:displayValue>
+ <jd2:text value="S2" visible="true">
+ <jd2:position rx="4" ry="6"/>
+ <jd2:font fontName="Arial" fontSize="8" fontColor="FF000000"/>
+ </jd2:text>
+ <jd2:complex id="DefaultMolecule" w="24" h="24" boundarySpeciesStyle="bsBox" boundaryStyleColor="FF0000FF" captionPosition="npCenter" aliasBoundaryColor="FFFF0000" aliasBoundaryThickness="3">
+ <jd2:subunit shape="suRoundSquare">
+ <jd2:boundingBox rx="0" ry="0" w="24" h="24"/>
+ <jd2:text value="S1" visible="false">
+ <jd2:position rx="6" ry="5"/>
+ <jd2:font fontName="Arial" fontSize="8" fontColor="FF000000"/>
+ </jd2:text>
+ <jd2:color scheme="gtHorizLinear" startColor="FFCCFFFF" endColor="FFFFFFFF"/>
+ <jd2:edgeStyle color="FF969696" thickness="1" stroke="dsSolid"/>
+ </jd2:subunit>
+ </jd2:complex>
+ </jd2:species>
+ <jd2:species id="S3" boundaryCondition="false" compartment="compartment" initialConcentration="0">
+ <jd2:positionLocked value="false"/>
+ <jd2:boundingBox x="318" y="178"/>
+ <jd2:displayValue visible="false">
+ <jd2:position rx="0" ry="0"/>
+ <jd2:font fontName="Arial" fontSize="8" fontColor="FF000000"/>
+ </jd2:displayValue>
+ <jd2:text value="S3" visible="true">
+ <jd2:position rx="4" ry="6"/>
+ <jd2:font fontName="Arial" fontSize="8" fontColor="FF000000"/>
+ </jd2:text>
+ <jd2:complex id="DefaultMolecule" w="24" h="24" boundarySpeciesStyle="bsBox" boundaryStyleColor="FF0000FF" captionPosition="npCenter" aliasBoundaryColor="FFFF0000" aliasBoundaryThickness="3">
+ <jd2:subunit shape="suRoundSquare">
+ <jd2:boundingBox rx="0" ry="0" w="24" h="24"/>
+ <jd2:text value="S1" visible="false">
+ <jd2:position rx="6" ry="5"/>
+ <jd2:font fontName="Arial" fontSize="8" fontColor="FF000000"/>
+ </jd2:text>
+ <jd2:color scheme="gtHorizLinear" startColor="FFCCFFFF" endColor="FFFFFFFF"/>
+ <jd2:edgeStyle color="FF969696" thickness="1" stroke="dsSolid"/>
+ </jd2:subunit>
+ </jd2:complex>
+ </jd2:species>
+ <jd2:species id="S4" boundaryCondition="false" compartment="compartment" initialConcentration="0">
+ <jd2:positionLocked value="false"/>
+ <jd2:boundingBox x="411" y="212"/>
+ <jd2:displayValue visible="false">
+ <jd2:position rx="0" ry="0"/>
+ <jd2:font fontName="Arial" fontSize="8" fontColor="FF000000"/>
+ </jd2:displayValue>
+ <jd2:text value="S4" visible="true">
+ <jd2:position rx="4" ry="6"/>
+ <jd2:font fontName="Arial" fontSize="8" fontColor="FF000000"/>
+ </jd2:text>
+ <jd2:complex id="DefaultMolecule" w="24" h="24" boundarySpeciesStyle="bsBox" boundaryStyleColor="FF0000FF" captionPosition="npCenter" aliasBoundaryColor="FFFF0000" aliasBoundaryThickness="3">
+ <jd2:subunit shape="suRoundSquare">
+ <jd2:boundingBox rx="0" ry="0" w="24" h="24"/>
+ <jd2:text value="S1" visible="false">
+ <jd2:position rx="6" ry="5"/>
+ <jd2:font fontName="Arial" fontSize="8" fontColor="FF000000"/>
+ </jd2:text>
+ <jd2:color scheme="gtHorizLinear" startColor="FFCCFFFF" endColor="FFFFFFFF"/>
+ <jd2:edgeStyle color="FF969696" thickness="1" stroke="dsSolid"/>
+ </jd2:subunit>
+ </jd2:complex>
+ </jd2:species>
+ <jd2:species id="X0" boundaryCondition="true" compartment="compartment" initialConcentration="10">
+ <jd2:positionLocked value="false"/>
+ <jd2:boundingBox x="33" y="60"/>
+ <jd2:displayValue visible="false">
+ <jd2:position rx="0" ry="0"/>
+ <jd2:font fontName="Arial" fontSize="8" fontColor="FF000000"/>
+ </jd2:displayValue>
+ <jd2:text value="X0" visible="true">
+ <jd2:position rx="4" ry="6"/>
+ <jd2:font fontName="Arial" fontSize="8" fontColor="FF000000"/>
+ </jd2:text>
+ <jd2:complex id="DefaultMolecule" w="24" h="24" boundarySpeciesStyle="bsBox" boundaryStyleColor="FF0000FF" captionPosition="npCenter" aliasBoundaryColor="FFFF0000" aliasBoundaryThickness="3">
+ <jd2:subunit shape="suRoundSquare">
+ <jd2:boundingBox rx="0" ry="0" w="24" h="24"/>
+ <jd2:text value="S1" visible="false">
+ <jd2:position rx="6" ry="5"/>
+ <jd2:font fontName="Arial" fontSize="8" fontColor="FF000000"/>
+ </jd2:text>
+ <jd2:color scheme="gtHorizLinear" startColor="FFCCFFFF" endColor="FFFFFFFF"/>
+ <jd2:edgeStyle color="FF969696" thickness="1" stroke="dsSolid"/>
+ </jd2:subunit>
+ </jd2:complex>
+ </jd2:species>
+ <jd2:species id="X1" boundaryCondition="true" compartment="compartment" initialConcentration="0">
+ <jd2:positionLocked value="false"/>
+ <jd2:boundingBox x="415" y="292"/>
+ <jd2:displayValue visible="false">
+ <jd2:position rx="0" ry="0"/>
+ <jd2:font fontName="Arial" fontSize="8" fontColor="FF000000"/>
+ </jd2:displayValue>
+ <jd2:text value="X1" visible="true">
+ <jd2:position rx="4" ry="6"/>
+ <jd2:font fontName="Arial" fontSize="8" fontColor="FF000000"/>
+ </jd2:text>
+ <jd2:complex id="DefaultMolecule" w="24" h="24" boundarySpeciesStyle="bsBox" boundaryStyleColor="FF0000FF" captionPosition="npCenter" aliasBoundaryColor="FFFF0000" aliasBoundaryThickness="3">
+ <jd2:subunit shape="suRoundSquare">
+ <jd2:boundingBox rx="0" ry="0" w="24" h="24"/>
+ <jd2:text value="S1" visible="false">
+ <jd2:position rx="6" ry="5"/>
+ <jd2:font fontName="Arial" fontSize="8" fontColor="FF000000"/>
+ </jd2:text>
+ <jd2:color scheme="gtHorizLinear" startColor="FFCCFFFF" endColor="FFFFFFFF"/>
+ <jd2:edgeStyle color="FF969696" thickness="1" stroke="dsSolid"/>
+ </jd2:subunit>
+ </jd2:complex>
+ </jd2:species>
+ </jd2:listOfSpecies>
+ <jd2:listOfReactions>
+ <jd2:reaction id="J0" reversible="false">
+ <jd2:listOfReactants>
+ <jd2:speciesReference species="X0" stoichiometry="1"/>
+ </jd2:listOfReactants>
+ <jd2:listOfProducts>
+ <jd2:speciesReference species="S1" stoichiometry="1"/>
+ </jd2:listOfProducts>
+ <jd2:listOfModifierEdges>
+ <jd2:modifierEdge>
+ <jd2:speciesReference species="S4"/>
+ <jd2:destinationReaction name="J0" regulatorType="rtNegative" relativePosition="0.415929203539823" destinationArcId="0" destinationLineSegmentId="0"/>
+ <jd2:display lineThickness="2" lineColor="FF0000FF" lineDashStyle="dsSolid" negativeMarkerStyle="rmBar">
+ <jd2:lineType type="ltSegmentedLine">
+ <jd2:pt x="423" y="224" type="modifier" speciesRef="S4"/>
+ <jd2:pt x="353" y="243"/>
+ <jd2:pt x="69" y="127"/>
+ <jd2:pt x="84" y="101"/>
+ </jd2:lineType>
+ </jd2:display>
+ </jd2:modifierEdge>
+ </jd2:listOfModifierEdges>
+ <jd2:kineticLaw type="explicit">
+ <jd2:rateEquation value="J0_VM1*(X0-S1/J0_Keq1)/(1+X0+S1+pow(S4,J0_h))"/>
+ </jd2:kineticLaw>
+ <jd2:display arrowStyle="ar1" arrowFillColor="FF000000" lineColor="FF838464" lineThickness="2">
+ <jd2:lineType type="ltLine">
+ <jd2:edge>
+ <jd2:pt x="45" y="72" type="substrate" speciesRef="X0"/>
+ <jd2:pt x="150" y="116" type="product" speciesRef="S1"/>
+ </jd2:edge>
+ </jd2:lineType>
+ </jd2:display>
+ </jd2:reaction>
+ <jd2:reaction id="J1" reversible="false">
+ <jd2:listOfReactants>
+ <jd2:speciesReference species="S1" stoichiometry="1"/>
+ </jd2:listOfReactants>
+ <jd2:listOfProducts>
+ <jd2:speciesReference species="S2" stoichiometry="1"/>
+ </jd2:listOfProducts>
+ <jd2:listOfModifierEdges/>
+ <jd2:kineticLaw type="explicit">
+ <jd2:rateEquation value="(10*S1-2*S2)/(1+S1+S2)"/>
+ </jd2:kineticLaw>
+ <jd2:display arrowStyle="ar1" arrowFillColor="FF000000" lineColor="FF838464" lineThickness="2">
+ <jd2:lineType type="ltLine">
+ <jd2:edge>
+ <jd2:pt x="150" y="116" type="substrate" speciesRef="S1"/>
+ <jd2:pt x="246" y="155" type="product" speciesRef="S2"/>
+ </jd2:edge>
+ </jd2:lineType>
+ </jd2:display>
+ </jd2:reaction>
+ <jd2:reaction id="J2" reversible="false">
+ <jd2:listOfReactants>
+ <jd2:speciesReference species="S2" stoichiometry="1"/>
+ </jd2:listOfReactants>
+ <jd2:listOfProducts>
+ <jd2:speciesReference species="S3" stoichiometry="1"/>
+ </jd2:listOfProducts>
+ <jd2:listOfModifierEdges/>
+ <jd2:kineticLaw type="explicit">
+ <jd2:rateEquation value="(10*S2-2*S3)/(1+S2+S3)"/>
+ </jd2:kineticLaw>
+ <jd2:display arrowStyle="ar1" arrowFillColor="FF000000" lineColor="FF838464" lineThickness="2">
+ <jd2:lineType type="ltLine">
+ <jd2:edge>
+ <jd2:pt x="246" y="155" type="substrate" speciesRef="S2"/>
+ <jd2:pt x="330" y="190" type="product" speciesRef="S3"/>
+ </jd2:edge>
+ </jd2:lineType>
+ </jd2:display>
+ </jd2:reaction>
+ <jd2:reaction id="J3" reversible="false">
+ <jd2:listOfReactants>
+ <jd2:speciesReference species="S3" stoichiometry="1"/>
+ </jd2:listOfReactants>
+ <jd2:listOfProducts>
+ <jd2:speciesReference species="S4" stoichiometry="1"/>
+ </jd2:listOfProducts>
+ <jd2:listOfModifierEdges/>
+ <jd2:kineticLaw type="explicit">
+ <jd2:rateEquation value="(10*S3-2*S4)/(1+S3+S4)"/>
+ </jd2:kineticLaw>
+ <jd2:display arrowStyle="ar1" arrowFillColor="FF000000" lineColor="FF838464" lineThickness="2">
+ <jd2:lineType type="ltLine">
+ <jd2:edge>
+ <jd2:pt x="330" y="190" type="substrate" speciesRef="S3"/>
+ <jd2:pt x="423" y="224" type="product" speciesRef="S4"/>
+ </jd2:edge>
+ </jd2:lineType>
+ </jd2:display>
+ </jd2:reaction>
+ <jd2:reaction id="J4" reversible="false">
+ <jd2:listOfReactants>
+ <jd2:speciesReference species="S4" stoichiometry="1"/>
+ </jd2:listOfReactants>
+ <jd2:listOfProducts>
+ <jd2:speciesReference species="X1" stoichiometry="1"/>
+ </jd2:listOfProducts>
+ <jd2:listOfModifierEdges/>
+ <jd2:kineticLaw type="explicit">
+ <jd2:rateEquation value="J4_V4*S4/(J4_KS4+S4)"/>
+ </jd2:kineticLaw>
+ <jd2:display arrowStyle="ar1" arrowFillColor="FF000000" lineColor="FF838464" lineThickness="2">
+ <jd2:lineType type="ltLine">
+ <jd2:edge>
+ <jd2:pt x="423" y="224" type="substrate" speciesRef="S4"/>
+ <jd2:pt x="427" y="304" type="product" speciesRef="X1"/>
+ </jd2:edge>
+ </jd2:lineType>
+ </jd2:display>
+ </jd2:reaction>
+ </jd2:listOfReactions>
+ </jd2:JDesignerLayout>
+ </annotation>
+ <listOfCompartments>
+ <compartment id="compartment" size="1"/>
+ </listOfCompartments>
+ <listOfSpecies>
+ <species id="S1" compartment="compartment" initialConcentration="0"/>
+ <species id="S2" compartment="compartment" initialConcentration="0"/>
+ <species id="S3" compartment="compartment" initialConcentration="0"/>
+ <species id="S4" compartment="compartment" initialConcentration="0"/>
+ <species id="X0" compartment="compartment" initialConcentration="10" boundaryCondition="true"/>
+ <species id="X1" compartment="compartment" initialConcentration="0" boundaryCondition="true"/>
+ </listOfSpecies>
+ <listOfParameters>
+ <parameter id="J0_VM1" value="10"/>
+ <parameter id="J0_Keq1" value="10"/>
+ <parameter id="J0_h" value="10"/>
+ <parameter id="J4_V4" value="2.5"/>
+ <parameter id="J4_KS4" value="0.5"/>
+ </listOfParameters>
+ <listOfReactions>
+ <reaction id="J0" reversible="false">
+ <listOfReactants>
+ <speciesReference species="X0"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="S1"/>
+ </listOfProducts>
+ <listOfModifiers>
+ <modifierSpeciesReference species="S4"/>
+ <modifierSpeciesReference species="S4"/>
+ </listOfModifiers>
+ <kineticLaw>
+ <math xmlns="http://www.w3.org/1998/Math/MathML">
+ <apply>
+ <divide/>
+ <apply>
+ <times/>
+ <ci> J0_VM1 </ci>
+ <apply>
+ <minus/>
+ <ci> X0 </ci>
+ <apply>
+ <divide/>
+ <ci> S1 </ci>
+ <ci> J0_Keq1 </ci>
+ </apply>
+ </apply>
+ </apply>
+ <apply>
+ <plus/>
+ <cn type="integer"> 1 </cn>
+ <ci> X0 </ci>
+ <ci> S1 </ci>
+ <apply>
+ <power/>
+ <ci> S4 </ci>
+ <ci> J0_h </ci>
+ </apply>
+ </apply>
+ </apply>
+ </math>
+ </kineticLaw>
+ </reaction>
+ <reaction id="J1" reversible="false">
+ <listOfReactants>
+ <speciesReference species="S1"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="S2"/>
+ </listOfProducts>
+ <kineticLaw>
+ <math xmlns="http://www.w3.org/1998/Math/MathML">
+ <apply>
+ <divide/>
+ <apply>
+ <minus/>
+ <apply>
+ <times/>
+ <cn type="integer"> 10 </cn>
+ <ci> S1 </ci>
+ </apply>
+ <apply>
+ <times/>
+ <cn type="integer"> 2 </cn>
+ <ci> S2 </ci>
+ </apply>
+ </apply>
+ <apply>
+ <plus/>
+ <cn type="integer"> 1 </cn>
+ <ci> S1 </ci>
+ <ci> S2 </ci>
+ </apply>
+ </apply>
+ </math>
+ </kineticLaw>
+ </reaction>
+ <reaction id="J2" reversible="false">
+ <listOfReactants>
+ <speciesReference species="S2"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="S3"/>
+ </listOfProducts>
+ <kineticLaw>
+ <math xmlns="http://www.w3.org/1998/Math/MathML">
+ <apply>
+ <divide/>
+ <apply>
+ <minus/>
+ <apply>
+ <times/>
+ <cn type="integer"> 10 </cn>
+ <ci> S2 </ci>
+ </apply>
+ <apply>
+ <times/>
+ <cn type="integer"> 2 </cn>
+ <ci> S3 </ci>
+ </apply>
+ </apply>
+ <apply>
+ <plus/>
+ <cn type="integer"> 1 </cn>
+ <ci> S2 </ci>
+ <ci> S3 </ci>
+ </apply>
+ </apply>
+ </math>
+ </kineticLaw>
+ </reaction>
+ <reaction id="J3" reversible="false">
+ <listOfReactants>
+ <speciesReference species="S3"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="S4"/>
+ </listOfProducts>
+ <kineticLaw>
+ <math xmlns="http://www.w3.org/1998/Math/MathML">
+ <apply>
+ <divide/>
+ <apply>
+ <minus/>
+ <apply>
+ <times/>
+ <cn type="integer"> 10 </cn>
+ <ci> S3 </ci>
+ </apply>
+ <apply>
+ <times/>
+ <cn type="integer"> 2 </cn>
+ <ci> S4 </ci>
+ </apply>
+ </apply>
+ <apply>
+ <plus/>
+ <cn type="integer"> 1 </cn>
+ <ci> S3 </ci>
+ <ci> S4 </ci>
+ </apply>
+ </apply>
+ </math>
+ </kineticLaw>
+ </reaction>
+ <reaction id="J4" reversible="false">
+ <listOfReactants>
+ <speciesReference species="S4"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="X1"/>
+ </listOfProducts>
+ <kineticLaw>
+ <math xmlns="http://www.w3.org/1998/Math/MathML">
+ <apply>
+ <divide/>
+ <apply>
+ <times/>
+ <ci> J4_V4 </ci>
+ <ci> S4 </ci>
+ </apply>
+ <apply>
+ <plus/>
+ <ci> J4_KS4 </ci>
+ <ci> S4 </ci>
+ </apply>
+ </apply>
+ </math>
+ </kineticLaw>
+ </reaction>
+ </listOfReactions>
+ </model>
+</sbml>
diff --git a/examples/load_model_dll/CMakeLists.txt b/examples/load_model_dll/CMakeLists.txt
index df0d5f5..6c300e4 100644
--- a/examples/load_model_dll/CMakeLists.txt
+++ b/examples/load_model_dll/CMakeLists.txt
@@ -1,49 +1,49 @@
-cmake_minimum_required(VERSION 2.8)
-set(target load_model_dll)
-
-add_executable(${target}
-main.cpp
-)
-
-add_definitions(
--DPOCO_STATIC
--DSTATIC_PUGI
--DLIBSBML_STATIC
--DSTATIC_RR
--DSTATIC_LIBSTRUCT
--DLIBLAX_STATIC
--DSTATIC_NLEQ
-)
-
-if(WIN32)
-add_definitions(
--DWIN32
-)
-
-target_link_libraries (${target}
-roadrunner-static
-)
-endif()
-
-#Not sure why linux linker need all libraries at linktime?? All symbols 'should' be in roadrunner-static
-if(UNIX)
-target_link_libraries (${target}
-roadrunner-static
-nleq-static.a
-rr-libstruct-static
-lapack
-blas
-f2c
-libsbml-static.a
-xml2
-sundials_nvecserial.a
-sundials_cvode.a
-pthread
-dl
-)
-endif()
-
-
-install (TARGETS ${target}
- DESTINATION bin
- COMPONENT examples)
+cmake_minimum_required(VERSION 2.8)
+set(target load_model_dll)
+
+add_executable(${target}
+main.cpp
+)
+
+add_definitions(
+-DPOCO_STATIC
+-DSTATIC_PUGI
+-DLIBSBML_STATIC
+-DSTATIC_RR
+-DSTATIC_LIBSTRUCT
+-DLIBLAX_STATIC
+-DSTATIC_NLEQ
+)
+
+if(WIN32)
+add_definitions(
+-DWIN32
+)
+
+target_link_libraries (${target}
+roadrunner-static
+)
+endif()
+
+#Not sure why linux linker need all libraries at linktime?? All symbols 'should' be in roadrunner-static
+if(UNIX)
+target_link_libraries (${target}
+roadrunner-static
+nleq-static.a
+rr-libstruct-static
+lapack
+blas
+f2c
+libsbml-static.a
+xml2
+sundials_nvecserial.a
+sundials_cvode.a
+pthread
+dl
+)
+endif()
+
+
+install (TARGETS ${target}
+ DESTINATION bin
+ COMPONENT examples)
diff --git a/examples/load_model_dll/Readme.txt b/examples/load_model_dll/Readme.txt
index 449f52d..52ae6d2 100644
--- a/examples/load_model_dll/Readme.txt
+++ b/examples/load_model_dll/Readme.txt
@@ -1 +1 @@
-This example shows how to use the RoadRunner API to do jobs in Threads.
+This example shows how to use the RoadRunner API to do jobs in Threads.
diff --git a/examples/load_model_dll/main.cpp b/examples/load_model_dll/main.cpp
index ec90389..f58b6fa 100644
--- a/examples/load_model_dll/main.cpp
+++ b/examples/load_model_dll/main.cpp
@@ -1,46 +1,46 @@
-#include <iostream>
-#include "rrRoadRunner.h"
-#include "rrLogger.h"
-#include "rrUtils.h"
-#include "rrException.h"
-
-using namespace rr;
-
-int main(int argc, char** argv)
-{
- try
- {
- const char* rootPath = "..";
-
- gLog.setLevel(lInfo);
- string tmpFolder = joinPath(rootPath, "temp");
-
- const string modelFile = joinPath(rootPath, "models", "test_1.xml");
-
-
- //Load modelFiles..
- Log(lInfo)<<" ---------- LOADING/GENERATING MODEL: "<<modelFile;
-
- RoadRunner rr1("", tmpFolder);
- if(!rr1.load(modelFile)) //This will generate a model DLL
- {
+#include <iostream>
+#include "rrRoadRunner.h"
+#include "rrLogger.h"
+#include "rrUtils.h"
+#include "rrException.h"
+
+using namespace rr;
+
+int main(int argc, char** argv)
+{
+ try
+ {
+ const char* rootPath = "..";
+
+ gLog.setLevel(lInfo);
+ string tmpFolder = joinPath(rootPath, "temp");
+
+ const string modelFile = joinPath(rootPath, "models", "test_1.xml");
+
+
+ //Load modelFiles..
+ Log(lInfo)<<" ---------- LOADING/GENERATING MODEL: "<<modelFile;
+
+ RoadRunner rr1("", tmpFolder);
+ if(!rr1.load(modelFile)) //This will generate a model DLL
+ {
Log(Logger::LOG_ERROR)<<"Failed to create model DLL....";
- return -1;
- }
-
- }
- catch(const Exception& ex)
- {
+ return -1;
+ }
+
+ }
+ catch(const Exception& ex)
+ {
Log(Logger::LOG_ERROR)<<"There was a problem: "<<ex.getMessage();
- }
-
- //Pause(true);
- return 0;
-}
-#if defined(CG_IDE) || defined(MSVS)
-#pragma comment(lib, "roadrunner-static.lib")
-#pragma comment(lib, "poco_foundation-static.lib")
-#pragma comment(lib, "rr-libstruct-static.lib")
-#endif
+ }
+
+ //Pause(true);
+ return 0;
+}
+#if defined(CG_IDE) || defined(MSVS)
+#pragma comment(lib, "roadrunner-static.lib")
+#pragma comment(lib, "poco_foundation-static.lib")
+#pragma comment(lib, "rr-libstruct-static.lib")
+#endif
diff --git a/examples/one_rr/CMakeLists.txt b/examples/one_rr/CMakeLists.txt
index a124d51..352189f 100644
--- a/examples/one_rr/CMakeLists.txt
+++ b/examples/one_rr/CMakeLists.txt
@@ -1,49 +1,49 @@
-cmake_minimum_required(VERSION 2.8)
-set(target one_rr)
-
-add_executable(${target}
-main.cpp
-)
-
-add_definitions(
--DPOCO_STATIC
--DSTATIC_PUGI
--DLIBSBML_STATIC
--DSTATIC_RR
--DSTATIC_LIBSTRUCT
--DLIBLAX_STATIC
--DSTATIC_NLEQ
-)
-
-if(WIN32)
-add_definitions(
--DWIN32
-)
-
-target_link_libraries (${target}
-roadrunner-static
-)
-endif()
-
-#Not sure why linux linker need all libraries at linktime?? All symbols 'should' be in roadrunner-static
-if(UNIX)
-target_link_libraries (${target}
-roadrunner-static
-nleq-static.a
-rr-libstruct-static
-lapack
-blas
-f2c
-libsbml-static.a
-xml2
-sundials_nvecserial.a
-sundials_cvode.a
-pthread
-dl
-)
-endif()
-
-
-install (TARGETS ${target}
- DESTINATION bin
- COMPONENT examples)
+cmake_minimum_required(VERSION 2.8)
+set(target one_rr)
+
+add_executable(${target}
+main.cpp
+)
+
+add_definitions(
+-DPOCO_STATIC
+-DSTATIC_PUGI
+-DLIBSBML_STATIC
+-DSTATIC_RR
+-DSTATIC_LIBSTRUCT
+-DLIBLAX_STATIC
+-DSTATIC_NLEQ
+)
+
+if(WIN32)
+add_definitions(
+-DWIN32
+)
+
+target_link_libraries (${target}
+roadrunner-static
+)
+endif()
+
+#Not sure why linux linker need all libraries at linktime?? All symbols 'should' be in roadrunner-static
+if(UNIX)
+target_link_libraries (${target}
+roadrunner-static
+nleq-static.a
+rr-libstruct-static
+lapack
+blas
+f2c
+libsbml-static.a
+xml2
+sundials_nvecserial.a
+sundials_cvode.a
+pthread
+dl
+)
+endif()
+
+
+install (TARGETS ${target}
+ DESTINATION bin
+ COMPONENT examples)
diff --git a/examples/one_rr/Readme.txt b/examples/one_rr/Readme.txt
index 90c371b..85fe4c2 100644
--- a/examples/one_rr/Readme.txt
+++ b/examples/one_rr/Readme.txt
@@ -1,4 +1,4 @@
-This example shows how to
-1) Create a RoadRunner instance
-2) Simulate a model
-3) Write data to a terminal
+This example shows how to
+1) Create a RoadRunner instance
+2) Simulate a model
+3) Write data to a terminal
diff --git a/examples/one_rr/main.cpp b/examples/one_rr/main.cpp
index b10386f..8d2ba48 100644
--- a/examples/one_rr/main.cpp
+++ b/examples/one_rr/main.cpp
@@ -1,47 +1,47 @@
-#include <iostream>
-#include "rrRoadRunner.h"
-#include "rrException.h"
-#include "rrUtils.h"
-#include "rrLogger.h"
-using namespace rr;
-
-int main(int argc, char** argv)
-{
- const char* rootPath = "..";
-
- try
- {
- gLog.setLevel(lInfo);
- string tmpFolder = joinPath(rootPath, "temp");
-
- const string modelFile = joinPath(rootPath, "models", "test_1.xml");
-
- //Load modelFiles..
- Log(lInfo)<<" ---------- LOADING/GENERATING MODELS ------";
-
- RoadRunner rr1("", tmpFolder);
- LoadSBMLOptions opt;
- opt.modelGeneratorOpt |= LoadSBMLOptions::RECOMPILE;
- if(!rr1.load(modelFile, &opt))
- {
- Log(Logger::LOG_ERROR)<<"There was a problem loading model in file: "<<modelFile;
- throw(Exception("Bad things in loadSBMLFromFile function"));
- }
-
- Log(lInfo)<<" ---------- SIMULATE ---------------------";
-
- rr1.simulate();
- Log(lInfo)<<"Data:"<<*(rr1.getSimulationData());
- }
- catch(const Exception& ex)
- {
-
- Log(Logger::LOG_ERROR)<<"There was a problem: "<<ex.getMessage();
- }
-
- return 0;
-}
-
-
-
-
+#include <iostream>
+#include "rrRoadRunner.h"
+#include "rrException.h"
+#include "rrUtils.h"
+#include "rrLogger.h"
+using namespace rr;
+
+int main(int argc, char** argv)
+{
+ const char* rootPath = "..";
+
+ try
+ {
+ gLog.setLevel(lInfo);
+ string tmpFolder = joinPath(rootPath, "temp");
+
+ const string modelFile = joinPath(rootPath, "models", "test_1.xml");
+
+ //Load modelFiles..
+ Log(lInfo)<<" ---------- LOADING/GENERATING MODELS ------";
+
+ RoadRunner rr1("", tmpFolder);
+ LoadSBMLOptions opt;
+ opt.modelGeneratorOpt |= LoadSBMLOptions::RECOMPILE;
+ if(!rr1.load(modelFile, &opt))
+ {
+ Log(Logger::LOG_ERROR)<<"There was a problem loading model in file: "<<modelFile;
+ throw(Exception("Bad things in loadSBMLFromFile function"));
+ }
+
+ Log(lInfo)<<" ---------- SIMULATE ---------------------";
+
+ rr1.simulate();
+ Log(lInfo)<<"Data:"<<*(rr1.getSimulationData());
+ }
+ catch(const Exception& ex)
+ {
+
+ Log(Logger::LOG_ERROR)<<"There was a problem: "<<ex.getMessage();
+ }
+
+ return 0;
+}
+
+
+
+
diff --git a/examples/two_rrs/CMakeLists.txt b/examples/two_rrs/CMakeLists.txt
index 699d084..419e158 100644
--- a/examples/two_rrs/CMakeLists.txt
+++ b/examples/two_rrs/CMakeLists.txt
@@ -1,49 +1,49 @@
-cmake_minimum_required(VERSION 2.8)
-set(target many_threads)
-
-add_executable( ${target}
-main.cpp
-)
-
-add_definitions(
--DPOCO_STATIC
--DSTATIC_PUGI
--DLIBSBML_STATIC
--DSTATIC_RR
--DSTATIC_LIBSTRUCT
--DLIBLAX_STATIC
--DSTATIC_NLEQ
-)
-
-if(WIN32)
-add_definitions(
--DWIN32
-)
-
-target_link_libraries (${target}
-roadrunner-static
-)
-endif()
-
-#Not sure why linux linker need all libraries at linktime?? All symbols 'should' be in roadrunner-static
-if(UNIX)
-target_link_libraries (${target}
-roadrunner-static
-nleq-static.a
-rr-libstruct-static
-lapack
-blas
-f2c
-libsbml-static.a
-libxml2.so
-sundials_nvecserial.a
-sundials_cvode.a
-pthread
-dl
-)
-endif()
-
-
-install (TARGETS ${target}
- DESTINATION bin
- COMPONENT examples)
+cmake_minimum_required(VERSION 2.8)
+set(target many_threads)
+
+add_executable( ${target}
+main.cpp
+)
+
+add_definitions(
+-DPOCO_STATIC
+-DSTATIC_PUGI
+-DLIBSBML_STATIC
+-DSTATIC_RR
+-DSTATIC_LIBSTRUCT
+-DLIBLAX_STATIC
+-DSTATIC_NLEQ
+)
+
+if(WIN32)
+add_definitions(
+-DWIN32
+)
+
+target_link_libraries (${target}
+roadrunner-static
+)
+endif()
+
+#Not sure why linux linker need all libraries at linktime?? All symbols 'should' be in roadrunner-static
+if(UNIX)
+target_link_libraries (${target}
+roadrunner-static
+nleq-static.a
+rr-libstruct-static
+lapack
+blas
+f2c
+libsbml-static.a
+libxml2.so
+sundials_nvecserial.a
+sundials_cvode.a
+pthread
+dl
+)
+endif()
+
+
+install (TARGETS ${target}
+ DESTINATION bin
+ COMPONENT examples)
diff --git a/examples/two_rrs/Readme.txt b/examples/two_rrs/Readme.txt
index 449f52d..52ae6d2 100644
--- a/examples/two_rrs/Readme.txt
+++ b/examples/two_rrs/Readme.txt
@@ -1 +1 @@
-This example shows how to use the RoadRunner API to do jobs in Threads.
+This example shows how to use the RoadRunner API to do jobs in Threads.
diff --git a/examples/two_rrs/main.cpp b/examples/two_rrs/main.cpp
index 04ace20..9b4443a 100644
--- a/examples/two_rrs/main.cpp
+++ b/examples/two_rrs/main.cpp
@@ -1,49 +1,49 @@
-#include <iostream>
-#include "rrRoadRunner.h"
-#include "rrLogger.h"
-#include "rrUtils.h"
-#include "rrException.h"
-
-using namespace rr;
-
-int main(int argc, char** argv)
-{
-
- try
- {
- LogOutput::mLogToConsole = true;
-
- //Use a list of roadrunners
- const char* rootPath = "..";
-
-// gLog.SetCutOffLogLevel(lDebug1);
- gLog.setLevel(lInfo);
- string tmpFolder = joinPath(rootPath, "temp");
-
- const string modelFile = joinPath(rootPath, "models", "feedback.xml");
-
- //Load modelFiles..
- Log(lInfo)<<" ---------- LOADING/GENERATING MODELS ------";
-
- RoadRunner rr1("", tmpFolder);
- RoadRunner rr2("", tmpFolder);
- rr1.load(modelFile);
- rr2.load(modelFile);
-
- Log(lInfo)<<" ---------- SIMULATE ---------------------";
-
- Log(lInfo)<<"Data:"<<rr1.simulate();
- Log(lInfo)<<"Data:"<<rr2.simulate();
- }
- catch(const Exception& ex)
- {
- Log(Logger::ERROR)<<"There was a problem: "<<ex.getMessage();
- }
-
- //Pause(true);
- return 0;
-}
-
-#pragma comment(lib, "roadrunner.lib")
-#pragma comment(lib, "poco_foundation-static.lib")
-#pragma comment(lib, "rr-libstruct-static.lib")
+#include <iostream>
+#include "rrRoadRunner.h"
+#include "rrLogger.h"
+#include "rrUtils.h"
+#include "rrException.h"
+
+using namespace rr;
+
+int main(int argc, char** argv)
+{
+
+ try
+ {
+ LogOutput::mLogToConsole = true;
+
+ //Use a list of roadrunners
+ const char* rootPath = "..";
+
+// gLog.SetCutOffLogLevel(lDebug1);
+ gLog.setLevel(lInfo);
+ string tmpFolder = joinPath(rootPath, "temp");
+
+ const string modelFile = joinPath(rootPath, "models", "feedback.xml");
+
+ //Load modelFiles..
+ Log(lInfo)<<" ---------- LOADING/GENERATING MODELS ------";
+
+ RoadRunner rr1("", tmpFolder);
+ RoadRunner rr2("", tmpFolder);
+ rr1.load(modelFile);
+ rr2.load(modelFile);
+
+ Log(lInfo)<<" ---------- SIMULATE ---------------------";
+
+ Log(lInfo)<<"Data:"<<rr1.simulate();
+ Log(lInfo)<<"Data:"<<rr2.simulate();
+ }
+ catch(const Exception& ex)
+ {
+ Log(Logger::ERROR)<<"There was a problem: "<<ex.getMessage();
+ }
+
+ //Pause(true);
+ return 0;
+}
+
+#pragma comment(lib, "roadrunner.lib")
+#pragma comment(lib, "poco_foundation-static.lib")
+#pragma comment(lib, "rr-libstruct-static.lib")
diff --git a/models/BorisEJB.xml b/models/BorisEJB.xml
index dd4e675..c4d8eb6 100644
--- a/models/BorisEJB.xml
+++ b/models/BorisEJB.xml
@@ -1,929 +1,929 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!-- Created by XMLPrettyPrinter on 1/25/2011 from JDesigner 2.3.45 -->
-<sbml xmlns = "http://www.sbml.org/sbml/level2" level = "2" version = "1" xmlns:jd2 = "http://www.sys-bio.org/sbml/jd2">
- <!-- -->
- <!-- Model Starts Here -->
- <!-- -->
- <model id = "BorisEJB" name = "BorisEJB">
- <annotation>
- <jd2:JDesignerLayout version = "2.0" MajorVersion = "2" MinorVersion = "3" BuildVersion = "45"
- xmlns:jd2 = "http://www.sys-bio.org/sbml/jd2">
- <jd2:header>
- <jd2:VersionHeader JDesignerVersion = "1.0"/>
- <jd2:ModelHeader Author = "" ModelVersion = "" ModelTitle = "BorisEJB"/>
- <jd2:TimeCourseDetails timeStart = "0" timeEnd = "4000" numberOfPoints = "1000"/>
- </jd2:header>
- <jd2:JDGraphicsHeader BackGroundColor = "FFFFFFEF"/>
- <jd2:listOfCompartments>
- <jd2:compartment id = "compartment" size = "1" visible = "false">
- <jd2:boundingBox x = "0" y = "0" w = "0" h = "0"/>
- <jd2:membraneStyle thickness = "12" color = "FF00A5FF"/>
- <jd2:interiorStyle color = "FFEEEEFF"/>
- <jd2:text value = "compartment" visible = "true">
- <jd2:position rx = "-31" ry = "-16"/>
- <jd2:font fontName = "Arial" fontSize = "8" fontStyle = "" fontColor = "FF000000"/>
- </jd2:text>
- </jd2:compartment>
- </jd2:listOfCompartments>
- <jd2:listOfSpecies>
- <jd2:species id = "MKKK" boundaryCondition = "false" compartment = "compartment" initialConcentration = "90">
- <jd2:positionLocked value = "false"/>
- <jd2:boundingBox x = "41" y = "74"/>
- <jd2:displayValue visible = "false">
- <jd2:position rx = "0" ry = "0"/>
- <jd2:font fontName = "Arial" fontSize = "8" fontColor = "FF000000" fontStyle = ""/>
- </jd2:displayValue>
- <jd2:text value = "MKKK" visible = "true">
- <jd2:position rx = "4" ry = "6"/>
- <jd2:font fontName = "Arial" fontSize = "8" fontStyle = "" fontColor = "FF000000"/>
- </jd2:text>
- <jd2:complex id = "DefaultMolecule" w = "43" h = "24" boundarySpeciesStyle = "bsBox"
- boundaryStyleColor = "FF0000FF" captionPosition = "npCenter" aliasBoundaryColor = "FFFF0000" aliasBoundaryThickness = "3">
- <jd2:subunit shape = "suRoundSquare">
- <jd2:boundingBox rx = "0" ry = "0" w = "43" h = "24"/>
- <jd2:text value = "S1" visible = "false">
- <jd2:position rx = "15" ry = "5"/>
- <jd2:font fontName = "Arial" fontSize = "8" fontColor = "FF000000" fontStyle = ""/>
- </jd2:text>
- <jd2:color scheme = "gtHorizLinear" startColor = "FFCCFFFF" endColor = "FFFFFFFF"/>
- <jd2:edgeStyle color = "FF969696" thickness = "1" stroke = "dsSolid"/>
- </jd2:subunit>
- </jd2:complex>
- </jd2:species>
- <jd2:species id = "MKKK_P" boundaryCondition = "false" compartment = "compartment" initialConcentration = "10">
- <jd2:positionLocked value = "false"/>
- <jd2:boundingBox x = "179" y = "74"/>
- <jd2:displayValue visible = "false">
- <jd2:position rx = "0" ry = "0"/>
- <jd2:font fontName = "Arial" fontSize = "8" fontColor = "FF000000" fontStyle = ""/>
- </jd2:displayValue>
- <jd2:text value = "MKKK_P" visible = "true">
- <jd2:position rx = "3" ry = "6"/>
- <jd2:font fontName = "Arial" fontSize = "8" fontStyle = "" fontColor = "FF000000"/>
- </jd2:text>
- <jd2:complex id = "DefaultMolecule" w = "55" h = "24" boundarySpeciesStyle = "bsBox"
- boundaryStyleColor = "FF0000FF" captionPosition = "npCenter" aliasBoundaryColor = "FFFF0000" aliasBoundaryThickness = "3">
- <jd2:subunit shape = "suRoundSquare">
- <jd2:boundingBox rx = "0" ry = "0" w = "55" h = "24"/>
- <jd2:text value = "S1" visible = "false">
- <jd2:position rx = "21" ry = "5"/>
- <jd2:font fontName = "Arial" fontSize = "8" fontColor = "FF000000" fontStyle = ""/>
- </jd2:text>
- <jd2:color scheme = "gtHorizLinear" startColor = "FFCCFFFF" endColor = "FFFFFFFF"/>
- <jd2:edgeStyle color = "FF969696" thickness = "1" stroke = "dsSolid"/>
- </jd2:subunit>
- </jd2:complex>
- </jd2:species>
- <jd2:species id = "MKK" boundaryCondition = "false" compartment = "compartment" initialConcentration = "280">
- <jd2:positionLocked value = "false"/>
- <jd2:boundingBox x = "78" y = "197"/>
- <jd2:displayValue visible = "false">
- <jd2:position rx = "0" ry = "0"/>
- <jd2:font fontName = "Arial" fontSize = "8" fontColor = "FF000000" fontStyle = ""/>
- </jd2:displayValue>
- <jd2:text value = "MKK" visible = "true">
- <jd2:position rx = "4" ry = "6"/>
- <jd2:font fontName = "Arial" fontSize = "8" fontStyle = "" fontColor = "FF000000"/>
- </jd2:text>
- <jd2:complex id = "DefaultMolecule" w = "36" h = "24" boundarySpeciesStyle = "bsBox"
- boundaryStyleColor = "FF0000FF" captionPosition = "npCenter" aliasBoundaryColor = "FFFF0000" aliasBoundaryThickness = "3">
- <jd2:subunit shape = "suRoundSquare">
- <jd2:boundingBox rx = "0" ry = "0" w = "36" h = "24"/>
- <jd2:text value = "S1" visible = "false">
- <jd2:position rx = "12" ry = "5"/>
- <jd2:font fontName = "Arial" fontSize = "8" fontColor = "FF000000" fontStyle = ""/>
- </jd2:text>
- <jd2:color scheme = "gtHorizLinear" startColor = "FFCCFFFF" endColor = "FFFFFFFF"/>
- <jd2:edgeStyle color = "FF969696" thickness = "1" stroke = "dsSolid"/>
- </jd2:subunit>
- </jd2:complex>
- </jd2:species>
- <jd2:species id = "MKK_P" boundaryCondition = "false" compartment = "compartment" initialConcentration = "10">
- <jd2:positionLocked value = "false"/>
- <jd2:boundingBox x = "195" y = "197"/>
- <jd2:displayValue visible = "false">
- <jd2:position rx = "0" ry = "0"/>
- <jd2:font fontName = "Arial" fontSize = "8" fontColor = "FF000000" fontStyle = ""/>
- </jd2:displayValue>
- <jd2:text value = "MKK_P" visible = "true">
- <jd2:position rx = "3" ry = "6"/>
- <jd2:font fontName = "Arial" fontSize = "8" fontStyle = "" fontColor = "FF000000"/>
- </jd2:text>
- <jd2:complex id = "DefaultMolecule" w = "48" h = "24" boundarySpeciesStyle = "bsBox"
- boundaryStyleColor = "FF0000FF" captionPosition = "npCenter" aliasBoundaryColor = "FFFF0000" aliasBoundaryThickness = "3">
- <jd2:subunit shape = "suRoundSquare">
- <jd2:boundingBox rx = "0" ry = "0" w = "48" h = "24"/>
- <jd2:text value = "S1" visible = "false">
- <jd2:position rx = "18" ry = "5"/>
- <jd2:font fontName = "Arial" fontSize = "8" fontColor = "FF000000" fontStyle = ""/>
- </jd2:text>
- <jd2:color scheme = "gtHorizLinear" startColor = "FFCCFFFF" endColor = "FFFFFFFF"/>
- <jd2:edgeStyle color = "FF969696" thickness = "1" stroke = "dsSolid"/>
- </jd2:subunit>
- </jd2:complex>
- </jd2:species>
- <jd2:species id = "MKK_PP" boundaryCondition = "false" compartment = "compartment" initialConcentration = "10">
- <jd2:positionLocked value = "false"/>
- <jd2:boundingBox x = "312" y = "197"/>
- <jd2:displayValue visible = "false">
- <jd2:position rx = "0" ry = "0"/>
- <jd2:font fontName = "Arial" fontSize = "8" fontColor = "FF000000" fontStyle = ""/>
- </jd2:displayValue>
- <jd2:text value = "MKK_PP" visible = "true">
- <jd2:position rx = "3" ry = "6"/>
- <jd2:font fontName = "Arial" fontSize = "8" fontStyle = "" fontColor = "FF000000"/>
- </jd2:text>
- <jd2:complex id = "DefaultMolecule" w = "54" h = "24" boundarySpeciesStyle = "bsBox"
- boundaryStyleColor = "FF0000FF" captionPosition = "npCenter" aliasBoundaryColor = "FFFF0000" aliasBoundaryThickness = "3">
- <jd2:subunit shape = "suRoundSquare">
- <jd2:boundingBox rx = "0" ry = "0" w = "54" h = "24"/>
- <jd2:text value = "S1" visible = "false">
- <jd2:position rx = "21" ry = "5"/>
- <jd2:font fontName = "Arial" fontSize = "8" fontColor = "FF000000" fontStyle = ""/>
- </jd2:text>
- <jd2:color scheme = "gtHorizLinear" startColor = "FFCCFFFF" endColor = "FFFFFFFF"/>
- <jd2:edgeStyle color = "FF969696" thickness = "1" stroke = "dsSolid"/>
- </jd2:subunit>
- </jd2:complex>
- </jd2:species>
- <jd2:species id = "MAPK" boundaryCondition = "false" compartment = "compartment" initialConcentration = "280">
- <jd2:positionLocked value = "false"/>
- <jd2:boundingBox x = "166" y = "318"/>
- <jd2:displayValue visible = "false">
- <jd2:position rx = "0" ry = "0"/>
- <jd2:font fontName = "Arial" fontSize = "8" fontColor = "FF000000" fontStyle = ""/>
- </jd2:displayValue>
- <jd2:text value = "MAPK" visible = "true">
- <jd2:position rx = "4" ry = "6"/>
- <jd2:font fontName = "Arial" fontSize = "8" fontStyle = "" fontColor = "FF000000"/>
- </jd2:text>
- <jd2:complex id = "DefaultMolecule" w = "43" h = "24" boundarySpeciesStyle = "bsBox"
- boundaryStyleColor = "FF0000FF" captionPosition = "npCenter" aliasBoundaryColor = "FFFF0000" aliasBoundaryThickness = "3">
- <jd2:subunit shape = "suRoundSquare">
- <jd2:boundingBox rx = "0" ry = "0" w = "43" h = "24"/>
- <jd2:text value = "S1" visible = "false">
- <jd2:position rx = "15" ry = "5"/>
- <jd2:font fontName = "Arial" fontSize = "8" fontColor = "FF000000" fontStyle = ""/>
- </jd2:text>
- <jd2:color scheme = "gtHorizLinear" startColor = "FFCCFFFF" endColor = "FFFFFFFF"/>
- <jd2:edgeStyle color = "FF969696" thickness = "1" stroke = "dsSolid"/>
- </jd2:subunit>
- </jd2:complex>
- </jd2:species>
- <jd2:species id = "MAPK_P" boundaryCondition = "false" compartment = "compartment" initialConcentration = "10">
- <jd2:positionLocked value = "false"/>
- <jd2:boundingBox x = "326" y = "318"/>
- <jd2:displayValue visible = "false">
- <jd2:position rx = "0" ry = "0"/>
- <jd2:font fontName = "Arial" fontSize = "8" fontColor = "FF000000" fontStyle = ""/>
- </jd2:displayValue>
- <jd2:text value = "MAPK_P" visible = "true">
- <jd2:position rx = "3" ry = "6"/>
- <jd2:font fontName = "Arial" fontSize = "8" fontStyle = "" fontColor = "FF000000"/>
- </jd2:text>
- <jd2:complex id = "DefaultMolecule" w = "55" h = "24" boundarySpeciesStyle = "bsBox"
- boundaryStyleColor = "FF0000FF" captionPosition = "npCenter" aliasBoundaryColor = "FFFF0000" aliasBoundaryThickness = "3">
- <jd2:subunit shape = "suRoundSquare">
- <jd2:boundingBox rx = "0" ry = "0" w = "55" h = "24"/>
- <jd2:text value = "S1" visible = "false">
- <jd2:position rx = "21" ry = "5"/>
- <jd2:font fontName = "Arial" fontSize = "8" fontColor = "FF000000" fontStyle = ""/>
- </jd2:text>
- <jd2:color scheme = "gtHorizLinear" startColor = "FFCCFFFF" endColor = "FFFFFFFF"/>
- <jd2:edgeStyle color = "FF969696" thickness = "1" stroke = "dsSolid"/>
- </jd2:subunit>
- </jd2:complex>
- </jd2:species>
- <jd2:species id = "MAPK_PP" boundaryCondition = "false" compartment = "compartment" initialConcentration = "10">
- <jd2:positionLocked value = "false"/>
- <jd2:boundingBox x = "486" y = "312"/>
- <jd2:displayValue visible = "false">
- <jd2:position rx = "0" ry = "0"/>
- <jd2:font fontName = "Arial" fontSize = "8" fontColor = "FF000000" fontStyle = ""/>
- </jd2:displayValue>
- <jd2:text value = "MAPK_PP" visible = "true">
- <jd2:position rx = "2" ry = "6"/>
- <jd2:font fontName = "Arial" fontSize = "8" fontStyle = "" fontColor = "FF000000"/>
- </jd2:text>
- <jd2:complex id = "DefaultMolecule" w = "61" h = "24" boundarySpeciesStyle = "bsBox"
- boundaryStyleColor = "FF0000FF" captionPosition = "npCenter" aliasBoundaryColor = "FFFF0000" aliasBoundaryThickness = "3">
- <jd2:subunit shape = "suRoundSquare">
- <jd2:boundingBox rx = "0" ry = "0" w = "61" h = "24"/>
- <jd2:text value = "S1" visible = "false">
- <jd2:position rx = "24" ry = "5"/>
- <jd2:font fontName = "Arial" fontSize = "8" fontColor = "FF000000" fontStyle = ""/>
- </jd2:text>
- <jd2:color scheme = "gtHorizLinear" startColor = "FFCCFFFF" endColor = "FFFFFFFF"/>
- <jd2:edgeStyle color = "FF969696" thickness = "1" stroke = "dsSolid"/>
- </jd2:subunit>
- </jd2:complex>
- </jd2:species>
- </jd2:listOfSpecies>
- <jd2:listOfReactions>
- <jd2:reaction id = "J0" reversible = "false">
- <jd2:listOfReactants>
- <jd2:speciesReference species = "MKKK" stoichiometry = "1"/>
- </jd2:listOfReactants>
- <jd2:listOfProducts>
- <jd2:speciesReference species = "MKKK_P" stoichiometry = "1"/>
- </jd2:listOfProducts>
- <jd2:listOfModifierEdges>
- <jd2:modifierEdge>
- <jd2:speciesReference species = "MAPK_PP"/>
- <jd2:destinationReaction name = "J0" regulatorType = "rtNegative" relativePosition = "0.555555555555556" destinationArcId = "0"
- destinationLineSegmentId = "0"/>
- <jd2:display lineThickness = "2" lineColor = "FFFF0000" lineDashStyle = "dsSolid" negativeMarkerStyle = "rmBar">
- <jd2:lineType type = "ltSegmentedLine">
- <jd2:pt x = "516" y = "324" type = "modifier" speciesRef = "MAPK_PP"/>
- <jd2:pt x = "305" y = "11"/>
- <jd2:pt x = "131" y = "11"/>
- <jd2:pt x = "132" y = "35"/>
- </jd2:lineType>
- </jd2:display>
- </jd2:modifierEdge>
- </jd2:listOfModifierEdges>
- <jd2:kineticLaw type = "explicit">
- <jd2:rateEquation value = "J0_V1*MKKK/((1+pow(MAPK_PP/J0_Ki,J0_n))*(J0_K1+MKKK))"/>
- </jd2:kineticLaw>
- <jd2:display arrowStyle = "ar1" arrowFillColor = "FFC0C0C0" lineColor = "FFFF9900" lineThickness = "2">
- <jd2:lineType type = "ltBezier">
- <jd2:edge>
- <jd2:pt x = "62" y = "86" type = "substrate" speciesRef = "MKKK"/>
- <jd2:pt x = "127" y = "34" type = "controlPoint"/>
- <jd2:pt x = "128" y = "34" type = "controlPoint"/>
- <jd2:pt x = "206" y = "86" type = "product" speciesRef = "MKKK_P"/>
- </jd2:edge>
- </jd2:lineType>
- </jd2:display>
- </jd2:reaction>
- <jd2:reaction id = "J1" reversible = "false">
- <jd2:listOfReactants>
- <jd2:speciesReference species = "MKKK_P" stoichiometry = "1"/>
- </jd2:listOfReactants>
- <jd2:listOfProducts>
- <jd2:speciesReference species = "MKKK" stoichiometry = "1"/>
- </jd2:listOfProducts>
- <jd2:listOfModifierEdges/>
- <jd2:kineticLaw type = "explicit">
- <jd2:rateEquation value = "J1_V2*MKKK_P/(J1_KK2+MKKK_P)"/>
- </jd2:kineticLaw>
- <jd2:display arrowStyle = "ar1" arrowFillColor = "FFC0C0C0" lineColor = "FFFF9900" lineThickness = "2">
- <jd2:lineType type = "ltBezier">
- <jd2:edge>
- <jd2:pt x = "206" y = "86" type = "substrate" speciesRef = "MKKK_P"/>
- <jd2:pt x = "131" y = "115" type = "controlPoint"/>
- <jd2:pt x = "131" y = "115" type = "controlPoint"/>
- <jd2:pt x = "62" y = "86" type = "product" speciesRef = "MKKK"/>
- </jd2:edge>
- </jd2:lineType>
- </jd2:display>
- </jd2:reaction>
- <jd2:reaction id = "J2" reversible = "false">
- <jd2:listOfReactants>
- <jd2:speciesReference species = "MKK" stoichiometry = "1"/>
- </jd2:listOfReactants>
- <jd2:listOfProducts>
- <jd2:speciesReference species = "MKK_P" stoichiometry = "1"/>
- </jd2:listOfProducts>
- <jd2:listOfModifierEdges>
- <jd2:modifierEdge>
- <jd2:speciesReference species = "MKKK_P"/>
- <jd2:destinationReaction name = "J2" regulatorType = "rtPositive" relativePosition = "0.577235772357724" destinationArcId = "0"
- destinationLineSegmentId = "0"/>
- <jd2:display lineThickness = "2" lineColor = "FF0000FF" lineDashStyle = "dsSolid" positiveMarkerStyle = "rmEmptyCircle">
- <jd2:lineType type = "ltLine">
- <jd2:pt x = "206" y = "86" type = "modifier" speciesRef = "MKKK_P"/>
- <jd2:pt x = "156" y = "162"/>
- </jd2:lineType>
- </jd2:display>
- </jd2:modifierEdge>
- </jd2:listOfModifierEdges>
- <jd2:kineticLaw type = "explicit">
- <jd2:rateEquation value = "J2_k3*MKKK_P*MKK/(J2_KK3+MKK)"/>
- </jd2:kineticLaw>
- <jd2:display arrowStyle = "ar1" arrowFillColor = "FFC0C0C0" lineColor = "FFFF9900" lineThickness = "2">
- <jd2:lineType type = "ltBezier">
- <jd2:edge>
- <jd2:pt x = "96" y = "209" type = "substrate" speciesRef = "MKK"/>
- <jd2:pt x = "153" y = "163" type = "controlPoint"/>
- <jd2:pt x = "153" y = "163" type = "controlPoint"/>
- <jd2:pt x = "219" y = "209" type = "product" speciesRef = "MKK_P"/>
- </jd2:edge>
- </jd2:lineType>
- </jd2:display>
- </jd2:reaction>
- <jd2:reaction id = "J3" reversible = "false">
- <jd2:listOfReactants>
- <jd2:speciesReference species = "MKK_P" stoichiometry = "1"/>
- </jd2:listOfReactants>
- <jd2:listOfProducts>
- <jd2:speciesReference species = "MKK_PP" stoichiometry = "1"/>
- </jd2:listOfProducts>
- <jd2:listOfModifierEdges>
- <jd2:modifierEdge>
- <jd2:speciesReference species = "MKKK_P"/>
- <jd2:destinationReaction name = "J3" regulatorType = "rtPositive" relativePosition = "0.55" destinationArcId = "0"
- destinationLineSegmentId = "0"/>
- <jd2:display lineThickness = "2" lineColor = "FF0000FF" lineDashStyle = "dsSolid" positiveMarkerStyle = "rmEmptyCircle">
- <jd2:lineType type = "ltLine">
- <jd2:pt x = "206" y = "86" type = "modifier" speciesRef = "MKKK_P"/>
- <jd2:pt x = "271" y = "162"/>
- </jd2:lineType>
- </jd2:display>
- </jd2:modifierEdge>
- </jd2:listOfModifierEdges>
- <jd2:kineticLaw type = "explicit">
- <jd2:rateEquation value = "J3_k4*MKKK_P*MKK_P/(J3_KK4+MKK_P)"/>
- </jd2:kineticLaw>
- <jd2:display arrowStyle = "ar1" arrowFillColor = "FFC0C0C0" lineColor = "FFFF9900" lineThickness = "2">
- <jd2:lineType type = "ltBezier">
- <jd2:edge>
- <jd2:pt x = "219" y = "209" type = "substrate" speciesRef = "MKK_P"/>
- <jd2:pt x = "270" y = "163" type = "controlPoint"/>
- <jd2:pt x = "270" y = "163" type = "controlPoint"/>
- <jd2:pt x = "339" y = "209" type = "product" speciesRef = "MKK_PP"/>
- </jd2:edge>
- </jd2:lineType>
- </jd2:display>
- </jd2:reaction>
- <jd2:reaction id = "J4" reversible = "false">
- <jd2:listOfReactants>
- <jd2:speciesReference species = "MKK_PP" stoichiometry = "1"/>
- </jd2:listOfReactants>
- <jd2:listOfProducts>
- <jd2:speciesReference species = "MKK_P" stoichiometry = "1"/>
- </jd2:listOfProducts>
- <jd2:listOfModifierEdges/>
- <jd2:kineticLaw type = "explicit">
- <jd2:rateEquation value = "J4_V5*MKK_PP/(J4_KK5+MKK_PP)"/>
- </jd2:kineticLaw>
- <jd2:display arrowStyle = "ar1" arrowFillColor = "FFC0C0C0" lineColor = "FFFF9900" lineThickness = "2">
- <jd2:lineType type = "ltBezier">
- <jd2:edge>
- <jd2:pt x = "339" y = "209" type = "substrate" speciesRef = "MKK_PP"/>
- <jd2:pt x = "277" y = "233" type = "controlPoint"/>
- <jd2:pt x = "277" y = "233" type = "controlPoint"/>
- <jd2:pt x = "219" y = "209" type = "product" speciesRef = "MKK_P"/>
- </jd2:edge>
- </jd2:lineType>
- </jd2:display>
- </jd2:reaction>
- <jd2:reaction id = "J5" reversible = "false">
- <jd2:listOfReactants>
- <jd2:speciesReference species = "MKK_P" stoichiometry = "1"/>
- </jd2:listOfReactants>
- <jd2:listOfProducts>
- <jd2:speciesReference species = "MKK" stoichiometry = "1"/>
- </jd2:listOfProducts>
- <jd2:listOfModifierEdges/>
- <jd2:kineticLaw type = "explicit">
- <jd2:rateEquation value = "J5_V6*MKK_P/(J5_KK6+MKK_P)"/>
- </jd2:kineticLaw>
- <jd2:display arrowStyle = "ar1" arrowFillColor = "FFC0C0C0" lineColor = "FFFF9900" lineThickness = "2">
- <jd2:lineType type = "ltBezier">
- <jd2:edge>
- <jd2:pt x = "219" y = "209" type = "substrate" speciesRef = "MKK_P"/>
- <jd2:pt x = "154" y = "233" type = "controlPoint"/>
- <jd2:pt x = "154" y = "233" type = "controlPoint"/>
- <jd2:pt x = "96" y = "209" type = "product" speciesRef = "MKK"/>
- </jd2:edge>
- </jd2:lineType>
- </jd2:display>
- </jd2:reaction>
- <jd2:reaction id = "J6" reversible = "false">
- <jd2:listOfReactants>
- <jd2:speciesReference species = "MAPK" stoichiometry = "1"/>
- </jd2:listOfReactants>
- <jd2:listOfProducts>
- <jd2:speciesReference species = "MAPK_P" stoichiometry = "1"/>
- </jd2:listOfProducts>
- <jd2:listOfModifierEdges>
- <jd2:modifierEdge>
- <jd2:speciesReference species = "MKK_PP"/>
- <jd2:destinationReaction name = "J6" regulatorType = "rtPositive" relativePosition = "0.542168674698795" destinationArcId = "0"
- destinationLineSegmentId = "0"/>
- <jd2:display lineThickness = "2" lineColor = "FF0000FF" lineDashStyle = "dsSolid" positiveMarkerStyle = "rmEmptyCircle">
- <jd2:lineType type = "ltLine">
- <jd2:pt x = "339" y = "209" type = "modifier" speciesRef = "MKK_PP"/>
- <jd2:pt x = "266" y = "283"/>
- </jd2:lineType>
- </jd2:display>
- </jd2:modifierEdge>
- </jd2:listOfModifierEdges>
- <jd2:kineticLaw type = "explicit">
- <jd2:rateEquation value = "J6_k7*MKK_PP*MAPK/(J6_KK7+MAPK)"/>
- </jd2:kineticLaw>
- <jd2:display arrowStyle = "ar1" arrowFillColor = "FFC0C0C0" lineColor = "FFFF9900" lineThickness = "2">
- <jd2:lineType type = "ltBezier">
- <jd2:edge>
- <jd2:pt x = "187" y = "330" type = "substrate" speciesRef = "MAPK"/>
- <jd2:pt x = "266" y = "284" type = "controlPoint"/>
- <jd2:pt x = "266" y = "284" type = "controlPoint"/>
- <jd2:pt x = "353" y = "330" type = "product" speciesRef = "MAPK_P"/>
- </jd2:edge>
- </jd2:lineType>
- </jd2:display>
- </jd2:reaction>
- <jd2:reaction id = "J7" reversible = "false">
- <jd2:listOfReactants>
- <jd2:speciesReference species = "MAPK_P" stoichiometry = "1"/>
- </jd2:listOfReactants>
- <jd2:listOfProducts>
- <jd2:speciesReference species = "MAPK_PP" stoichiometry = "1"/>
- </jd2:listOfProducts>
- <jd2:listOfModifierEdges>
- <jd2:modifierEdge>
- <jd2:speciesReference species = "MKK_PP"/>
- <jd2:destinationReaction name = "J7" regulatorType = "rtPositive" relativePosition = "0.496932515337423" destinationArcId = "0"
- destinationLineSegmentId = "0"/>
- <jd2:display lineThickness = "2" lineColor = "FF0000FF" lineDashStyle = "dsSolid" positiveMarkerStyle = "rmEmptyCircle">
- <jd2:lineType type = "ltLine">
- <jd2:pt x = "339" y = "209" type = "modifier" speciesRef = "MKK_PP"/>
- <jd2:pt x = "421" y = "284"/>
- </jd2:lineType>
- </jd2:display>
- </jd2:modifierEdge>
- </jd2:listOfModifierEdges>
- <jd2:kineticLaw type = "explicit">
- <jd2:rateEquation value = "J7_k8*MKK_PP*MAPK_P/(J7_KK8+MAPK_P)"/>
- </jd2:kineticLaw>
- <jd2:display arrowStyle = "ar1" arrowFillColor = "FFC0C0C0" lineColor = "FFFF9900" lineThickness = "2">
- <jd2:lineType type = "ltBezier">
- <jd2:edge>
- <jd2:pt x = "353" y = "330" type = "substrate" speciesRef = "MAPK_P"/>
- <jd2:pt x = "427" y = "284" type = "controlPoint"/>
- <jd2:pt x = "427" y = "284" type = "controlPoint"/>
- <jd2:pt x = "516" y = "324" type = "product" speciesRef = "MAPK_PP"/>
- </jd2:edge>
- </jd2:lineType>
- </jd2:display>
- </jd2:reaction>
- <jd2:reaction id = "J8" reversible = "false">
- <jd2:listOfReactants>
- <jd2:speciesReference species = "MAPK_PP" stoichiometry = "1"/>
- </jd2:listOfReactants>
- <jd2:listOfProducts>
- <jd2:speciesReference species = "MAPK_P" stoichiometry = "1"/>
- </jd2:listOfProducts>
- <jd2:listOfModifierEdges/>
- <jd2:kineticLaw type = "explicit">
- <jd2:rateEquation value = "J8_V9*MAPK_PP/(J8_KK9+MAPK_PP)"/>
- </jd2:kineticLaw>
- <jd2:display arrowStyle = "ar1" arrowFillColor = "FFC0C0C0" lineColor = "FFFF9900" lineThickness = "2">
- <jd2:lineType type = "ltBezier">
- <jd2:edge>
- <jd2:pt x = "516" y = "324" type = "substrate" speciesRef = "MAPK_PP"/>
- <jd2:pt x = "433" y = "355" type = "controlPoint"/>
- <jd2:pt x = "433" y = "355" type = "controlPoint"/>
- <jd2:pt x = "353" y = "330" type = "product" speciesRef = "MAPK_P"/>
- </jd2:edge>
- </jd2:lineType>
- </jd2:display>
- </jd2:reaction>
- <jd2:reaction id = "J9" reversible = "false">
- <jd2:listOfReactants>
- <jd2:speciesReference species = "MAPK_P" stoichiometry = "1"/>
- </jd2:listOfReactants>
- <jd2:listOfProducts>
- <jd2:speciesReference species = "MAPK" stoichiometry = "1"/>
- </jd2:listOfProducts>
- <jd2:listOfModifierEdges/>
- <jd2:kineticLaw type = "explicit">
- <jd2:rateEquation value = "J9_V10*MAPK_P/(J9_KK10+MAPK_P)"/>
- </jd2:kineticLaw>
- <jd2:display arrowStyle = "ar1" arrowFillColor = "FFC0C0C0" lineColor = "FFFF9900" lineThickness = "2">
- <jd2:lineType type = "ltBezier">
- <jd2:edge>
- <jd2:pt x = "353" y = "330" type = "substrate" speciesRef = "MAPK_P"/>
- <jd2:pt x = "266" y = "349" type = "controlPoint"/>
- <jd2:pt x = "266" y = "349" type = "controlPoint"/>
- <jd2:pt x = "187" y = "330" type = "product" speciesRef = "MAPK"/>
- </jd2:edge>
- </jd2:lineType>
- </jd2:display>
- </jd2:reaction>
- </jd2:listOfReactions>
- </jd2:JDesignerLayout>
- </annotation>
- <listOfCompartments>
- <compartment id = "compartment" size = "1"/>
- </listOfCompartments>
- <listOfSpecies>
- <species id = "MKKK" boundaryCondition = "false" initialConcentration = "90" compartment = "compartment"/>
- <species id = "MKKK_P" boundaryCondition = "false" initialConcentration = "10" compartment = "compartment"/>
- <species id = "MKK" boundaryCondition = "false" initialConcentration = "280" compartment = "compartment"/>
- <species id = "MKK_P" boundaryCondition = "false" initialConcentration = "10" compartment = "compartment"/>
- <species id = "MKK_PP" boundaryCondition = "false" initialConcentration = "10" compartment = "compartment"/>
- <species id = "MAPK" boundaryCondition = "false" initialConcentration = "280" compartment = "compartment"/>
- <species id = "MAPK_P" boundaryCondition = "false" initialConcentration = "10" compartment = "compartment"/>
- <species id = "MAPK_PP" boundaryCondition = "false" initialConcentration = "10" compartment = "compartment"/>
- </listOfSpecies>
- <listOfParameters>
- <parameter id = "J0_V1" value = "2.5"/>
- <parameter id = "J0_Ki" value = "9"/>
- <parameter id = "J0_n" value = "1"/>
- <parameter id = "J0_K1" value = "10"/>
- <parameter id = "J1_V2" value = "0.25"/>
- <parameter id = "J1_KK2" value = "8"/>
- <parameter id = "J2_k3" value = "0.025"/>
- <parameter id = "J2_KK3" value = "15"/>
- <parameter id = "J3_k4" value = "0.025"/>
- <parameter id = "J3_KK4" value = "15"/>
- <parameter id = "J4_V5" value = "0.75"/>
- <parameter id = "J4_KK5" value = "15"/>
- <parameter id = "J5_V6" value = "0.75"/>
- <parameter id = "J5_KK6" value = "15"/>
- <parameter id = "J6_k7" value = "0.025"/>
- <parameter id = "J6_KK7" value = "15"/>
- <parameter id = "J7_k8" value = "0.025"/>
- <parameter id = "J7_KK8" value = "15"/>
- <parameter id = "J8_V9" value = "0.5"/>
- <parameter id = "J8_KK9" value = "15"/>
- <parameter id = "J9_V10" value = "0.5"/>
- <parameter id = "J9_KK10" value = "15"/>
- </listOfParameters>
- <listOfReactions>
- <reaction id = "J0" reversible = "false">
- <listOfReactants>
- <speciesReference species = "MKKK" stoichiometry = "1"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species = "MKKK_P" stoichiometry = "1"/>
- </listOfProducts>
- <listOfModifiers>
- <modifierSpeciesReference species = "MAPK_PP"/>
- </listOfModifiers>
- <kineticLaw>
- <math xmlns = "http://www.w3.org/1998/Math/MathML">
- <apply>
- <divide/>
- <apply>
- <times/>
- <ci>
- J0_V1
- </ci>
- <ci>
- MKKK
- </ci>
- </apply>
- <apply>
- <times/>
- <apply>
- <plus/>
- <cn type = "integer">
- 1
- </cn>
- <apply>
- <power/>
- <apply>
- <divide/>
- <ci>
- MAPK_PP
- </ci>
- <ci>
- J0_Ki
- </ci>
- </apply>
- <ci>
- J0_n
- </ci>
- </apply>
- </apply>
- <apply>
- <plus/>
- <ci>
- J0_K1
- </ci>
- <ci>
- MKKK
- </ci>
- </apply>
- </apply>
- </apply>
- </math>
- </kineticLaw>
- </reaction>
- <reaction id = "J1" reversible = "false">
- <listOfReactants>
- <speciesReference species = "MKKK_P" stoichiometry = "1"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species = "MKKK" stoichiometry = "1"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns = "http://www.w3.org/1998/Math/MathML">
- <apply>
- <divide/>
- <apply>
- <times/>
- <ci>
- J1_V2
- </ci>
- <ci>
- MKKK_P
- </ci>
- </apply>
- <apply>
- <plus/>
- <ci>
- J1_KK2
- </ci>
- <ci>
- MKKK_P
- </ci>
- </apply>
- </apply>
- </math>
- </kineticLaw>
- </reaction>
- <reaction id = "J2" reversible = "false">
- <listOfReactants>
- <speciesReference species = "MKK" stoichiometry = "1"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species = "MKK_P" stoichiometry = "1"/>
- </listOfProducts>
- <listOfModifiers>
- <modifierSpeciesReference species = "MKKK_P"/>
- </listOfModifiers>
- <kineticLaw>
- <math xmlns = "http://www.w3.org/1998/Math/MathML">
- <apply>
- <divide/>
- <apply>
- <times/>
- <ci>
- J2_k3
- </ci>
- <ci>
- MKKK_P
- </ci>
- <ci>
- MKK
- </ci>
- </apply>
- <apply>
- <plus/>
- <ci>
- J2_KK3
- </ci>
- <ci>
- MKK
- </ci>
- </apply>
- </apply>
- </math>
- </kineticLaw>
- </reaction>
- <reaction id = "J3" reversible = "false">
- <listOfReactants>
- <speciesReference species = "MKK_P" stoichiometry = "1"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species = "MKK_PP" stoichiometry = "1"/>
- </listOfProducts>
- <listOfModifiers>
- <modifierSpeciesReference species = "MKKK_P"/>
- </listOfModifiers>
- <kineticLaw>
- <math xmlns = "http://www.w3.org/1998/Math/MathML">
- <apply>
- <divide/>
- <apply>
- <times/>
- <ci>
- J3_k4
- </ci>
- <ci>
- MKKK_P
- </ci>
- <ci>
- MKK_P
- </ci>
- </apply>
- <apply>
- <plus/>
- <ci>
- J3_KK4
- </ci>
- <ci>
- MKK_P
- </ci>
- </apply>
- </apply>
- </math>
- </kineticLaw>
- </reaction>
- <reaction id = "J4" reversible = "false">
- <listOfReactants>
- <speciesReference species = "MKK_PP" stoichiometry = "1"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species = "MKK_P" stoichiometry = "1"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns = "http://www.w3.org/1998/Math/MathML">
- <apply>
- <divide/>
- <apply>
- <times/>
- <ci>
- J4_V5
- </ci>
- <ci>
- MKK_PP
- </ci>
- </apply>
- <apply>
- <plus/>
- <ci>
- J4_KK5
- </ci>
- <ci>
- MKK_PP
- </ci>
- </apply>
- </apply>
- </math>
- </kineticLaw>
- </reaction>
- <reaction id = "J5" reversible = "false">
- <listOfReactants>
- <speciesReference species = "MKK_P" stoichiometry = "1"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species = "MKK" stoichiometry = "1"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns = "http://www.w3.org/1998/Math/MathML">
- <apply>
- <divide/>
- <apply>
- <times/>
- <ci>
- J5_V6
- </ci>
- <ci>
- MKK_P
- </ci>
- </apply>
- <apply>
- <plus/>
- <ci>
- J5_KK6
- </ci>
- <ci>
- MKK_P
- </ci>
- </apply>
- </apply>
- </math>
- </kineticLaw>
- </reaction>
- <reaction id = "J6" reversible = "false">
- <listOfReactants>
- <speciesReference species = "MAPK" stoichiometry = "1"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species = "MAPK_P" stoichiometry = "1"/>
- </listOfProducts>
- <listOfModifiers>
- <modifierSpeciesReference species = "MKK_PP"/>
- </listOfModifiers>
- <kineticLaw>
- <math xmlns = "http://www.w3.org/1998/Math/MathML">
- <apply>
- <divide/>
- <apply>
- <times/>
- <ci>
- J6_k7
- </ci>
- <ci>
- MKK_PP
- </ci>
- <ci>
- MAPK
- </ci>
- </apply>
- <apply>
- <plus/>
- <ci>
- J6_KK7
- </ci>
- <ci>
- MAPK
- </ci>
- </apply>
- </apply>
- </math>
- </kineticLaw>
- </reaction>
- <reaction id = "J7" reversible = "false">
- <listOfReactants>
- <speciesReference species = "MAPK_P" stoichiometry = "1"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species = "MAPK_PP" stoichiometry = "1"/>
- </listOfProducts>
- <listOfModifiers>
- <modifierSpeciesReference species = "MKK_PP"/>
- </listOfModifiers>
- <kineticLaw>
- <math xmlns = "http://www.w3.org/1998/Math/MathML">
- <apply>
- <divide/>
- <apply>
- <times/>
- <ci>
- J7_k8
- </ci>
- <ci>
- MKK_PP
- </ci>
- <ci>
- MAPK_P
- </ci>
- </apply>
- <apply>
- <plus/>
- <ci>
- J7_KK8
- </ci>
- <ci>
- MAPK_P
- </ci>
- </apply>
- </apply>
- </math>
- </kineticLaw>
- </reaction>
- <reaction id = "J8" reversible = "false">
- <listOfReactants>
- <speciesReference species = "MAPK_PP" stoichiometry = "1"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species = "MAPK_P" stoichiometry = "1"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns = "http://www.w3.org/1998/Math/MathML">
- <apply>
- <divide/>
- <apply>
- <times/>
- <ci>
- J8_V9
- </ci>
- <ci>
- MAPK_PP
- </ci>
- </apply>
- <apply>
- <plus/>
- <ci>
- J8_KK9
- </ci>
- <ci>
- MAPK_PP
- </ci>
- </apply>
- </apply>
- </math>
- </kineticLaw>
- </reaction>
- <reaction id = "J9" reversible = "false">
- <listOfReactants>
- <speciesReference species = "MAPK_P" stoichiometry = "1"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species = "MAPK" stoichiometry = "1"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns = "http://www.w3.org/1998/Math/MathML">
- <apply>
- <divide/>
- <apply>
- <times/>
- <ci>
- J9_V10
- </ci>
- <ci>
- MAPK_P
- </ci>
- </apply>
- <apply>
- <plus/>
- <ci>
- J9_KK10
- </ci>
- <ci>
- MAPK_P
- </ci>
- </apply>
- </apply>
- </math>
- </kineticLaw>
- </reaction>
- </listOfReactions>
- </model>
-</sbml>
+<?xml version="1.0" encoding="UTF-8"?>
+<!-- Created by XMLPrettyPrinter on 1/25/2011 from JDesigner 2.3.45 -->
+<sbml xmlns = "http://www.sbml.org/sbml/level2" level = "2" version = "1" xmlns:jd2 = "http://www.sys-bio.org/sbml/jd2">
+ <!-- -->
+ <!-- Model Starts Here -->
+ <!-- -->
+ <model id = "BorisEJB" name = "BorisEJB">
+ <annotation>
+ <jd2:JDesignerLayout version = "2.0" MajorVersion = "2" MinorVersion = "3" BuildVersion = "45"
+ xmlns:jd2 = "http://www.sys-bio.org/sbml/jd2">
+ <jd2:header>
+ <jd2:VersionHeader JDesignerVersion = "1.0"/>
+ <jd2:ModelHeader Author = "" ModelVersion = "" ModelTitle = "BorisEJB"/>
+ <jd2:TimeCourseDetails timeStart = "0" timeEnd = "4000" numberOfPoints = "1000"/>
+ </jd2:header>
+ <jd2:JDGraphicsHeader BackGroundColor = "FFFFFFEF"/>
+ <jd2:listOfCompartments>
+ <jd2:compartment id = "compartment" size = "1" visible = "false">
+ <jd2:boundingBox x = "0" y = "0" w = "0" h = "0"/>
+ <jd2:membraneStyle thickness = "12" color = "FF00A5FF"/>
+ <jd2:interiorStyle color = "FFEEEEFF"/>
+ <jd2:text value = "compartment" visible = "true">
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+ <jd2:font fontName = "Arial" fontSize = "8" fontStyle = "" fontColor = "FF000000"/>
+ </jd2:text>
+ </jd2:compartment>
+ </jd2:listOfCompartments>
+ <jd2:listOfSpecies>
+ <jd2:species id = "MKKK" boundaryCondition = "false" compartment = "compartment" initialConcentration = "90">
+ <jd2:positionLocked value = "false"/>
+ <jd2:boundingBox x = "41" y = "74"/>
+ <jd2:displayValue visible = "false">
+ <jd2:position rx = "0" ry = "0"/>
+ <jd2:font fontName = "Arial" fontSize = "8" fontColor = "FF000000" fontStyle = ""/>
+ </jd2:displayValue>
+ <jd2:text value = "MKKK" visible = "true">
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+ <jd2:font fontName = "Arial" fontSize = "8" fontStyle = "" fontColor = "FF000000"/>
+ </jd2:text>
+ <jd2:complex id = "DefaultMolecule" w = "43" h = "24" boundarySpeciesStyle = "bsBox"
+ boundaryStyleColor = "FF0000FF" captionPosition = "npCenter" aliasBoundaryColor = "FFFF0000" aliasBoundaryThickness = "3">
+ <jd2:subunit shape = "suRoundSquare">
+ <jd2:boundingBox rx = "0" ry = "0" w = "43" h = "24"/>
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+ <jd2:font fontName = "Arial" fontSize = "8" fontColor = "FF000000" fontStyle = ""/>
+ </jd2:text>
+ <jd2:color scheme = "gtHorizLinear" startColor = "FFCCFFFF" endColor = "FFFFFFFF"/>
+ <jd2:edgeStyle color = "FF969696" thickness = "1" stroke = "dsSolid"/>
+ </jd2:subunit>
+ </jd2:complex>
+ </jd2:species>
+ <jd2:species id = "MKKK_P" boundaryCondition = "false" compartment = "compartment" initialConcentration = "10">
+ <jd2:positionLocked value = "false"/>
+ <jd2:boundingBox x = "179" y = "74"/>
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+ <jd2:font fontName = "Arial" fontSize = "8" fontColor = "FF000000" fontStyle = ""/>
+ </jd2:displayValue>
+ <jd2:text value = "MKKK_P" visible = "true">
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+ <jd2:font fontName = "Arial" fontSize = "8" fontStyle = "" fontColor = "FF000000"/>
+ </jd2:text>
+ <jd2:complex id = "DefaultMolecule" w = "55" h = "24" boundarySpeciesStyle = "bsBox"
+ boundaryStyleColor = "FF0000FF" captionPosition = "npCenter" aliasBoundaryColor = "FFFF0000" aliasBoundaryThickness = "3">
+ <jd2:subunit shape = "suRoundSquare">
+ <jd2:boundingBox rx = "0" ry = "0" w = "55" h = "24"/>
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+ <jd2:font fontName = "Arial" fontSize = "8" fontColor = "FF000000" fontStyle = ""/>
+ </jd2:text>
+ <jd2:color scheme = "gtHorizLinear" startColor = "FFCCFFFF" endColor = "FFFFFFFF"/>
+ <jd2:edgeStyle color = "FF969696" thickness = "1" stroke = "dsSolid"/>
+ </jd2:subunit>
+ </jd2:complex>
+ </jd2:species>
+ <jd2:species id = "MKK" boundaryCondition = "false" compartment = "compartment" initialConcentration = "280">
+ <jd2:positionLocked value = "false"/>
+ <jd2:boundingBox x = "78" y = "197"/>
+ <jd2:displayValue visible = "false">
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+ <jd2:font fontName = "Arial" fontSize = "8" fontColor = "FF000000" fontStyle = ""/>
+ </jd2:displayValue>
+ <jd2:text value = "MKK" visible = "true">
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+ <jd2:font fontName = "Arial" fontSize = "8" fontStyle = "" fontColor = "FF000000"/>
+ </jd2:text>
+ <jd2:complex id = "DefaultMolecule" w = "36" h = "24" boundarySpeciesStyle = "bsBox"
+ boundaryStyleColor = "FF0000FF" captionPosition = "npCenter" aliasBoundaryColor = "FFFF0000" aliasBoundaryThickness = "3">
+ <jd2:subunit shape = "suRoundSquare">
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+ <jd2:color scheme = "gtHorizLinear" startColor = "FFCCFFFF" endColor = "FFFFFFFF"/>
+ <jd2:edgeStyle color = "FF969696" thickness = "1" stroke = "dsSolid"/>
+ </jd2:subunit>
+ </jd2:complex>
+ </jd2:species>
+ <jd2:species id = "MKK_P" boundaryCondition = "false" compartment = "compartment" initialConcentration = "10">
+ <jd2:positionLocked value = "false"/>
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+ </jd2:displayValue>
+ <jd2:text value = "MKK_P" visible = "true">
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+ <jd2:font fontName = "Arial" fontSize = "8" fontStyle = "" fontColor = "FF000000"/>
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+ boundaryStyleColor = "FF0000FF" captionPosition = "npCenter" aliasBoundaryColor = "FFFF0000" aliasBoundaryThickness = "3">
+ <jd2:subunit shape = "suRoundSquare">
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+ <jd2:edgeStyle color = "FF969696" thickness = "1" stroke = "dsSolid"/>
+ </jd2:subunit>
+ </jd2:complex>
+ </jd2:species>
+ <jd2:species id = "MKK_PP" boundaryCondition = "false" compartment = "compartment" initialConcentration = "10">
+ <jd2:positionLocked value = "false"/>
+ <jd2:boundingBox x = "312" y = "197"/>
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+ <jd2:text value = "MKK_PP" visible = "true">
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+ <jd2:font fontName = "Arial" fontSize = "8" fontStyle = "" fontColor = "FF000000"/>
+ </jd2:text>
+ <jd2:complex id = "DefaultMolecule" w = "54" h = "24" boundarySpeciesStyle = "bsBox"
+ boundaryStyleColor = "FF0000FF" captionPosition = "npCenter" aliasBoundaryColor = "FFFF0000" aliasBoundaryThickness = "3">
+ <jd2:subunit shape = "suRoundSquare">
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+ <jd2:font fontName = "Arial" fontSize = "8" fontColor = "FF000000" fontStyle = ""/>
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+ <jd2:color scheme = "gtHorizLinear" startColor = "FFCCFFFF" endColor = "FFFFFFFF"/>
+ <jd2:edgeStyle color = "FF969696" thickness = "1" stroke = "dsSolid"/>
+ </jd2:subunit>
+ </jd2:complex>
+ </jd2:species>
+ <jd2:species id = "MAPK" boundaryCondition = "false" compartment = "compartment" initialConcentration = "280">
+ <jd2:positionLocked value = "false"/>
+ <jd2:boundingBox x = "166" y = "318"/>
+ <jd2:displayValue visible = "false">
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+ <jd2:font fontName = "Arial" fontSize = "8" fontColor = "FF000000" fontStyle = ""/>
+ </jd2:displayValue>
+ <jd2:text value = "MAPK" visible = "true">
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+ <jd2:font fontName = "Arial" fontSize = "8" fontStyle = "" fontColor = "FF000000"/>
+ </jd2:text>
+ <jd2:complex id = "DefaultMolecule" w = "43" h = "24" boundarySpeciesStyle = "bsBox"
+ boundaryStyleColor = "FF0000FF" captionPosition = "npCenter" aliasBoundaryColor = "FFFF0000" aliasBoundaryThickness = "3">
+ <jd2:subunit shape = "suRoundSquare">
+ <jd2:boundingBox rx = "0" ry = "0" w = "43" h = "24"/>
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+ <jd2:edgeStyle color = "FF969696" thickness = "1" stroke = "dsSolid"/>
+ </jd2:subunit>
+ </jd2:complex>
+ </jd2:species>
+ <jd2:species id = "MAPK_P" boundaryCondition = "false" compartment = "compartment" initialConcentration = "10">
+ <jd2:positionLocked value = "false"/>
+ <jd2:boundingBox x = "326" y = "318"/>
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+ <jd2:font fontName = "Arial" fontSize = "8" fontColor = "FF000000" fontStyle = ""/>
+ </jd2:displayValue>
+ <jd2:text value = "MAPK_P" visible = "true">
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+ <jd2:font fontName = "Arial" fontSize = "8" fontStyle = "" fontColor = "FF000000"/>
+ </jd2:text>
+ <jd2:complex id = "DefaultMolecule" w = "55" h = "24" boundarySpeciesStyle = "bsBox"
+ boundaryStyleColor = "FF0000FF" captionPosition = "npCenter" aliasBoundaryColor = "FFFF0000" aliasBoundaryThickness = "3">
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+ <jd2:color scheme = "gtHorizLinear" startColor = "FFCCFFFF" endColor = "FFFFFFFF"/>
+ <jd2:edgeStyle color = "FF969696" thickness = "1" stroke = "dsSolid"/>
+ </jd2:subunit>
+ </jd2:complex>
+ </jd2:species>
+ <jd2:species id = "MAPK_PP" boundaryCondition = "false" compartment = "compartment" initialConcentration = "10">
+ <jd2:positionLocked value = "false"/>
+ <jd2:boundingBox x = "486" y = "312"/>
+ <jd2:displayValue visible = "false">
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+ <jd2:font fontName = "Arial" fontSize = "8" fontColor = "FF000000" fontStyle = ""/>
+ </jd2:displayValue>
+ <jd2:text value = "MAPK_PP" visible = "true">
+ <jd2:position rx = "2" ry = "6"/>
+ <jd2:font fontName = "Arial" fontSize = "8" fontStyle = "" fontColor = "FF000000"/>
+ </jd2:text>
+ <jd2:complex id = "DefaultMolecule" w = "61" h = "24" boundarySpeciesStyle = "bsBox"
+ boundaryStyleColor = "FF0000FF" captionPosition = "npCenter" aliasBoundaryColor = "FFFF0000" aliasBoundaryThickness = "3">
+ <jd2:subunit shape = "suRoundSquare">
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+ <jd2:color scheme = "gtHorizLinear" startColor = "FFCCFFFF" endColor = "FFFFFFFF"/>
+ <jd2:edgeStyle color = "FF969696" thickness = "1" stroke = "dsSolid"/>
+ </jd2:subunit>
+ </jd2:complex>
+ </jd2:species>
+ </jd2:listOfSpecies>
+ <jd2:listOfReactions>
+ <jd2:reaction id = "J0" reversible = "false">
+ <jd2:listOfReactants>
+ <jd2:speciesReference species = "MKKK" stoichiometry = "1"/>
+ </jd2:listOfReactants>
+ <jd2:listOfProducts>
+ <jd2:speciesReference species = "MKKK_P" stoichiometry = "1"/>
+ </jd2:listOfProducts>
+ <jd2:listOfModifierEdges>
+ <jd2:modifierEdge>
+ <jd2:speciesReference species = "MAPK_PP"/>
+ <jd2:destinationReaction name = "J0" regulatorType = "rtNegative" relativePosition = "0.555555555555556" destinationArcId = "0"
+ destinationLineSegmentId = "0"/>
+ <jd2:display lineThickness = "2" lineColor = "FFFF0000" lineDashStyle = "dsSolid" negativeMarkerStyle = "rmBar">
+ <jd2:lineType type = "ltSegmentedLine">
+ <jd2:pt x = "516" y = "324" type = "modifier" speciesRef = "MAPK_PP"/>
+ <jd2:pt x = "305" y = "11"/>
+ <jd2:pt x = "131" y = "11"/>
+ <jd2:pt x = "132" y = "35"/>
+ </jd2:lineType>
+ </jd2:display>
+ </jd2:modifierEdge>
+ </jd2:listOfModifierEdges>
+ <jd2:kineticLaw type = "explicit">
+ <jd2:rateEquation value = "J0_V1*MKKK/((1+pow(MAPK_PP/J0_Ki,J0_n))*(J0_K1+MKKK))"/>
+ </jd2:kineticLaw>
+ <jd2:display arrowStyle = "ar1" arrowFillColor = "FFC0C0C0" lineColor = "FFFF9900" lineThickness = "2">
+ <jd2:lineType type = "ltBezier">
+ <jd2:edge>
+ <jd2:pt x = "62" y = "86" type = "substrate" speciesRef = "MKKK"/>
+ <jd2:pt x = "127" y = "34" type = "controlPoint"/>
+ <jd2:pt x = "128" y = "34" type = "controlPoint"/>
+ <jd2:pt x = "206" y = "86" type = "product" speciesRef = "MKKK_P"/>
+ </jd2:edge>
+ </jd2:lineType>
+ </jd2:display>
+ </jd2:reaction>
+ <jd2:reaction id = "J1" reversible = "false">
+ <jd2:listOfReactants>
+ <jd2:speciesReference species = "MKKK_P" stoichiometry = "1"/>
+ </jd2:listOfReactants>
+ <jd2:listOfProducts>
+ <jd2:speciesReference species = "MKKK" stoichiometry = "1"/>
+ </jd2:listOfProducts>
+ <jd2:listOfModifierEdges/>
+ <jd2:kineticLaw type = "explicit">
+ <jd2:rateEquation value = "J1_V2*MKKK_P/(J1_KK2+MKKK_P)"/>
+ </jd2:kineticLaw>
+ <jd2:display arrowStyle = "ar1" arrowFillColor = "FFC0C0C0" lineColor = "FFFF9900" lineThickness = "2">
+ <jd2:lineType type = "ltBezier">
+ <jd2:edge>
+ <jd2:pt x = "206" y = "86" type = "substrate" speciesRef = "MKKK_P"/>
+ <jd2:pt x = "131" y = "115" type = "controlPoint"/>
+ <jd2:pt x = "131" y = "115" type = "controlPoint"/>
+ <jd2:pt x = "62" y = "86" type = "product" speciesRef = "MKKK"/>
+ </jd2:edge>
+ </jd2:lineType>
+ </jd2:display>
+ </jd2:reaction>
+ <jd2:reaction id = "J2" reversible = "false">
+ <jd2:listOfReactants>
+ <jd2:speciesReference species = "MKK" stoichiometry = "1"/>
+ </jd2:listOfReactants>
+ <jd2:listOfProducts>
+ <jd2:speciesReference species = "MKK_P" stoichiometry = "1"/>
+ </jd2:listOfProducts>
+ <jd2:listOfModifierEdges>
+ <jd2:modifierEdge>
+ <jd2:speciesReference species = "MKKK_P"/>
+ <jd2:destinationReaction name = "J2" regulatorType = "rtPositive" relativePosition = "0.577235772357724" destinationArcId = "0"
+ destinationLineSegmentId = "0"/>
+ <jd2:display lineThickness = "2" lineColor = "FF0000FF" lineDashStyle = "dsSolid" positiveMarkerStyle = "rmEmptyCircle">
+ <jd2:lineType type = "ltLine">
+ <jd2:pt x = "206" y = "86" type = "modifier" speciesRef = "MKKK_P"/>
+ <jd2:pt x = "156" y = "162"/>
+ </jd2:lineType>
+ </jd2:display>
+ </jd2:modifierEdge>
+ </jd2:listOfModifierEdges>
+ <jd2:kineticLaw type = "explicit">
+ <jd2:rateEquation value = "J2_k3*MKKK_P*MKK/(J2_KK3+MKK)"/>
+ </jd2:kineticLaw>
+ <jd2:display arrowStyle = "ar1" arrowFillColor = "FFC0C0C0" lineColor = "FFFF9900" lineThickness = "2">
+ <jd2:lineType type = "ltBezier">
+ <jd2:edge>
+ <jd2:pt x = "96" y = "209" type = "substrate" speciesRef = "MKK"/>
+ <jd2:pt x = "153" y = "163" type = "controlPoint"/>
+ <jd2:pt x = "153" y = "163" type = "controlPoint"/>
+ <jd2:pt x = "219" y = "209" type = "product" speciesRef = "MKK_P"/>
+ </jd2:edge>
+ </jd2:lineType>
+ </jd2:display>
+ </jd2:reaction>
+ <jd2:reaction id = "J3" reversible = "false">
+ <jd2:listOfReactants>
+ <jd2:speciesReference species = "MKK_P" stoichiometry = "1"/>
+ </jd2:listOfReactants>
+ <jd2:listOfProducts>
+ <jd2:speciesReference species = "MKK_PP" stoichiometry = "1"/>
+ </jd2:listOfProducts>
+ <jd2:listOfModifierEdges>
+ <jd2:modifierEdge>
+ <jd2:speciesReference species = "MKKK_P"/>
+ <jd2:destinationReaction name = "J3" regulatorType = "rtPositive" relativePosition = "0.55" destinationArcId = "0"
+ destinationLineSegmentId = "0"/>
+ <jd2:display lineThickness = "2" lineColor = "FF0000FF" lineDashStyle = "dsSolid" positiveMarkerStyle = "rmEmptyCircle">
+ <jd2:lineType type = "ltLine">
+ <jd2:pt x = "206" y = "86" type = "modifier" speciesRef = "MKKK_P"/>
+ <jd2:pt x = "271" y = "162"/>
+ </jd2:lineType>
+ </jd2:display>
+ </jd2:modifierEdge>
+ </jd2:listOfModifierEdges>
+ <jd2:kineticLaw type = "explicit">
+ <jd2:rateEquation value = "J3_k4*MKKK_P*MKK_P/(J3_KK4+MKK_P)"/>
+ </jd2:kineticLaw>
+ <jd2:display arrowStyle = "ar1" arrowFillColor = "FFC0C0C0" lineColor = "FFFF9900" lineThickness = "2">
+ <jd2:lineType type = "ltBezier">
+ <jd2:edge>
+ <jd2:pt x = "219" y = "209" type = "substrate" speciesRef = "MKK_P"/>
+ <jd2:pt x = "270" y = "163" type = "controlPoint"/>
+ <jd2:pt x = "270" y = "163" type = "controlPoint"/>
+ <jd2:pt x = "339" y = "209" type = "product" speciesRef = "MKK_PP"/>
+ </jd2:edge>
+ </jd2:lineType>
+ </jd2:display>
+ </jd2:reaction>
+ <jd2:reaction id = "J4" reversible = "false">
+ <jd2:listOfReactants>
+ <jd2:speciesReference species = "MKK_PP" stoichiometry = "1"/>
+ </jd2:listOfReactants>
+ <jd2:listOfProducts>
+ <jd2:speciesReference species = "MKK_P" stoichiometry = "1"/>
+ </jd2:listOfProducts>
+ <jd2:listOfModifierEdges/>
+ <jd2:kineticLaw type = "explicit">
+ <jd2:rateEquation value = "J4_V5*MKK_PP/(J4_KK5+MKK_PP)"/>
+ </jd2:kineticLaw>
+ <jd2:display arrowStyle = "ar1" arrowFillColor = "FFC0C0C0" lineColor = "FFFF9900" lineThickness = "2">
+ <jd2:lineType type = "ltBezier">
+ <jd2:edge>
+ <jd2:pt x = "339" y = "209" type = "substrate" speciesRef = "MKK_PP"/>
+ <jd2:pt x = "277" y = "233" type = "controlPoint"/>
+ <jd2:pt x = "277" y = "233" type = "controlPoint"/>
+ <jd2:pt x = "219" y = "209" type = "product" speciesRef = "MKK_P"/>
+ </jd2:edge>
+ </jd2:lineType>
+ </jd2:display>
+ </jd2:reaction>
+ <jd2:reaction id = "J5" reversible = "false">
+ <jd2:listOfReactants>
+ <jd2:speciesReference species = "MKK_P" stoichiometry = "1"/>
+ </jd2:listOfReactants>
+ <jd2:listOfProducts>
+ <jd2:speciesReference species = "MKK" stoichiometry = "1"/>
+ </jd2:listOfProducts>
+ <jd2:listOfModifierEdges/>
+ <jd2:kineticLaw type = "explicit">
+ <jd2:rateEquation value = "J5_V6*MKK_P/(J5_KK6+MKK_P)"/>
+ </jd2:kineticLaw>
+ <jd2:display arrowStyle = "ar1" arrowFillColor = "FFC0C0C0" lineColor = "FFFF9900" lineThickness = "2">
+ <jd2:lineType type = "ltBezier">
+ <jd2:edge>
+ <jd2:pt x = "219" y = "209" type = "substrate" speciesRef = "MKK_P"/>
+ <jd2:pt x = "154" y = "233" type = "controlPoint"/>
+ <jd2:pt x = "154" y = "233" type = "controlPoint"/>
+ <jd2:pt x = "96" y = "209" type = "product" speciesRef = "MKK"/>
+ </jd2:edge>
+ </jd2:lineType>
+ </jd2:display>
+ </jd2:reaction>
+ <jd2:reaction id = "J6" reversible = "false">
+ <jd2:listOfReactants>
+ <jd2:speciesReference species = "MAPK" stoichiometry = "1"/>
+ </jd2:listOfReactants>
+ <jd2:listOfProducts>
+ <jd2:speciesReference species = "MAPK_P" stoichiometry = "1"/>
+ </jd2:listOfProducts>
+ <jd2:listOfModifierEdges>
+ <jd2:modifierEdge>
+ <jd2:speciesReference species = "MKK_PP"/>
+ <jd2:destinationReaction name = "J6" regulatorType = "rtPositive" relativePosition = "0.542168674698795" destinationArcId = "0"
+ destinationLineSegmentId = "0"/>
+ <jd2:display lineThickness = "2" lineColor = "FF0000FF" lineDashStyle = "dsSolid" positiveMarkerStyle = "rmEmptyCircle">
+ <jd2:lineType type = "ltLine">
+ <jd2:pt x = "339" y = "209" type = "modifier" speciesRef = "MKK_PP"/>
+ <jd2:pt x = "266" y = "283"/>
+ </jd2:lineType>
+ </jd2:display>
+ </jd2:modifierEdge>
+ </jd2:listOfModifierEdges>
+ <jd2:kineticLaw type = "explicit">
+ <jd2:rateEquation value = "J6_k7*MKK_PP*MAPK/(J6_KK7+MAPK)"/>
+ </jd2:kineticLaw>
+ <jd2:display arrowStyle = "ar1" arrowFillColor = "FFC0C0C0" lineColor = "FFFF9900" lineThickness = "2">
+ <jd2:lineType type = "ltBezier">
+ <jd2:edge>
+ <jd2:pt x = "187" y = "330" type = "substrate" speciesRef = "MAPK"/>
+ <jd2:pt x = "266" y = "284" type = "controlPoint"/>
+ <jd2:pt x = "266" y = "284" type = "controlPoint"/>
+ <jd2:pt x = "353" y = "330" type = "product" speciesRef = "MAPK_P"/>
+ </jd2:edge>
+ </jd2:lineType>
+ </jd2:display>
+ </jd2:reaction>
+ <jd2:reaction id = "J7" reversible = "false">
+ <jd2:listOfReactants>
+ <jd2:speciesReference species = "MAPK_P" stoichiometry = "1"/>
+ </jd2:listOfReactants>
+ <jd2:listOfProducts>
+ <jd2:speciesReference species = "MAPK_PP" stoichiometry = "1"/>
+ </jd2:listOfProducts>
+ <jd2:listOfModifierEdges>
+ <jd2:modifierEdge>
+ <jd2:speciesReference species = "MKK_PP"/>
+ <jd2:destinationReaction name = "J7" regulatorType = "rtPositive" relativePosition = "0.496932515337423" destinationArcId = "0"
+ destinationLineSegmentId = "0"/>
+ <jd2:display lineThickness = "2" lineColor = "FF0000FF" lineDashStyle = "dsSolid" positiveMarkerStyle = "rmEmptyCircle">
+ <jd2:lineType type = "ltLine">
+ <jd2:pt x = "339" y = "209" type = "modifier" speciesRef = "MKK_PP"/>
+ <jd2:pt x = "421" y = "284"/>
+ </jd2:lineType>
+ </jd2:display>
+ </jd2:modifierEdge>
+ </jd2:listOfModifierEdges>
+ <jd2:kineticLaw type = "explicit">
+ <jd2:rateEquation value = "J7_k8*MKK_PP*MAPK_P/(J7_KK8+MAPK_P)"/>
+ </jd2:kineticLaw>
+ <jd2:display arrowStyle = "ar1" arrowFillColor = "FFC0C0C0" lineColor = "FFFF9900" lineThickness = "2">
+ <jd2:lineType type = "ltBezier">
+ <jd2:edge>
+ <jd2:pt x = "353" y = "330" type = "substrate" speciesRef = "MAPK_P"/>
+ <jd2:pt x = "427" y = "284" type = "controlPoint"/>
+ <jd2:pt x = "427" y = "284" type = "controlPoint"/>
+ <jd2:pt x = "516" y = "324" type = "product" speciesRef = "MAPK_PP"/>
+ </jd2:edge>
+ </jd2:lineType>
+ </jd2:display>
+ </jd2:reaction>
+ <jd2:reaction id = "J8" reversible = "false">
+ <jd2:listOfReactants>
+ <jd2:speciesReference species = "MAPK_PP" stoichiometry = "1"/>
+ </jd2:listOfReactants>
+ <jd2:listOfProducts>
+ <jd2:speciesReference species = "MAPK_P" stoichiometry = "1"/>
+ </jd2:listOfProducts>
+ <jd2:listOfModifierEdges/>
+ <jd2:kineticLaw type = "explicit">
+ <jd2:rateEquation value = "J8_V9*MAPK_PP/(J8_KK9+MAPK_PP)"/>
+ </jd2:kineticLaw>
+ <jd2:display arrowStyle = "ar1" arrowFillColor = "FFC0C0C0" lineColor = "FFFF9900" lineThickness = "2">
+ <jd2:lineType type = "ltBezier">
+ <jd2:edge>
+ <jd2:pt x = "516" y = "324" type = "substrate" speciesRef = "MAPK_PP"/>
+ <jd2:pt x = "433" y = "355" type = "controlPoint"/>
+ <jd2:pt x = "433" y = "355" type = "controlPoint"/>
+ <jd2:pt x = "353" y = "330" type = "product" speciesRef = "MAPK_P"/>
+ </jd2:edge>
+ </jd2:lineType>
+ </jd2:display>
+ </jd2:reaction>
+ <jd2:reaction id = "J9" reversible = "false">
+ <jd2:listOfReactants>
+ <jd2:speciesReference species = "MAPK_P" stoichiometry = "1"/>
+ </jd2:listOfReactants>
+ <jd2:listOfProducts>
+ <jd2:speciesReference species = "MAPK" stoichiometry = "1"/>
+ </jd2:listOfProducts>
+ <jd2:listOfModifierEdges/>
+ <jd2:kineticLaw type = "explicit">
+ <jd2:rateEquation value = "J9_V10*MAPK_P/(J9_KK10+MAPK_P)"/>
+ </jd2:kineticLaw>
+ <jd2:display arrowStyle = "ar1" arrowFillColor = "FFC0C0C0" lineColor = "FFFF9900" lineThickness = "2">
+ <jd2:lineType type = "ltBezier">
+ <jd2:edge>
+ <jd2:pt x = "353" y = "330" type = "substrate" speciesRef = "MAPK_P"/>
+ <jd2:pt x = "266" y = "349" type = "controlPoint"/>
+ <jd2:pt x = "266" y = "349" type = "controlPoint"/>
+ <jd2:pt x = "187" y = "330" type = "product" speciesRef = "MAPK"/>
+ </jd2:edge>
+ </jd2:lineType>
+ </jd2:display>
+ </jd2:reaction>
+ </jd2:listOfReactions>
+ </jd2:JDesignerLayout>
+ </annotation>
+ <listOfCompartments>
+ <compartment id = "compartment" size = "1"/>
+ </listOfCompartments>
+ <listOfSpecies>
+ <species id = "MKKK" boundaryCondition = "false" initialConcentration = "90" compartment = "compartment"/>
+ <species id = "MKKK_P" boundaryCondition = "false" initialConcentration = "10" compartment = "compartment"/>
+ <species id = "MKK" boundaryCondition = "false" initialConcentration = "280" compartment = "compartment"/>
+ <species id = "MKK_P" boundaryCondition = "false" initialConcentration = "10" compartment = "compartment"/>
+ <species id = "MKK_PP" boundaryCondition = "false" initialConcentration = "10" compartment = "compartment"/>
+ <species id = "MAPK" boundaryCondition = "false" initialConcentration = "280" compartment = "compartment"/>
+ <species id = "MAPK_P" boundaryCondition = "false" initialConcentration = "10" compartment = "compartment"/>
+ <species id = "MAPK_PP" boundaryCondition = "false" initialConcentration = "10" compartment = "compartment"/>
+ </listOfSpecies>
+ <listOfParameters>
+ <parameter id = "J0_V1" value = "2.5"/>
+ <parameter id = "J0_Ki" value = "9"/>
+ <parameter id = "J0_n" value = "1"/>
+ <parameter id = "J0_K1" value = "10"/>
+ <parameter id = "J1_V2" value = "0.25"/>
+ <parameter id = "J1_KK2" value = "8"/>
+ <parameter id = "J2_k3" value = "0.025"/>
+ <parameter id = "J2_KK3" value = "15"/>
+ <parameter id = "J3_k4" value = "0.025"/>
+ <parameter id = "J3_KK4" value = "15"/>
+ <parameter id = "J4_V5" value = "0.75"/>
+ <parameter id = "J4_KK5" value = "15"/>
+ <parameter id = "J5_V6" value = "0.75"/>
+ <parameter id = "J5_KK6" value = "15"/>
+ <parameter id = "J6_k7" value = "0.025"/>
+ <parameter id = "J6_KK7" value = "15"/>
+ <parameter id = "J7_k8" value = "0.025"/>
+ <parameter id = "J7_KK8" value = "15"/>
+ <parameter id = "J8_V9" value = "0.5"/>
+ <parameter id = "J8_KK9" value = "15"/>
+ <parameter id = "J9_V10" value = "0.5"/>
+ <parameter id = "J9_KK10" value = "15"/>
+ </listOfParameters>
+ <listOfReactions>
+ <reaction id = "J0" reversible = "false">
+ <listOfReactants>
+ <speciesReference species = "MKKK" stoichiometry = "1"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species = "MKKK_P" stoichiometry = "1"/>
+ </listOfProducts>
+ <listOfModifiers>
+ <modifierSpeciesReference species = "MAPK_PP"/>
+ </listOfModifiers>
+ <kineticLaw>
+ <math xmlns = "http://www.w3.org/1998/Math/MathML">
+ <apply>
+ <divide/>
+ <apply>
+ <times/>
+ <ci>
+ J0_V1
+ </ci>
+ <ci>
+ MKKK
+ </ci>
+ </apply>
+ <apply>
+ <times/>
+ <apply>
+ <plus/>
+ <cn type = "integer">
+ 1
+ </cn>
+ <apply>
+ <power/>
+ <apply>
+ <divide/>
+ <ci>
+ MAPK_PP
+ </ci>
+ <ci>
+ J0_Ki
+ </ci>
+ </apply>
+ <ci>
+ J0_n
+ </ci>
+ </apply>
+ </apply>
+ <apply>
+ <plus/>
+ <ci>
+ J0_K1
+ </ci>
+ <ci>
+ MKKK
+ </ci>
+ </apply>
+ </apply>
+ </apply>
+ </math>
+ </kineticLaw>
+ </reaction>
+ <reaction id = "J1" reversible = "false">
+ <listOfReactants>
+ <speciesReference species = "MKKK_P" stoichiometry = "1"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species = "MKKK" stoichiometry = "1"/>
+ </listOfProducts>
+ <kineticLaw>
+ <math xmlns = "http://www.w3.org/1998/Math/MathML">
+ <apply>
+ <divide/>
+ <apply>
+ <times/>
+ <ci>
+ J1_V2
+ </ci>
+ <ci>
+ MKKK_P
+ </ci>
+ </apply>
+ <apply>
+ <plus/>
+ <ci>
+ J1_KK2
+ </ci>
+ <ci>
+ MKKK_P
+ </ci>
+ </apply>
+ </apply>
+ </math>
+ </kineticLaw>
+ </reaction>
+ <reaction id = "J2" reversible = "false">
+ <listOfReactants>
+ <speciesReference species = "MKK" stoichiometry = "1"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species = "MKK_P" stoichiometry = "1"/>
+ </listOfProducts>
+ <listOfModifiers>
+ <modifierSpeciesReference species = "MKKK_P"/>
+ </listOfModifiers>
+ <kineticLaw>
+ <math xmlns = "http://www.w3.org/1998/Math/MathML">
+ <apply>
+ <divide/>
+ <apply>
+ <times/>
+ <ci>
+ J2_k3
+ </ci>
+ <ci>
+ MKKK_P
+ </ci>
+ <ci>
+ MKK
+ </ci>
+ </apply>
+ <apply>
+ <plus/>
+ <ci>
+ J2_KK3
+ </ci>
+ <ci>
+ MKK
+ </ci>
+ </apply>
+ </apply>
+ </math>
+ </kineticLaw>
+ </reaction>
+ <reaction id = "J3" reversible = "false">
+ <listOfReactants>
+ <speciesReference species = "MKK_P" stoichiometry = "1"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species = "MKK_PP" stoichiometry = "1"/>
+ </listOfProducts>
+ <listOfModifiers>
+ <modifierSpeciesReference species = "MKKK_P"/>
+ </listOfModifiers>
+ <kineticLaw>
+ <math xmlns = "http://www.w3.org/1998/Math/MathML">
+ <apply>
+ <divide/>
+ <apply>
+ <times/>
+ <ci>
+ J3_k4
+ </ci>
+ <ci>
+ MKKK_P
+ </ci>
+ <ci>
+ MKK_P
+ </ci>
+ </apply>
+ <apply>
+ <plus/>
+ <ci>
+ J3_KK4
+ </ci>
+ <ci>
+ MKK_P
+ </ci>
+ </apply>
+ </apply>
+ </math>
+ </kineticLaw>
+ </reaction>
+ <reaction id = "J4" reversible = "false">
+ <listOfReactants>
+ <speciesReference species = "MKK_PP" stoichiometry = "1"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species = "MKK_P" stoichiometry = "1"/>
+ </listOfProducts>
+ <kineticLaw>
+ <math xmlns = "http://www.w3.org/1998/Math/MathML">
+ <apply>
+ <divide/>
+ <apply>
+ <times/>
+ <ci>
+ J4_V5
+ </ci>
+ <ci>
+ MKK_PP
+ </ci>
+ </apply>
+ <apply>
+ <plus/>
+ <ci>
+ J4_KK5
+ </ci>
+ <ci>
+ MKK_PP
+ </ci>
+ </apply>
+ </apply>
+ </math>
+ </kineticLaw>
+ </reaction>
+ <reaction id = "J5" reversible = "false">
+ <listOfReactants>
+ <speciesReference species = "MKK_P" stoichiometry = "1"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species = "MKK" stoichiometry = "1"/>
+ </listOfProducts>
+ <kineticLaw>
+ <math xmlns = "http://www.w3.org/1998/Math/MathML">
+ <apply>
+ <divide/>
+ <apply>
+ <times/>
+ <ci>
+ J5_V6
+ </ci>
+ <ci>
+ MKK_P
+ </ci>
+ </apply>
+ <apply>
+ <plus/>
+ <ci>
+ J5_KK6
+ </ci>
+ <ci>
+ MKK_P
+ </ci>
+ </apply>
+ </apply>
+ </math>
+ </kineticLaw>
+ </reaction>
+ <reaction id = "J6" reversible = "false">
+ <listOfReactants>
+ <speciesReference species = "MAPK" stoichiometry = "1"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species = "MAPK_P" stoichiometry = "1"/>
+ </listOfProducts>
+ <listOfModifiers>
+ <modifierSpeciesReference species = "MKK_PP"/>
+ </listOfModifiers>
+ <kineticLaw>
+ <math xmlns = "http://www.w3.org/1998/Math/MathML">
+ <apply>
+ <divide/>
+ <apply>
+ <times/>
+ <ci>
+ J6_k7
+ </ci>
+ <ci>
+ MKK_PP
+ </ci>
+ <ci>
+ MAPK
+ </ci>
+ </apply>
+ <apply>
+ <plus/>
+ <ci>
+ J6_KK7
+ </ci>
+ <ci>
+ MAPK
+ </ci>
+ </apply>
+ </apply>
+ </math>
+ </kineticLaw>
+ </reaction>
+ <reaction id = "J7" reversible = "false">
+ <listOfReactants>
+ <speciesReference species = "MAPK_P" stoichiometry = "1"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species = "MAPK_PP" stoichiometry = "1"/>
+ </listOfProducts>
+ <listOfModifiers>
+ <modifierSpeciesReference species = "MKK_PP"/>
+ </listOfModifiers>
+ <kineticLaw>
+ <math xmlns = "http://www.w3.org/1998/Math/MathML">
+ <apply>
+ <divide/>
+ <apply>
+ <times/>
+ <ci>
+ J7_k8
+ </ci>
+ <ci>
+ MKK_PP
+ </ci>
+ <ci>
+ MAPK_P
+ </ci>
+ </apply>
+ <apply>
+ <plus/>
+ <ci>
+ J7_KK8
+ </ci>
+ <ci>
+ MAPK_P
+ </ci>
+ </apply>
+ </apply>
+ </math>
+ </kineticLaw>
+ </reaction>
+ <reaction id = "J8" reversible = "false">
+ <listOfReactants>
+ <speciesReference species = "MAPK_PP" stoichiometry = "1"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species = "MAPK_P" stoichiometry = "1"/>
+ </listOfProducts>
+ <kineticLaw>
+ <math xmlns = "http://www.w3.org/1998/Math/MathML">
+ <apply>
+ <divide/>
+ <apply>
+ <times/>
+ <ci>
+ J8_V9
+ </ci>
+ <ci>
+ MAPK_PP
+ </ci>
+ </apply>
+ <apply>
+ <plus/>
+ <ci>
+ J8_KK9
+ </ci>
+ <ci>
+ MAPK_PP
+ </ci>
+ </apply>
+ </apply>
+ </math>
+ </kineticLaw>
+ </reaction>
+ <reaction id = "J9" reversible = "false">
+ <listOfReactants>
+ <speciesReference species = "MAPK_P" stoichiometry = "1"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species = "MAPK" stoichiometry = "1"/>
+ </listOfProducts>
+ <kineticLaw>
+ <math xmlns = "http://www.w3.org/1998/Math/MathML">
+ <apply>
+ <divide/>
+ <apply>
+ <times/>
+ <ci>
+ J9_V10
+ </ci>
+ <ci>
+ MAPK_P
+ </ci>
+ </apply>
+ <apply>
+ <plus/>
+ <ci>
+ J9_KK10
+ </ci>
+ <ci>
+ MAPK_P
+ </ci>
+ </apply>
+ </apply>
+ </math>
+ </kineticLaw>
+ </reaction>
+ </listOfReactions>
+ </model>
+</sbml>
diff --git a/models/CMakeLists.txt b/models/CMakeLists.txt
index 8521f1a..bbf22ed 100644
--- a/models/CMakeLists.txt
+++ b/models/CMakeLists.txt
@@ -1,24 +1,24 @@
-cmake_minimum_required(VERSION 2.8)
-
-PROJECT(rrModels)
-
-set(models
-README.txt
-bistable.xml
-feedback.xml
-sbml_test_0001.xml
-#ss_threestep.xml
-#ss_threeSpecies.xml
-)
-
-if(BUILD_TESTS)
-add_subdirectory(test_models)
-endif()
-
-install( FILES ${models}
- DESTINATION models
- COMPONENT sbml_models)
-
-install( FILES README.txt
- DESTINATION models
- COMPONENT sbml_models)
+cmake_minimum_required(VERSION 2.8)
+
+PROJECT(rrModels)
+
+set(models
+README.txt
+bistable.xml
+feedback.xml
+sbml_test_0001.xml
+#ss_threestep.xml
+#ss_threeSpecies.xml
+)
+
+if(BUILD_TESTS)
+add_subdirectory(test_models)
+endif()
+
+install( FILES ${models}
+ DESTINATION models
+ COMPONENT sbml_models)
+
+install( FILES README.txt
+ DESTINATION models
+ COMPONENT sbml_models)
diff --git a/models/MinimizationTest_A.xml b/models/MinimizationTest_A.xml
index cb0f1ca..b3e45b8 100644
--- a/models/MinimizationTest_A.xml
+++ b/models/MinimizationTest_A.xml
@@ -1,73 +1,73 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!-- Created by JarnacLite version 1.0.4424.32089 on 2013-05-03 15:46 with libSBML version 5.3.0. -->
-<sbml xmlns="http://www.sbml.org/sbml/level2/version4" level="2" version="4">
- <model id="cell" name="cell">
- <listOfCompartments>
- <compartment id="compartment" size="1" />
- </listOfCompartments>
- <listOfSpecies>
- <species id="x0" compartment="compartment" initialConcentration="1" boundaryCondition="true" />
- <species id="x1" compartment="compartment" initialConcentration="0" boundaryCondition="true" />
- <species id="s1" compartment="compartment" initialConcentration="0" boundaryCondition="false" />
- <species id="s2" compartment="compartment" initialConcentration="0" boundaryCondition="false" />
- </listOfSpecies>
- <listOfParameters>
- <parameter id="k1" value="1.2" constant="true" />
- <parameter id="k2" value="4.5" constant="true" />
- <parameter id="k3" value="3.4" constant="true" />
- </listOfParameters>
- <listOfReactions>
- <reaction id="_J0" reversible="false">
- <listOfReactants>
- <speciesReference species="x0" stoichiometry="1" />
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="s1" stoichiometry="1" />
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <apply>
- <times />
- <ci> k1 </ci>
- <ci> x0 </ci>
- </apply>
- </math>
- </kineticLaw>
- </reaction>
- <reaction id="_J1" reversible="false">
- <listOfReactants>
- <speciesReference species="s1" stoichiometry="1" />
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="s2" stoichiometry="1" />
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <apply>
- <times />
- <ci> k2 </ci>
- <ci> s1 </ci>
- </apply>
- </math>
- </kineticLaw>
- </reaction>
- <reaction id="_J2" reversible="false">
- <listOfReactants>
- <speciesReference species="s2" stoichiometry="1" />
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="x1" stoichiometry="1" />
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <apply>
- <times />
- <ci> k3 </ci>
- <ci> s2 </ci>
- </apply>
- </math>
- </kineticLaw>
- </reaction>
- </listOfReactions>
- </model>
-</sbml>
+<?xml version="1.0" encoding="UTF-8"?>
+<!-- Created by JarnacLite version 1.0.4424.32089 on 2013-05-03 15:46 with libSBML version 5.3.0. -->
+<sbml xmlns="http://www.sbml.org/sbml/level2/version4" level="2" version="4">
+ <model id="cell" name="cell">
+ <listOfCompartments>
+ <compartment id="compartment" size="1" />
+ </listOfCompartments>
+ <listOfSpecies>
+ <species id="x0" compartment="compartment" initialConcentration="1" boundaryCondition="true" />
+ <species id="x1" compartment="compartment" initialConcentration="0" boundaryCondition="true" />
+ <species id="s1" compartment="compartment" initialConcentration="0" boundaryCondition="false" />
+ <species id="s2" compartment="compartment" initialConcentration="0" boundaryCondition="false" />
+ </listOfSpecies>
+ <listOfParameters>
+ <parameter id="k1" value="1.2" constant="true" />
+ <parameter id="k2" value="4.5" constant="true" />
+ <parameter id="k3" value="3.4" constant="true" />
+ </listOfParameters>
+ <listOfReactions>
+ <reaction id="_J0" reversible="false">
+ <listOfReactants>
+ <speciesReference species="x0" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="s1" stoichiometry="1" />
+ </listOfProducts>
+ <kineticLaw>
+ <math xmlns="http://www.w3.org/1998/Math/MathML">
+ <apply>
+ <times />
+ <ci> k1 </ci>
+ <ci> x0 </ci>
+ </apply>
+ </math>
+ </kineticLaw>
+ </reaction>
+ <reaction id="_J1" reversible="false">
+ <listOfReactants>
+ <speciesReference species="s1" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="s2" stoichiometry="1" />
+ </listOfProducts>
+ <kineticLaw>
+ <math xmlns="http://www.w3.org/1998/Math/MathML">
+ <apply>
+ <times />
+ <ci> k2 </ci>
+ <ci> s1 </ci>
+ </apply>
+ </math>
+ </kineticLaw>
+ </reaction>
+ <reaction id="_J2" reversible="false">
+ <listOfReactants>
+ <speciesReference species="s2" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="x1" stoichiometry="1" />
+ </listOfProducts>
+ <kineticLaw>
+ <math xmlns="http://www.w3.org/1998/Math/MathML">
+ <apply>
+ <times />
+ <ci> k3 </ci>
+ <ci> s2 </ci>
+ </apply>
+ </math>
+ </kineticLaw>
+ </reaction>
+ </listOfReactions>
+ </model>
+</sbml>
diff --git a/models/bug.xml b/models/bug.xml
index 50ed940..4804c88 100644
--- a/models/bug.xml
+++ b/models/bug.xml
@@ -1,452 +1,452 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!-- Created by XMLPrettyPrinter on 10/4/2012 from JDesigner 2.4.3 -->
-<sbml xmlns = "http://www.sbml.org/sbml/level2" level = "2" version = "1" xmlns:jd2 = "http://www.sys-bio.org/sbml/jd2">
- <!-- -->
- <!-- Model Starts Here -->
- <!-- -->
- <model id = "untitled">
- <notes>
- <p xmlns = "http://www.w3.org/1999/xhtml">
- <body/>
- </p>
- </notes>
- <annotation>
- <jd2:JDesignerLayout version = "2.0" MajorVersion = "2" MinorVersion = "4" BuildVersion = "54"
- xmlns:jd2 = "http://www.sys-bio.org/sbml/jd2">
- <jd2:header>
- <jd2:VersionHeader JDesignerVersion = "2.0"/>
- <jd2:ModelHeader Author = "" ModelVersion = "0.0" ModelTitle = "untitled"/>
- <jd2:TimeCourseDetails timeStart = "0" timeEnd = "10" numberOfPoints = "1000"/>
- </jd2:header>
- <jd2:JDGraphicsHeader BackGroundColor = "FFFFFFEF"/>
- <jd2:listOfCompartments>
- <jd2:compartment id = "compartment" size = "1" visible = "false">
- <jd2:boundingBox x = "0" y = "0" w = "64" h = "64"/>
- <jd2:membraneStyle thickness = "12" color = "FF00A5FF"/>
- <jd2:interiorStyle color = "FFEEEEFF"/>
- <jd2:text value = "compartment" visible = "true">
- <jd2:position rx = "32" ry = "58"/>
- <jd2:font fontName = "Arial" fontSize = "8" fontStyle = "" fontColor = "FF000000"/>
- </jd2:text>
- </jd2:compartment>
- </jd2:listOfCompartments>
- <jd2:listOfSpecies>
- <jd2:species id = "Node0" boundaryCondition = "false" compartment = "compartment" initialConcentration = "0">
- <jd2:positionLocked value = "false"/>
- <jd2:boundingBox x = "93" y = "83"/>
- <jd2:displayValue visible = "false">
- <jd2:position rx = "0" ry = "0"/>
- <jd2:font fontName = "Arial" fontSize = "8" fontColor = "FF000000" fontStyle = ""/>
- </jd2:displayValue>
- <jd2:text value = "Node0" visible = "true">
- <jd2:position rx = "13" ry = "14"/>
- <jd2:font fontName = "Arial" fontSize = "8" fontStyle = "" fontColor = "FF000000"/>
- </jd2:text>
- <jd2:complex id = "C2592840" w = "62" h = "40" boundarySpeciesStyle = "bsShadow"
- boundaryStyleColor = "FF0000FF" captionPosition = "npCenter" aliasBoundaryColor = "FFFF0000" aliasBoundaryThickness = "3">
- <jd2:subunit shape = "suOvalSquare">
- <jd2:boundingBox rx = "0" ry = "0" w = "62" h = "40"/>
- <jd2:text value = "S13" visible = "false">
- <jd2:position rx = "22" ry = "13"/>
- <jd2:font fontName = "Arial" fontSize = "8" fontColor = "FF000000" fontStyle = ""/>
- </jd2:text>
- <jd2:color scheme = "gtVertLinear" startColor = "FFFFCC99" endColor = "FFFFFFFF"/>
- <jd2:edgeStyle color = "FFFF6600" thickness = "2" stroke = "dsSolid"/>
- </jd2:subunit>
- </jd2:complex>
- </jd2:species>
- <jd2:species id = "Node1" boundaryCondition = "false" compartment = "compartment" initialConcentration = "0">
- <jd2:positionLocked value = "false"/>
- <jd2:boundingBox x = "223" y = "159"/>
- <jd2:displayValue visible = "false">
- <jd2:position rx = "0" ry = "0"/>
- <jd2:font fontName = "Arial" fontSize = "8" fontColor = "FF000000" fontStyle = ""/>
- </jd2:displayValue>
- <jd2:text value = "Node1" visible = "true">
- <jd2:position rx = "13" ry = "14"/>
- <jd2:font fontName = "Arial" fontSize = "8" fontStyle = "" fontColor = "FF000000"/>
- </jd2:text>
- <jd2:complex id = "C2592840" w = "62" h = "40" boundarySpeciesStyle = "bsShadow"
- boundaryStyleColor = "FF0000FF" captionPosition = "npCenter" aliasBoundaryColor = "FFFF0000" aliasBoundaryThickness = "3">
- <jd2:subunit shape = "suOvalSquare">
- <jd2:boundingBox rx = "0" ry = "0" w = "62" h = "40"/>
- <jd2:text value = "S13" visible = "false">
- <jd2:position rx = "22" ry = "13"/>
- <jd2:font fontName = "Arial" fontSize = "8" fontColor = "FF000000" fontStyle = ""/>
- </jd2:text>
- <jd2:color scheme = "gtVertLinear" startColor = "FFFFCC99" endColor = "FFFFFFFF"/>
- <jd2:edgeStyle color = "FFFF6600" thickness = "2" stroke = "dsSolid"/>
- </jd2:subunit>
- </jd2:complex>
- </jd2:species>
- </jd2:listOfSpecies>
- <jd2:listOfReactions>
- <jd2:reaction id = "J0" reversible = "false">
- <jd2:listOfReactants>
- <jd2:speciesReference species = "Node0" stoichiometry = "1"/>
- </jd2:listOfReactants>
- <jd2:listOfProducts>
- <jd2:speciesReference species = "Node1" stoichiometry = "1"/>
- </jd2:listOfProducts>
- <jd2:listOfModifierEdges/>
- <jd2:kineticLaw type = "builtin">
- <jd2:rateEquation value = "imm"/>
- <jd2:listOfSymbols>
- <jd2:parameter id = "J0_k" value = "0.1"/>
- </jd2:listOfSymbols>
- </jd2:kineticLaw>
- <jd2:display arrowStyle = "ar1" arrowFillColor = "FF808080" lineColor = "FF339966" lineThickness = "2">
- <jd2:lineType type = "ltBezier">
- <jd2:edge>
- <jd2:pt x = "124" y = "103" type = "substrate" speciesRef = "Node0"/>
- <jd2:pt x = "188" y = "140" type = "controlPoint"/>
- <jd2:pt x = "188" y = "140" type = "controlPoint"/>
- <jd2:pt x = "254" y = "179" type = "product" speciesRef = "Node1"/>
- </jd2:edge>
- </jd2:lineType>
- <jd2:displayValue visible = "false" showValue = "false" value = "0">
- <jd2:position rx = "0" ry = "0"/>
- <jd2:font fontName = "Arial" fontSize = "8" fontColor = "FF000000" fontStyle = ""/>
- </jd2:displayValue>
- </jd2:display>
- </jd2:reaction>
- </jd2:listOfReactions>
- </jd2:JDesignerLayout>
- </annotation>
- <listOfFunctionDefinitions>
- <functionDefinition id = "mod">
- <math xmlns = "http://www.w3.org/1998/Math/MathML">
- <lambda>
- <bvar>
- <ci>
- x
- </ci>
- </bvar>
- <bvar>
- <ci>
- y
- </ci>
- </bvar>
- <apply>
- <minus/>
- <ci>
- x
- </ci>
- <apply>
- <times/>
- <ci>
- y
- </ci>
- <apply>
- <floor/>
- <apply>
- <divide/>
- <ci>
- x
- </ci>
- <ci>
- y
- </ci>
- </apply>
- </apply>
- </apply>
- </apply>
- </lambda>
- </math>
- </functionDefinition>
- <functionDefinition id = "normal">
- <annotation>
- <distribution xmlns = "http://sbml.org/annotations/distribution" definition = "http://en.wikipedia.org/wiki/Normal_distribution"/>
- </annotation>
- <math xmlns = "http://www.w3.org/1998/Math/MathML">
- <lambda>
- <bvar>
- <ci>
- m
- </ci>
- </bvar>
- <bvar>
- <ci>
- s
- </ci>
- </bvar>
- <ci>
- m
- </ci>
- </lambda>
- </math>
- </functionDefinition>
- <functionDefinition id = "uniform">
- <annotation>
- <distribution xmlns = "http://sbml.org/annotations/distribution" definition = "http://en.wikipedia.org/wiki/Uniform_distribution_(continuous)"/>
- </annotation>
- <math xmlns = "http://www.w3.org/1998/Math/MathML">
- <lambda>
- <bvar>
- <ci>
- a
- </ci>
- </bvar>
- <bvar>
- <ci>
- b
- </ci>
- </bvar>
- <apply>
- <divide/>
- <apply>
- <plus/>
- <ci>
- a
- </ci>
- <ci>
- b
- </ci>
- </apply>
- <cn type = "integer">
- 2
- </cn>
- </apply>
- </lambda>
- </math>
- </functionDefinition>
- <functionDefinition id = "sawTooth">
- <math xmlns = "http://www.w3.org/1998/Math/MathML">
- <lambda>
- <bvar>
- <ci>
- time
- </ci>
- </bvar>
- <bvar>
- <ci>
- period
- </ci>
- </bvar>
- <bvar>
- <ci>
- center
- </ci>
- </bvar>
- <bvar>
- <ci>
- amplitude
- </ci>
- </bvar>
- <apply>
- <plus/>
- <ci>
- center
- </ci>
- <apply>
- <times/>
- <ci>
- amplitude
- </ci>
- <apply>
- <minus/>
- <apply>
- <divide/>
- <ci>
- time
- </ci>
- <ci>
- period
- </ci>
- </apply>
- <apply>
- <floor/>
- <apply>
- <plus/>
- <apply>
- <divide/>
- <ci>
- time
- </ci>
- <ci>
- period
- </ci>
- </apply>
- <cn>
- 0.5
- </cn>
- </apply>
- </apply>
- </apply>
- </apply>
- </apply>
- </lambda>
- </math>
- </functionDefinition>
- <functionDefinition id = "squareWave">
- <math xmlns = "http://www.w3.org/1998/Math/MathML">
- <lambda>
- <bvar>
- <ci>
- time
- </ci>
- </bvar>
- <bvar>
- <ci>
- period
- </ci>
- </bvar>
- <bvar>
- <ci>
- center
- </ci>
- </bvar>
- <bvar>
- <ci>
- amplitude
- </ci>
- </bvar>
- <apply>
- <plus/>
- <apply>
- <times/>
- <ci>
- amplitude
- </ci>
- <apply>
- <gt/>
- <apply>
- <sin/>
- <apply>
- <divide/>
- <apply>
- <times/>
- <cn type = "integer">
- 2
- </cn>
- <cn>
- 3.1414926
- </cn>
- <ci>
- time
- </ci>
- </apply>
- <ci>
- period
- </ci>
- </apply>
- </apply>
- <cn type = "integer">
- 0
- </cn>
- </apply>
- </apply>
- <ci>
- center
- </ci>
- </apply>
- </lambda>
- </math>
- </functionDefinition>
- <functionDefinition id = "triangleWave">
- <math xmlns = "http://www.w3.org/1998/Math/MathML">
- <lambda>
- <bvar>
- <ci>
- time
- </ci>
- </bvar>
- <bvar>
- <ci>
- period
- </ci>
- </bvar>
- <bvar>
- <ci>
- center
- </ci>
- </bvar>
- <bvar>
- <ci>
- amplitude
- </ci>
- </bvar>
- <apply>
- <plus/>
- <ci>
- center
- </ci>
- <apply>
- <times/>
- <ci>
- amplitude
- </ci>
- <apply>
- <abs/>
- <apply>
- <minus/>
- <apply>
- <divide/>
- <ci>
- time
- </ci>
- <ci>
- period
- </ci>
- </apply>
- <apply>
- <floor/>
- <apply>
- <plus/>
- <apply>
- <divide/>
- <ci>
- time
- </ci>
- <ci>
- period
- </ci>
- </apply>
- <cn>
- 0.5
- </cn>
- </apply>
- </apply>
- </apply>
- </apply>
- </apply>
- </apply>
- </lambda>
- </math>
- </functionDefinition>
- </listOfFunctionDefinitions>
- <listOfCompartments>
- <compartment id = "compartment" size = "1"/>
- </listOfCompartments>
- <listOfSpecies>
- <species id = "Node0" boundaryCondition = "false" initialConcentration = "0" compartment = "compartment"/>
- <species id = "Node1" boundaryCondition = "false" initialConcentration = "0" compartment = "compartment"/>
- </listOfSpecies>
- <listOfParameters>
- <parameter id = "J0_k" value = "0.1"/>
- </listOfParameters>
- <listOfReactions>
- <reaction id = "J0" reversible = "false">
- <listOfReactants>
- <speciesReference species = "Node0" stoichiometry = "1"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species = "Node1" stoichiometry = "1"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns = "http://www.w3.org/1998/Math/MathML">
- <apply>
- <times/>
- <ci>
- J0_k
- </ci>
- <ci>
- Node0
- </ci>
- </apply>
- </math>
- </kineticLaw>
- </reaction>
- </listOfReactions>
- </model>
-</sbml>
+<?xml version="1.0" encoding="UTF-8"?>
+<!-- Created by XMLPrettyPrinter on 10/4/2012 from JDesigner 2.4.3 -->
+<sbml xmlns = "http://www.sbml.org/sbml/level2" level = "2" version = "1" xmlns:jd2 = "http://www.sys-bio.org/sbml/jd2">
+ <!-- -->
+ <!-- Model Starts Here -->
+ <!-- -->
+ <model id = "untitled">
+ <notes>
+ <p xmlns = "http://www.w3.org/1999/xhtml">
+ <body/>
+ </p>
+ </notes>
+ <annotation>
+ <jd2:JDesignerLayout version = "2.0" MajorVersion = "2" MinorVersion = "4" BuildVersion = "54"
+ xmlns:jd2 = "http://www.sys-bio.org/sbml/jd2">
+ <jd2:header>
+ <jd2:VersionHeader JDesignerVersion = "2.0"/>
+ <jd2:ModelHeader Author = "" ModelVersion = "0.0" ModelTitle = "untitled"/>
+ <jd2:TimeCourseDetails timeStart = "0" timeEnd = "10" numberOfPoints = "1000"/>
+ </jd2:header>
+ <jd2:JDGraphicsHeader BackGroundColor = "FFFFFFEF"/>
+ <jd2:listOfCompartments>
+ <jd2:compartment id = "compartment" size = "1" visible = "false">
+ <jd2:boundingBox x = "0" y = "0" w = "64" h = "64"/>
+ <jd2:membraneStyle thickness = "12" color = "FF00A5FF"/>
+ <jd2:interiorStyle color = "FFEEEEFF"/>
+ <jd2:text value = "compartment" visible = "true">
+ <jd2:position rx = "32" ry = "58"/>
+ <jd2:font fontName = "Arial" fontSize = "8" fontStyle = "" fontColor = "FF000000"/>
+ </jd2:text>
+ </jd2:compartment>
+ </jd2:listOfCompartments>
+ <jd2:listOfSpecies>
+ <jd2:species id = "Node0" boundaryCondition = "false" compartment = "compartment" initialConcentration = "0">
+ <jd2:positionLocked value = "false"/>
+ <jd2:boundingBox x = "93" y = "83"/>
+ <jd2:displayValue visible = "false">
+ <jd2:position rx = "0" ry = "0"/>
+ <jd2:font fontName = "Arial" fontSize = "8" fontColor = "FF000000" fontStyle = ""/>
+ </jd2:displayValue>
+ <jd2:text value = "Node0" visible = "true">
+ <jd2:position rx = "13" ry = "14"/>
+ <jd2:font fontName = "Arial" fontSize = "8" fontStyle = "" fontColor = "FF000000"/>
+ </jd2:text>
+ <jd2:complex id = "C2592840" w = "62" h = "40" boundarySpeciesStyle = "bsShadow"
+ boundaryStyleColor = "FF0000FF" captionPosition = "npCenter" aliasBoundaryColor = "FFFF0000" aliasBoundaryThickness = "3">
+ <jd2:subunit shape = "suOvalSquare">
+ <jd2:boundingBox rx = "0" ry = "0" w = "62" h = "40"/>
+ <jd2:text value = "S13" visible = "false">
+ <jd2:position rx = "22" ry = "13"/>
+ <jd2:font fontName = "Arial" fontSize = "8" fontColor = "FF000000" fontStyle = ""/>
+ </jd2:text>
+ <jd2:color scheme = "gtVertLinear" startColor = "FFFFCC99" endColor = "FFFFFFFF"/>
+ <jd2:edgeStyle color = "FFFF6600" thickness = "2" stroke = "dsSolid"/>
+ </jd2:subunit>
+ </jd2:complex>
+ </jd2:species>
+ <jd2:species id = "Node1" boundaryCondition = "false" compartment = "compartment" initialConcentration = "0">
+ <jd2:positionLocked value = "false"/>
+ <jd2:boundingBox x = "223" y = "159"/>
+ <jd2:displayValue visible = "false">
+ <jd2:position rx = "0" ry = "0"/>
+ <jd2:font fontName = "Arial" fontSize = "8" fontColor = "FF000000" fontStyle = ""/>
+ </jd2:displayValue>
+ <jd2:text value = "Node1" visible = "true">
+ <jd2:position rx = "13" ry = "14"/>
+ <jd2:font fontName = "Arial" fontSize = "8" fontStyle = "" fontColor = "FF000000"/>
+ </jd2:text>
+ <jd2:complex id = "C2592840" w = "62" h = "40" boundarySpeciesStyle = "bsShadow"
+ boundaryStyleColor = "FF0000FF" captionPosition = "npCenter" aliasBoundaryColor = "FFFF0000" aliasBoundaryThickness = "3">
+ <jd2:subunit shape = "suOvalSquare">
+ <jd2:boundingBox rx = "0" ry = "0" w = "62" h = "40"/>
+ <jd2:text value = "S13" visible = "false">
+ <jd2:position rx = "22" ry = "13"/>
+ <jd2:font fontName = "Arial" fontSize = "8" fontColor = "FF000000" fontStyle = ""/>
+ </jd2:text>
+ <jd2:color scheme = "gtVertLinear" startColor = "FFFFCC99" endColor = "FFFFFFFF"/>
+ <jd2:edgeStyle color = "FFFF6600" thickness = "2" stroke = "dsSolid"/>
+ </jd2:subunit>
+ </jd2:complex>
+ </jd2:species>
+ </jd2:listOfSpecies>
+ <jd2:listOfReactions>
+ <jd2:reaction id = "J0" reversible = "false">
+ <jd2:listOfReactants>
+ <jd2:speciesReference species = "Node0" stoichiometry = "1"/>
+ </jd2:listOfReactants>
+ <jd2:listOfProducts>
+ <jd2:speciesReference species = "Node1" stoichiometry = "1"/>
+ </jd2:listOfProducts>
+ <jd2:listOfModifierEdges/>
+ <jd2:kineticLaw type = "builtin">
+ <jd2:rateEquation value = "imm"/>
+ <jd2:listOfSymbols>
+ <jd2:parameter id = "J0_k" value = "0.1"/>
+ </jd2:listOfSymbols>
+ </jd2:kineticLaw>
+ <jd2:display arrowStyle = "ar1" arrowFillColor = "FF808080" lineColor = "FF339966" lineThickness = "2">
+ <jd2:lineType type = "ltBezier">
+ <jd2:edge>
+ <jd2:pt x = "124" y = "103" type = "substrate" speciesRef = "Node0"/>
+ <jd2:pt x = "188" y = "140" type = "controlPoint"/>
+ <jd2:pt x = "188" y = "140" type = "controlPoint"/>
+ <jd2:pt x = "254" y = "179" type = "product" speciesRef = "Node1"/>
+ </jd2:edge>
+ </jd2:lineType>
+ <jd2:displayValue visible = "false" showValue = "false" value = "0">
+ <jd2:position rx = "0" ry = "0"/>
+ <jd2:font fontName = "Arial" fontSize = "8" fontColor = "FF000000" fontStyle = ""/>
+ </jd2:displayValue>
+ </jd2:display>
+ </jd2:reaction>
+ </jd2:listOfReactions>
+ </jd2:JDesignerLayout>
+ </annotation>
+ <listOfFunctionDefinitions>
+ <functionDefinition id = "mod">
+ <math xmlns = "http://www.w3.org/1998/Math/MathML">
+ <lambda>
+ <bvar>
+ <ci>
+ x
+ </ci>
+ </bvar>
+ <bvar>
+ <ci>
+ y
+ </ci>
+ </bvar>
+ <apply>
+ <minus/>
+ <ci>
+ x
+ </ci>
+ <apply>
+ <times/>
+ <ci>
+ y
+ </ci>
+ <apply>
+ <floor/>
+ <apply>
+ <divide/>
+ <ci>
+ x
+ </ci>
+ <ci>
+ y
+ </ci>
+ </apply>
+ </apply>
+ </apply>
+ </apply>
+ </lambda>
+ </math>
+ </functionDefinition>
+ <functionDefinition id = "normal">
+ <annotation>
+ <distribution xmlns = "http://sbml.org/annotations/distribution" definition = "http://en.wikipedia.org/wiki/Normal_distribution"/>
+ </annotation>
+ <math xmlns = "http://www.w3.org/1998/Math/MathML">
+ <lambda>
+ <bvar>
+ <ci>
+ m
+ </ci>
+ </bvar>
+ <bvar>
+ <ci>
+ s
+ </ci>
+ </bvar>
+ <ci>
+ m
+ </ci>
+ </lambda>
+ </math>
+ </functionDefinition>
+ <functionDefinition id = "uniform">
+ <annotation>
+ <distribution xmlns = "http://sbml.org/annotations/distribution" definition = "http://en.wikipedia.org/wiki/Uniform_distribution_(continuous)"/>
+ </annotation>
+ <math xmlns = "http://www.w3.org/1998/Math/MathML">
+ <lambda>
+ <bvar>
+ <ci>
+ a
+ </ci>
+ </bvar>
+ <bvar>
+ <ci>
+ b
+ </ci>
+ </bvar>
+ <apply>
+ <divide/>
+ <apply>
+ <plus/>
+ <ci>
+ a
+ </ci>
+ <ci>
+ b
+ </ci>
+ </apply>
+ <cn type = "integer">
+ 2
+ </cn>
+ </apply>
+ </lambda>
+ </math>
+ </functionDefinition>
+ <functionDefinition id = "sawTooth">
+ <math xmlns = "http://www.w3.org/1998/Math/MathML">
+ <lambda>
+ <bvar>
+ <ci>
+ time
+ </ci>
+ </bvar>
+ <bvar>
+ <ci>
+ period
+ </ci>
+ </bvar>
+ <bvar>
+ <ci>
+ center
+ </ci>
+ </bvar>
+ <bvar>
+ <ci>
+ amplitude
+ </ci>
+ </bvar>
+ <apply>
+ <plus/>
+ <ci>
+ center
+ </ci>
+ <apply>
+ <times/>
+ <ci>
+ amplitude
+ </ci>
+ <apply>
+ <minus/>
+ <apply>
+ <divide/>
+ <ci>
+ time
+ </ci>
+ <ci>
+ period
+ </ci>
+ </apply>
+ <apply>
+ <floor/>
+ <apply>
+ <plus/>
+ <apply>
+ <divide/>
+ <ci>
+ time
+ </ci>
+ <ci>
+ period
+ </ci>
+ </apply>
+ <cn>
+ 0.5
+ </cn>
+ </apply>
+ </apply>
+ </apply>
+ </apply>
+ </apply>
+ </lambda>
+ </math>
+ </functionDefinition>
+ <functionDefinition id = "squareWave">
+ <math xmlns = "http://www.w3.org/1998/Math/MathML">
+ <lambda>
+ <bvar>
+ <ci>
+ time
+ </ci>
+ </bvar>
+ <bvar>
+ <ci>
+ period
+ </ci>
+ </bvar>
+ <bvar>
+ <ci>
+ center
+ </ci>
+ </bvar>
+ <bvar>
+ <ci>
+ amplitude
+ </ci>
+ </bvar>
+ <apply>
+ <plus/>
+ <apply>
+ <times/>
+ <ci>
+ amplitude
+ </ci>
+ <apply>
+ <gt/>
+ <apply>
+ <sin/>
+ <apply>
+ <divide/>
+ <apply>
+ <times/>
+ <cn type = "integer">
+ 2
+ </cn>
+ <cn>
+ 3.1414926
+ </cn>
+ <ci>
+ time
+ </ci>
+ </apply>
+ <ci>
+ period
+ </ci>
+ </apply>
+ </apply>
+ <cn type = "integer">
+ 0
+ </cn>
+ </apply>
+ </apply>
+ <ci>
+ center
+ </ci>
+ </apply>
+ </lambda>
+ </math>
+ </functionDefinition>
+ <functionDefinition id = "triangleWave">
+ <math xmlns = "http://www.w3.org/1998/Math/MathML">
+ <lambda>
+ <bvar>
+ <ci>
+ time
+ </ci>
+ </bvar>
+ <bvar>
+ <ci>
+ period
+ </ci>
+ </bvar>
+ <bvar>
+ <ci>
+ center
+ </ci>
+ </bvar>
+ <bvar>
+ <ci>
+ amplitude
+ </ci>
+ </bvar>
+ <apply>
+ <plus/>
+ <ci>
+ center
+ </ci>
+ <apply>
+ <times/>
+ <ci>
+ amplitude
+ </ci>
+ <apply>
+ <abs/>
+ <apply>
+ <minus/>
+ <apply>
+ <divide/>
+ <ci>
+ time
+ </ci>
+ <ci>
+ period
+ </ci>
+ </apply>
+ <apply>
+ <floor/>
+ <apply>
+ <plus/>
+ <apply>
+ <divide/>
+ <ci>
+ time
+ </ci>
+ <ci>
+ period
+ </ci>
+ </apply>
+ <cn>
+ 0.5
+ </cn>
+ </apply>
+ </apply>
+ </apply>
+ </apply>
+ </apply>
+ </apply>
+ </lambda>
+ </math>
+ </functionDefinition>
+ </listOfFunctionDefinitions>
+ <listOfCompartments>
+ <compartment id = "compartment" size = "1"/>
+ </listOfCompartments>
+ <listOfSpecies>
+ <species id = "Node0" boundaryCondition = "false" initialConcentration = "0" compartment = "compartment"/>
+ <species id = "Node1" boundaryCondition = "false" initialConcentration = "0" compartment = "compartment"/>
+ </listOfSpecies>
+ <listOfParameters>
+ <parameter id = "J0_k" value = "0.1"/>
+ </listOfParameters>
+ <listOfReactions>
+ <reaction id = "J0" reversible = "false">
+ <listOfReactants>
+ <speciesReference species = "Node0" stoichiometry = "1"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species = "Node1" stoichiometry = "1"/>
+ </listOfProducts>
+ <kineticLaw>
+ <math xmlns = "http://www.w3.org/1998/Math/MathML">
+ <apply>
+ <times/>
+ <ci>
+ J0_k
+ </ci>
+ <ci>
+ Node0
+ </ci>
+ </apply>
+ </math>
+ </kineticLaw>
+ </reaction>
+ </listOfReactions>
+ </model>
+</sbml>
diff --git a/models/sbml_test_0001.xml b/models/sbml_test_0001.xml
index 60c5c4a..bd42e35 100644
--- a/models/sbml_test_0001.xml
+++ b/models/sbml_test_0001.xml
@@ -1,35 +1,35 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<sbml xmlns="http://www.sbml.org/sbml/level2/version4" level="2" version="4">
- <model metaid="_case00001" id="case00001" name="case00001">
- <listOfCompartments>
- <compartment id="compartment" name="compartment" size="1" units="volume"/>
- </listOfCompartments>
- <listOfSpecies>
- <species id="S1" name="S1" compartment="compartment" initialAmount="0.00015" substanceUnits="substance"/>
- <species id="S2" name="S2" compartment="compartment" initialAmount="0" substanceUnits="substance"/>
- </listOfSpecies>
- <listOfParameters>
- <parameter id="k1" name="k1" value="1"/>
- </listOfParameters>
- <listOfReactions>
- <reaction id="reaction1" name="reaction1" reversible="false" fast="false">
- <listOfReactants>
- <speciesReference species="S1"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="S2"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <apply>
- <times/>
- <ci> compartment </ci>
- <ci> k1 </ci>
- <ci> S1 </ci>
- </apply>
- </math>
- </kineticLaw>
- </reaction>
- </listOfReactions>
- </model>
-</sbml>
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level2/version4" level="2" version="4">
+ <model metaid="_case00001" id="case00001" name="case00001">
+ <listOfCompartments>
+ <compartment id="compartment" name="compartment" size="1" units="volume"/>
+ </listOfCompartments>
+ <listOfSpecies>
+ <species id="S1" name="S1" compartment="compartment" initialAmount="0.00015" substanceUnits="substance"/>
+ <species id="S2" name="S2" compartment="compartment" initialAmount="0" substanceUnits="substance"/>
+ </listOfSpecies>
+ <listOfParameters>
+ <parameter id="k1" name="k1" value="1"/>
+ </listOfParameters>
+ <listOfReactions>
+ <reaction id="reaction1" name="reaction1" reversible="false" fast="false">
+ <listOfReactants>
+ <speciesReference species="S1"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="S2"/>
+ </listOfProducts>
+ <kineticLaw>
+ <math xmlns="http://www.w3.org/1998/Math/MathML">
+ <apply>
+ <times/>
+ <ci> compartment </ci>
+ <ci> k1 </ci>
+ <ci> S1 </ci>
+ </apply>
+ </math>
+ </kineticLaw>
+ </reaction>
+ </listOfReactions>
+ </model>
+</sbml>
diff --git a/models/simple.xml b/models/simple.xml
index ee79016..2935af5 100644
--- a/models/simple.xml
+++ b/models/simple.xml
@@ -1,54 +1,54 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!-- Created by JarnacLite version 1.0.4092.22132 on 2012-03-21 15:10 with libSBML version 4.3.0. -->
-<sbml xmlns="http://www.sbml.org/sbml/level2/version4" level="2" version="4">
- <model id="cell" name="cell">
- <listOfCompartments>
- <compartment id="compartment" size="1" />
- </listOfCompartments>
- <listOfSpecies>
- <species id="Xo" compartment="compartment" initialConcentration="10" boundaryCondition="true" />
- <species id="X1" compartment="compartment" initialConcentration="0" boundaryCondition="true" />
- <species id="S1" compartment="compartment" initialConcentration="0" />
- </listOfSpecies>
- <listOfParameters>
- <parameter id="k1" value="1" />
- <parameter id="k2" value="2" />
- </listOfParameters>
- <listOfReactions>
- <reaction id="_J0" reversible="false">
- <listOfReactants>
- <speciesReference species="Xo" />
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="S1" />
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <apply>
- <times />
- <ci> k1 </ci>
- <ci> Xo </ci>
- </apply>
- </math>
- </kineticLaw>
- </reaction>
- <reaction id="_J1" reversible="false">
- <listOfReactants>
- <speciesReference species="S1" />
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="X1" />
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <apply>
- <times />
- <ci> k2 </ci>
- <ci> S1 </ci>
- </apply>
- </math>
- </kineticLaw>
- </reaction>
- </listOfReactions>
- </model>
+<?xml version="1.0" encoding="UTF-8"?>
+<!-- Created by JarnacLite version 1.0.4092.22132 on 2012-03-21 15:10 with libSBML version 4.3.0. -->
+<sbml xmlns="http://www.sbml.org/sbml/level2/version4" level="2" version="4">
+ <model id="cell" name="cell">
+ <listOfCompartments>
+ <compartment id="compartment" size="1" />
+ </listOfCompartments>
+ <listOfSpecies>
+ <species id="Xo" compartment="compartment" initialConcentration="10" boundaryCondition="true" />
+ <species id="X1" compartment="compartment" initialConcentration="0" boundaryCondition="true" />
+ <species id="S1" compartment="compartment" initialConcentration="0" />
+ </listOfSpecies>
+ <listOfParameters>
+ <parameter id="k1" value="1" />
+ <parameter id="k2" value="2" />
+ </listOfParameters>
+ <listOfReactions>
+ <reaction id="_J0" reversible="false">
+ <listOfReactants>
+ <speciesReference species="Xo" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="S1" />
+ </listOfProducts>
+ <kineticLaw>
+ <math xmlns="http://www.w3.org/1998/Math/MathML">
+ <apply>
+ <times />
+ <ci> k1 </ci>
+ <ci> Xo </ci>
+ </apply>
+ </math>
+ </kineticLaw>
+ </reaction>
+ <reaction id="_J1" reversible="false">
+ <listOfReactants>
+ <speciesReference species="S1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="X1" />
+ </listOfProducts>
+ <kineticLaw>
+ <math xmlns="http://www.w3.org/1998/Math/MathML">
+ <apply>
+ <times />
+ <ci> k2 </ci>
+ <ci> S1 </ci>
+ </apply>
+ </math>
+ </kineticLaw>
+ </reaction>
+ </listOfReactions>
+ </model>
</sbml>
\ No newline at end of file
diff --git a/models/squareWaveModel.xml b/models/squareWaveModel.xml
index ec36659..615e9f0 100644
--- a/models/squareWaveModel.xml
+++ b/models/squareWaveModel.xml
@@ -1,69 +1,69 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!-- Created by XMLPrettyPrinter on 7/25/2012 from -->
-<sbml xmlns = "http://www.sbml.org/sbml/level2" level = "2" version = "1">
- <model id = "cell">
- <listOfCompartments>
- <compartment id = "compartment" size = "1"/>
- </listOfCompartments>
- <listOfSpecies>
- <species id = "X1" boundaryCondition = "true" initialConcentration = "1" compartment = "compartment"/>
- <species id = "S1" boundaryCondition = "false" initialConcentration = "1.9039453559906" compartment = "compartment"/>
- </listOfSpecies>
- <listOfParameters>
- <parameter id = "k1" value = "1"/>
- </listOfParameters>
- <listOfReactions>
- <reaction id = "J0" reversible = "false">
- <listOfReactants>
- <speciesReference species = "X1" stoichiometry = "1"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species = "S1" stoichiometry = "1"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns = "http://www.w3.org/1998/Math/MathML">
- <apply>
- <plus/>
- <apply>
- <gt/>
- <apply>
- <sin/>
- <csymbol encoding = "text" definitionURL = "http://www.sbml.org/sbml/symbols/time">
- time
- </csymbol>
- </apply>
- <cn type = "integer">
- 0
- </cn>
- </apply>
- <cn type = "integer">
- 1
- </cn>
- </apply>
- </math>
- </kineticLaw>
- </reaction>
- <reaction id = "_J2" reversible = "false">
- <listOfReactants>
- <speciesReference species = "S1" stoichiometry = "1"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species = "X1" stoichiometry = "1"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns = "http://www.w3.org/1998/Math/MathML">
- <apply>
- <times/>
- <ci>
- k1
- </ci>
- <ci>
- S1
- </ci>
- </apply>
- </math>
- </kineticLaw>
- </reaction>
- </listOfReactions>
- </model>
-</sbml>
+<?xml version="1.0" encoding="UTF-8"?>
+<!-- Created by XMLPrettyPrinter on 7/25/2012 from -->
+<sbml xmlns = "http://www.sbml.org/sbml/level2" level = "2" version = "1">
+ <model id = "cell">
+ <listOfCompartments>
+ <compartment id = "compartment" size = "1"/>
+ </listOfCompartments>
+ <listOfSpecies>
+ <species id = "X1" boundaryCondition = "true" initialConcentration = "1" compartment = "compartment"/>
+ <species id = "S1" boundaryCondition = "false" initialConcentration = "1.9039453559906" compartment = "compartment"/>
+ </listOfSpecies>
+ <listOfParameters>
+ <parameter id = "k1" value = "1"/>
+ </listOfParameters>
+ <listOfReactions>
+ <reaction id = "J0" reversible = "false">
+ <listOfReactants>
+ <speciesReference species = "X1" stoichiometry = "1"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species = "S1" stoichiometry = "1"/>
+ </listOfProducts>
+ <kineticLaw>
+ <math xmlns = "http://www.w3.org/1998/Math/MathML">
+ <apply>
+ <plus/>
+ <apply>
+ <gt/>
+ <apply>
+ <sin/>
+ <csymbol encoding = "text" definitionURL = "http://www.sbml.org/sbml/symbols/time">
+ time
+ </csymbol>
+ </apply>
+ <cn type = "integer">
+ 0
+ </cn>
+ </apply>
+ <cn type = "integer">
+ 1
+ </cn>
+ </apply>
+ </math>
+ </kineticLaw>
+ </reaction>
+ <reaction id = "_J2" reversible = "false">
+ <listOfReactants>
+ <speciesReference species = "S1" stoichiometry = "1"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species = "X1" stoichiometry = "1"/>
+ </listOfProducts>
+ <kineticLaw>
+ <math xmlns = "http://www.w3.org/1998/Math/MathML">
+ <apply>
+ <times/>
+ <ci>
+ k1
+ </ci>
+ <ci>
+ S1
+ </ci>
+ </apply>
+ </math>
+ </kineticLaw>
+ </reaction>
+ </listOfReactions>
+ </model>
+</sbml>
diff --git a/models/ss_SimpleConservedCycle.xml b/models/ss_SimpleConservedCycle.xml
index 654325b..13afc55 100644
--- a/models/ss_SimpleConservedCycle.xml
+++ b/models/ss_SimpleConservedCycle.xml
@@ -1,61 +1,61 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!-- Created by XMLPrettyPrinter on 6/19/2012 from -->
-<sbml xmlns = "http://www.sbml.org/sbml/level2" level = "2" version = "1">
- <model id = "cell">
- <listOfCompartments>
- <compartment id = "compartment" size = "1"/>
- </listOfCompartments>
- <listOfSpecies>
- <species id = "S1" boundaryCondition = "false" initialConcentration = "7.5" compartment = "compartment"/>
- <species id = "S2" boundaryCondition = "false" initialConcentration = "2.5" compartment = "compartment"/>
- </listOfSpecies>
- <listOfParameters>
- <parameter id = "k1" value = "0.15"/>
- <parameter id = "k2" value = "0.45"/>
- </listOfParameters>
- <listOfReactions>
- <reaction id = "_J1" reversible = "false">
- <listOfReactants>
- <speciesReference species = "S1" stoichiometry = "1"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species = "S2" stoichiometry = "1"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns = "http://www.w3.org/1998/Math/MathML">
- <apply>
- <times/>
- <ci>
- k1
- </ci>
- <ci>
- S1
- </ci>
- </apply>
- </math>
- </kineticLaw>
- </reaction>
- <reaction id = "_J2" reversible = "false">
- <listOfReactants>
- <speciesReference species = "S2" stoichiometry = "1"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species = "S1" stoichiometry = "1"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns = "http://www.w3.org/1998/Math/MathML">
- <apply>
- <times/>
- <ci>
- k2
- </ci>
- <ci>
- S2
- </ci>
- </apply>
- </math>
- </kineticLaw>
- </reaction>
- </listOfReactions>
- </model>
-</sbml>
+<?xml version="1.0" encoding="UTF-8"?>
+<!-- Created by XMLPrettyPrinter on 6/19/2012 from -->
+<sbml xmlns = "http://www.sbml.org/sbml/level2" level = "2" version = "1">
+ <model id = "cell">
+ <listOfCompartments>
+ <compartment id = "compartment" size = "1"/>
+ </listOfCompartments>
+ <listOfSpecies>
+ <species id = "S1" boundaryCondition = "false" initialConcentration = "7.5" compartment = "compartment"/>
+ <species id = "S2" boundaryCondition = "false" initialConcentration = "2.5" compartment = "compartment"/>
+ </listOfSpecies>
+ <listOfParameters>
+ <parameter id = "k1" value = "0.15"/>
+ <parameter id = "k2" value = "0.45"/>
+ </listOfParameters>
+ <listOfReactions>
+ <reaction id = "_J1" reversible = "false">
+ <listOfReactants>
+ <speciesReference species = "S1" stoichiometry = "1"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species = "S2" stoichiometry = "1"/>
+ </listOfProducts>
+ <kineticLaw>
+ <math xmlns = "http://www.w3.org/1998/Math/MathML">
+ <apply>
+ <times/>
+ <ci>
+ k1
+ </ci>
+ <ci>
+ S1
+ </ci>
+ </apply>
+ </math>
+ </kineticLaw>
+ </reaction>
+ <reaction id = "_J2" reversible = "false">
+ <listOfReactants>
+ <speciesReference species = "S2" stoichiometry = "1"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species = "S1" stoichiometry = "1"/>
+ </listOfProducts>
+ <kineticLaw>
+ <math xmlns = "http://www.w3.org/1998/Math/MathML">
+ <apply>
+ <times/>
+ <ci>
+ k2
+ </ci>
+ <ci>
+ S2
+ </ci>
+ </apply>
+ </math>
+ </kineticLaw>
+ </reaction>
+ </listOfReactions>
+ </model>
+</sbml>
diff --git a/models/ss_TurnOnConservationAnalysis.xml b/models/ss_TurnOnConservationAnalysis.xml
index 654325b..13afc55 100644
--- a/models/ss_TurnOnConservationAnalysis.xml
+++ b/models/ss_TurnOnConservationAnalysis.xml
@@ -1,61 +1,61 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!-- Created by XMLPrettyPrinter on 6/19/2012 from -->
-<sbml xmlns = "http://www.sbml.org/sbml/level2" level = "2" version = "1">
- <model id = "cell">
- <listOfCompartments>
- <compartment id = "compartment" size = "1"/>
- </listOfCompartments>
- <listOfSpecies>
- <species id = "S1" boundaryCondition = "false" initialConcentration = "7.5" compartment = "compartment"/>
- <species id = "S2" boundaryCondition = "false" initialConcentration = "2.5" compartment = "compartment"/>
- </listOfSpecies>
- <listOfParameters>
- <parameter id = "k1" value = "0.15"/>
- <parameter id = "k2" value = "0.45"/>
- </listOfParameters>
- <listOfReactions>
- <reaction id = "_J1" reversible = "false">
- <listOfReactants>
- <speciesReference species = "S1" stoichiometry = "1"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species = "S2" stoichiometry = "1"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns = "http://www.w3.org/1998/Math/MathML">
- <apply>
- <times/>
- <ci>
- k1
- </ci>
- <ci>
- S1
- </ci>
- </apply>
- </math>
- </kineticLaw>
- </reaction>
- <reaction id = "_J2" reversible = "false">
- <listOfReactants>
- <speciesReference species = "S2" stoichiometry = "1"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species = "S1" stoichiometry = "1"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns = "http://www.w3.org/1998/Math/MathML">
- <apply>
- <times/>
- <ci>
- k2
- </ci>
- <ci>
- S2
- </ci>
- </apply>
- </math>
- </kineticLaw>
- </reaction>
- </listOfReactions>
- </model>
-</sbml>
+<?xml version="1.0" encoding="UTF-8"?>
+<!-- Created by XMLPrettyPrinter on 6/19/2012 from -->
+<sbml xmlns = "http://www.sbml.org/sbml/level2" level = "2" version = "1">
+ <model id = "cell">
+ <listOfCompartments>
+ <compartment id = "compartment" size = "1"/>
+ </listOfCompartments>
+ <listOfSpecies>
+ <species id = "S1" boundaryCondition = "false" initialConcentration = "7.5" compartment = "compartment"/>
+ <species id = "S2" boundaryCondition = "false" initialConcentration = "2.5" compartment = "compartment"/>
+ </listOfSpecies>
+ <listOfParameters>
+ <parameter id = "k1" value = "0.15"/>
+ <parameter id = "k2" value = "0.45"/>
+ </listOfParameters>
+ <listOfReactions>
+ <reaction id = "_J1" reversible = "false">
+ <listOfReactants>
+ <speciesReference species = "S1" stoichiometry = "1"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species = "S2" stoichiometry = "1"/>
+ </listOfProducts>
+ <kineticLaw>
+ <math xmlns = "http://www.w3.org/1998/Math/MathML">
+ <apply>
+ <times/>
+ <ci>
+ k1
+ </ci>
+ <ci>
+ S1
+ </ci>
+ </apply>
+ </math>
+ </kineticLaw>
+ </reaction>
+ <reaction id = "_J2" reversible = "false">
+ <listOfReactants>
+ <speciesReference species = "S2" stoichiometry = "1"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species = "S1" stoichiometry = "1"/>
+ </listOfProducts>
+ <kineticLaw>
+ <math xmlns = "http://www.w3.org/1998/Math/MathML">
+ <apply>
+ <times/>
+ <ci>
+ k2
+ </ci>
+ <ci>
+ S2
+ </ci>
+ </apply>
+ </math>
+ </kineticLaw>
+ </reaction>
+ </listOfReactions>
+ </model>
+</sbml>
diff --git a/models/ss_threeSpecies.xml b/models/ss_threeSpecies.xml
index 19d8037..b565368 100644
--- a/models/ss_threeSpecies.xml
+++ b/models/ss_threeSpecies.xml
@@ -1,108 +1,108 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!-- Created by XMLPrettyPrinter on 6/19/2012 from -->
-<sbml xmlns = "http://www.sbml.org/sbml/level2" level = "2" version = "1">
- <model id = "cell">
- <listOfCompartments>
- <compartment id = "compartment" size = "1"/>
- </listOfCompartments>
- <listOfSpecies>
- <species id = "Xo" boundaryCondition = "true" initialConcentration = "1" compartment = "compartment"/>
- <species id = "X1" boundaryCondition = "true" initialConcentration = "0" compartment = "compartment"/>
- <species id = "S1" boundaryCondition = "false" initialConcentration = "0.666666666666667" compartment = "compartment"/>
- <species id = "S2" boundaryCondition = "false" initialConcentration = "0.25" compartment = "compartment"/>
- <species id = "S3" boundaryCondition = "false" initialConcentration = "0.181818181818182" compartment = "compartment"/>
- </listOfSpecies>
- <listOfParameters>
- <parameter id = "k1" value = "0.1"/>
- <parameter id = "k2" value = "0.15"/>
- <parameter id = "k3" value = "0.4"/>
- <parameter id = "k4" value = "0.55"/>
- </listOfParameters>
- <listOfReactions>
- <reaction id = "_J1" reversible = "false">
- <listOfReactants>
- <speciesReference species = "Xo" stoichiometry = "1"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species = "S1" stoichiometry = "1"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns = "http://www.w3.org/1998/Math/MathML">
- <apply>
- <times/>
- <ci>
- k1
- </ci>
- <ci>
- Xo
- </ci>
- </apply>
- </math>
- </kineticLaw>
- </reaction>
- <reaction id = "_J2" reversible = "false">
- <listOfReactants>
- <speciesReference species = "S1" stoichiometry = "1"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species = "S2" stoichiometry = "1"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns = "http://www.w3.org/1998/Math/MathML">
- <apply>
- <times/>
- <ci>
- k2
- </ci>
- <ci>
- S1
- </ci>
- </apply>
- </math>
- </kineticLaw>
- </reaction>
- <reaction id = "_J3" reversible = "false">
- <listOfReactants>
- <speciesReference species = "S2" stoichiometry = "1"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species = "S3" stoichiometry = "1"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns = "http://www.w3.org/1998/Math/MathML">
- <apply>
- <times/>
- <ci>
- k3
- </ci>
- <ci>
- S2
- </ci>
- </apply>
- </math>
- </kineticLaw>
- </reaction>
- <reaction id = "_J4" reversible = "false">
- <listOfReactants>
- <speciesReference species = "S3" stoichiometry = "1"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species = "X1" stoichiometry = "1"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns = "http://www.w3.org/1998/Math/MathML">
- <apply>
- <times/>
- <ci>
- k4
- </ci>
- <ci>
- S3
- </ci>
- </apply>
- </math>
- </kineticLaw>
- </reaction>
- </listOfReactions>
- </model>
-</sbml>
+<?xml version="1.0" encoding="UTF-8"?>
+<!-- Created by XMLPrettyPrinter on 6/19/2012 from -->
+<sbml xmlns = "http://www.sbml.org/sbml/level2" level = "2" version = "1">
+ <model id = "cell">
+ <listOfCompartments>
+ <compartment id = "compartment" size = "1"/>
+ </listOfCompartments>
+ <listOfSpecies>
+ <species id = "Xo" boundaryCondition = "true" initialConcentration = "1" compartment = "compartment"/>
+ <species id = "X1" boundaryCondition = "true" initialConcentration = "0" compartment = "compartment"/>
+ <species id = "S1" boundaryCondition = "false" initialConcentration = "0.666666666666667" compartment = "compartment"/>
+ <species id = "S2" boundaryCondition = "false" initialConcentration = "0.25" compartment = "compartment"/>
+ <species id = "S3" boundaryCondition = "false" initialConcentration = "0.181818181818182" compartment = "compartment"/>
+ </listOfSpecies>
+ <listOfParameters>
+ <parameter id = "k1" value = "0.1"/>
+ <parameter id = "k2" value = "0.15"/>
+ <parameter id = "k3" value = "0.4"/>
+ <parameter id = "k4" value = "0.55"/>
+ </listOfParameters>
+ <listOfReactions>
+ <reaction id = "_J1" reversible = "false">
+ <listOfReactants>
+ <speciesReference species = "Xo" stoichiometry = "1"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species = "S1" stoichiometry = "1"/>
+ </listOfProducts>
+ <kineticLaw>
+ <math xmlns = "http://www.w3.org/1998/Math/MathML">
+ <apply>
+ <times/>
+ <ci>
+ k1
+ </ci>
+ <ci>
+ Xo
+ </ci>
+ </apply>
+ </math>
+ </kineticLaw>
+ </reaction>
+ <reaction id = "_J2" reversible = "false">
+ <listOfReactants>
+ <speciesReference species = "S1" stoichiometry = "1"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species = "S2" stoichiometry = "1"/>
+ </listOfProducts>
+ <kineticLaw>
+ <math xmlns = "http://www.w3.org/1998/Math/MathML">
+ <apply>
+ <times/>
+ <ci>
+ k2
+ </ci>
+ <ci>
+ S1
+ </ci>
+ </apply>
+ </math>
+ </kineticLaw>
+ </reaction>
+ <reaction id = "_J3" reversible = "false">
+ <listOfReactants>
+ <speciesReference species = "S2" stoichiometry = "1"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species = "S3" stoichiometry = "1"/>
+ </listOfProducts>
+ <kineticLaw>
+ <math xmlns = "http://www.w3.org/1998/Math/MathML">
+ <apply>
+ <times/>
+ <ci>
+ k3
+ </ci>
+ <ci>
+ S2
+ </ci>
+ </apply>
+ </math>
+ </kineticLaw>
+ </reaction>
+ <reaction id = "_J4" reversible = "false">
+ <listOfReactants>
+ <speciesReference species = "S3" stoichiometry = "1"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species = "X1" stoichiometry = "1"/>
+ </listOfProducts>
+ <kineticLaw>
+ <math xmlns = "http://www.w3.org/1998/Math/MathML">
+ <apply>
+ <times/>
+ <ci>
+ k4
+ </ci>
+ <ci>
+ S3
+ </ci>
+ </apply>
+ </math>
+ </kineticLaw>
+ </reaction>
+ </listOfReactions>
+ </model>
+</sbml>
diff --git a/models/ss_threestep.xml b/models/ss_threestep.xml
index 75a115a..33d9810 100644
--- a/models/ss_threestep.xml
+++ b/models/ss_threestep.xml
@@ -1,108 +1,108 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!-- Created by XMLPrettyPrinter on 6/19/2012 from -->
-<sbml xmlns = "http://www.sbml.org/sbml/level2" level = "2" version = "1">
- <model id = "cell">
- <listOfCompartments>
- <compartment id = "compartment" size = "1"/>
- </listOfCompartments>
- <listOfSpecies>
- <species id = "Xo" boundaryCondition = "true" initialConcentration = "1" compartment = "compartment"/>
- <species id = "X1" boundaryCondition = "true" initialConcentration = "0" compartment = "compartment"/>
- <species id = "S1" boundaryCondition = "false" initialConcentration = "0.0" compartment = "compartment"/>
- <species id = "S2" boundaryCondition = "false" initialConcentration = "0.0" compartment = "compartment"/>
- <species id = "S3" boundaryCondition = "false" initialConcentration = "0.0" compartment = "compartment"/>
- </listOfSpecies>
- <listOfParameters>
- <parameter id = "k1" value = "0.1"/>
- <parameter id = "k2" value = "0.15"/>
- <parameter id = "k3" value = "0.4"/>
- <parameter id = "k4" value = "0.55"/>
- </listOfParameters>
- <listOfReactions>
- <reaction id = "_J1" reversible = "false">
- <listOfReactants>
- <speciesReference species = "Xo" stoichiometry = "1"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species = "S1" stoichiometry = "1"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns = "http://www.w3.org/1998/Math/MathML">
- <apply>
- <times/>
- <ci>
- k1
- </ci>
- <ci>
- Xo
- </ci>
- </apply>
- </math>
- </kineticLaw>
- </reaction>
- <reaction id = "_J2" reversible = "false">
- <listOfReactants>
- <speciesReference species = "S1" stoichiometry = "1"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species = "S2" stoichiometry = "1"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns = "http://www.w3.org/1998/Math/MathML">
- <apply>
- <times/>
- <ci>
- k2
- </ci>
- <ci>
- S1
- </ci>
- </apply>
- </math>
- </kineticLaw>
- </reaction>
- <reaction id = "_J3" reversible = "false">
- <listOfReactants>
- <speciesReference species = "S2" stoichiometry = "1"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species = "S3" stoichiometry = "1"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns = "http://www.w3.org/1998/Math/MathML">
- <apply>
- <times/>
- <ci>
- k3
- </ci>
- <ci>
- S2
- </ci>
- </apply>
- </math>
- </kineticLaw>
- </reaction>
- <reaction id = "_J4" reversible = "false">
- <listOfReactants>
- <speciesReference species = "S3" stoichiometry = "1"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species = "X1" stoichiometry = "1"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns = "http://www.w3.org/1998/Math/MathML">
- <apply>
- <times/>
- <ci>
- k4
- </ci>
- <ci>
- S3
- </ci>
- </apply>
- </math>
- </kineticLaw>
- </reaction>
- </listOfReactions>
- </model>
-</sbml>
+<?xml version="1.0" encoding="UTF-8"?>
+<!-- Created by XMLPrettyPrinter on 6/19/2012 from -->
+<sbml xmlns = "http://www.sbml.org/sbml/level2" level = "2" version = "1">
+ <model id = "cell">
+ <listOfCompartments>
+ <compartment id = "compartment" size = "1"/>
+ </listOfCompartments>
+ <listOfSpecies>
+ <species id = "Xo" boundaryCondition = "true" initialConcentration = "1" compartment = "compartment"/>
+ <species id = "X1" boundaryCondition = "true" initialConcentration = "0" compartment = "compartment"/>
+ <species id = "S1" boundaryCondition = "false" initialConcentration = "0.0" compartment = "compartment"/>
+ <species id = "S2" boundaryCondition = "false" initialConcentration = "0.0" compartment = "compartment"/>
+ <species id = "S3" boundaryCondition = "false" initialConcentration = "0.0" compartment = "compartment"/>
+ </listOfSpecies>
+ <listOfParameters>
+ <parameter id = "k1" value = "0.1"/>
+ <parameter id = "k2" value = "0.15"/>
+ <parameter id = "k3" value = "0.4"/>
+ <parameter id = "k4" value = "0.55"/>
+ </listOfParameters>
+ <listOfReactions>
+ <reaction id = "_J1" reversible = "false">
+ <listOfReactants>
+ <speciesReference species = "Xo" stoichiometry = "1"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species = "S1" stoichiometry = "1"/>
+ </listOfProducts>
+ <kineticLaw>
+ <math xmlns = "http://www.w3.org/1998/Math/MathML">
+ <apply>
+ <times/>
+ <ci>
+ k1
+ </ci>
+ <ci>
+ Xo
+ </ci>
+ </apply>
+ </math>
+ </kineticLaw>
+ </reaction>
+ <reaction id = "_J2" reversible = "false">
+ <listOfReactants>
+ <speciesReference species = "S1" stoichiometry = "1"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species = "S2" stoichiometry = "1"/>
+ </listOfProducts>
+ <kineticLaw>
+ <math xmlns = "http://www.w3.org/1998/Math/MathML">
+ <apply>
+ <times/>
+ <ci>
+ k2
+ </ci>
+ <ci>
+ S1
+ </ci>
+ </apply>
+ </math>
+ </kineticLaw>
+ </reaction>
+ <reaction id = "_J3" reversible = "false">
+ <listOfReactants>
+ <speciesReference species = "S2" stoichiometry = "1"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species = "S3" stoichiometry = "1"/>
+ </listOfProducts>
+ <kineticLaw>
+ <math xmlns = "http://www.w3.org/1998/Math/MathML">
+ <apply>
+ <times/>
+ <ci>
+ k3
+ </ci>
+ <ci>
+ S2
+ </ci>
+ </apply>
+ </math>
+ </kineticLaw>
+ </reaction>
+ <reaction id = "_J4" reversible = "false">
+ <listOfReactants>
+ <speciesReference species = "S3" stoichiometry = "1"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species = "X1" stoichiometry = "1"/>
+ </listOfProducts>
+ <kineticLaw>
+ <math xmlns = "http://www.w3.org/1998/Math/MathML">
+ <apply>
+ <times/>
+ <ci>
+ k4
+ </ci>
+ <ci>
+ S3
+ </ci>
+ </apply>
+ </math>
+ </kineticLaw>
+ </reaction>
+ </listOfReactions>
+ </model>
+</sbml>
diff --git a/models/test_models/CMakeLists.txt b/models/test_models/CMakeLists.txt
index eda3faf..7fafd72 100644
--- a/models/test_models/CMakeLists.txt
+++ b/models/test_models/CMakeLists.txt
@@ -1,17 +1,17 @@
-cmake_minimum_required(VERSION 2.8)
-
-PROJECT(rrModels)
-
-set(test_models
-TestModel_1.xml
-)
-
-if(BUILD_TESTS)
-add_subdirectory(reference_data)
-endif()
-
-install(
-FILES ${test_models}
-DESTINATION models/test_models
-COMPONENT testing
-)
+cmake_minimum_required(VERSION 2.8)
+
+PROJECT(rrModels)
+
+set(test_models
+TestModel_1.xml
+)
+
+if(BUILD_TESTS)
+add_subdirectory(reference_data)
+endif()
+
+install(
+FILES ${test_models}
+DESTINATION models/test_models
+COMPONENT testing
+)
diff --git a/models/test_models/TestModel_1.xml b/models/test_models/TestModel_1.xml
index d51e185..67e3327 100644
--- a/models/test_models/TestModel_1.xml
+++ b/models/test_models/TestModel_1.xml
@@ -1,162 +1,162 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!-- Created by XMLPrettyPrinter on 11/28/2012 from -->
-<sbml xmlns = "http://www.sbml.org/sbml/level2/version4" level = "2" version = "4">
- <model id = "cell">
- <listOfCompartments>
- <compartment id = "compartment" size = "1"/>
- </listOfCompartments>
- <listOfSpecies>
- <species id = "src" boundaryCondition = "true" initialConcentration = "0" compartment = "compartment"/>
- <species id = "waste" boundaryCondition = "true" initialConcentration = "0" compartment = "compartment"/>
- <species id = "Xo" boundaryCondition = "true" initialConcentration = "1" compartment = "compartment"/>
- <species id = "X1" boundaryCondition = "true" initialConcentration = "0" compartment = "compartment"/>
- <species id = "S1" boundaryCondition = "false" initialConcentration = "0.569694868238558" compartment = "compartment"/>
- <species id = "S2" boundaryCondition = "false" initialConcentration = "0.208044382801664" compartment = "compartment"/>
- <species id = "S3" boundaryCondition = "false" initialConcentration = "0.13002773925104" compartment = "compartment"/>
- </listOfSpecies>
- <listOfParameters>
- <parameter id = "k1" value = "0.1"/>
- <parameter id = "k_1" value = "0.05"/>
- <parameter id = "k2" value = "0.15"/>
- <parameter id = "k_2" value = "0.067"/>
- <parameter id = "k3" value = "0.4"/>
- <parameter id = "k_3" value = "0.09"/>
- <parameter id = "k4" value = "0.55"/>
- <parameter id = "k_4" value = "0.01"/>
- </listOfParameters>
- <listOfReactions>
- <reaction id = "J1" reversible = "false">
- <listOfReactants>
- <speciesReference species = "Xo" stoichiometry = "1"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species = "S1" stoichiometry = "1"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns = "http://www.w3.org/1998/Math/MathML">
- <apply>
- <minus/>
- <apply>
- <times/>
- <ci>
- k1
- </ci>
- <ci>
- Xo
- </ci>
- </apply>
- <apply>
- <times/>
- <ci>
- k_1
- </ci>
- <ci>
- S1
- </ci>
- </apply>
- </apply>
- </math>
- </kineticLaw>
- </reaction>
- <reaction id = "J2" reversible = "false">
- <listOfReactants>
- <speciesReference species = "S1" stoichiometry = "1"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species = "S2" stoichiometry = "1"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns = "http://www.w3.org/1998/Math/MathML">
- <apply>
- <minus/>
- <apply>
- <times/>
- <ci>
- k2
- </ci>
- <ci>
- S1
- </ci>
- </apply>
- <apply>
- <times/>
- <ci>
- k_2
- </ci>
- <ci>
- S2
- </ci>
- </apply>
- </apply>
- </math>
- </kineticLaw>
- </reaction>
- <reaction id = "J3" reversible = "false">
- <listOfReactants>
- <speciesReference species = "S2" stoichiometry = "1"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species = "S3" stoichiometry = "1"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns = "http://www.w3.org/1998/Math/MathML">
- <apply>
- <minus/>
- <apply>
- <times/>
- <ci>
- k3
- </ci>
- <ci>
- S2
- </ci>
- </apply>
- <apply>
- <times/>
- <ci>
- k_3
- </ci>
- <ci>
- S3
- </ci>
- </apply>
- </apply>
- </math>
- </kineticLaw>
- </reaction>
- <reaction id = "J4" reversible = "false">
- <listOfReactants>
- <speciesReference species = "S3" stoichiometry = "1"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species = "X1" stoichiometry = "1"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns = "http://www.w3.org/1998/Math/MathML">
- <apply>
- <minus/>
- <apply>
- <times/>
- <ci>
- k4
- </ci>
- <ci>
- S3
- </ci>
- </apply>
- <apply>
- <times/>
- <ci>
- k_4
- </ci>
- <ci>
- X1
- </ci>
- </apply>
- </apply>
- </math>
- </kineticLaw>
- </reaction>
- </listOfReactions>
- </model>
-</sbml>
+<?xml version="1.0" encoding="UTF-8"?>
+<!-- Created by XMLPrettyPrinter on 11/28/2012 from -->
+<sbml xmlns = "http://www.sbml.org/sbml/level2/version4" level = "2" version = "4">
+ <model id = "cell">
+ <listOfCompartments>
+ <compartment id = "compartment" size = "1"/>
+ </listOfCompartments>
+ <listOfSpecies>
+ <species id = "src" boundaryCondition = "true" initialConcentration = "0" compartment = "compartment"/>
+ <species id = "waste" boundaryCondition = "true" initialConcentration = "0" compartment = "compartment"/>
+ <species id = "Xo" boundaryCondition = "true" initialConcentration = "1" compartment = "compartment"/>
+ <species id = "X1" boundaryCondition = "true" initialConcentration = "0" compartment = "compartment"/>
+ <species id = "S1" boundaryCondition = "false" initialConcentration = "0.569694868238558" compartment = "compartment"/>
+ <species id = "S2" boundaryCondition = "false" initialConcentration = "0.208044382801664" compartment = "compartment"/>
+ <species id = "S3" boundaryCondition = "false" initialConcentration = "0.13002773925104" compartment = "compartment"/>
+ </listOfSpecies>
+ <listOfParameters>
+ <parameter id = "k1" value = "0.1"/>
+ <parameter id = "k_1" value = "0.05"/>
+ <parameter id = "k2" value = "0.15"/>
+ <parameter id = "k_2" value = "0.067"/>
+ <parameter id = "k3" value = "0.4"/>
+ <parameter id = "k_3" value = "0.09"/>
+ <parameter id = "k4" value = "0.55"/>
+ <parameter id = "k_4" value = "0.01"/>
+ </listOfParameters>
+ <listOfReactions>
+ <reaction id = "J1" reversible = "false">
+ <listOfReactants>
+ <speciesReference species = "Xo" stoichiometry = "1"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species = "S1" stoichiometry = "1"/>
+ </listOfProducts>
+ <kineticLaw>
+ <math xmlns = "http://www.w3.org/1998/Math/MathML">
+ <apply>
+ <minus/>
+ <apply>
+ <times/>
+ <ci>
+ k1
+ </ci>
+ <ci>
+ Xo
+ </ci>
+ </apply>
+ <apply>
+ <times/>
+ <ci>
+ k_1
+ </ci>
+ <ci>
+ S1
+ </ci>
+ </apply>
+ </apply>
+ </math>
+ </kineticLaw>
+ </reaction>
+ <reaction id = "J2" reversible = "false">
+ <listOfReactants>
+ <speciesReference species = "S1" stoichiometry = "1"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species = "S2" stoichiometry = "1"/>
+ </listOfProducts>
+ <kineticLaw>
+ <math xmlns = "http://www.w3.org/1998/Math/MathML">
+ <apply>
+ <minus/>
+ <apply>
+ <times/>
+ <ci>
+ k2
+ </ci>
+ <ci>
+ S1
+ </ci>
+ </apply>
+ <apply>
+ <times/>
+ <ci>
+ k_2
+ </ci>
+ <ci>
+ S2
+ </ci>
+ </apply>
+ </apply>
+ </math>
+ </kineticLaw>
+ </reaction>
+ <reaction id = "J3" reversible = "false">
+ <listOfReactants>
+ <speciesReference species = "S2" stoichiometry = "1"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species = "S3" stoichiometry = "1"/>
+ </listOfProducts>
+ <kineticLaw>
+ <math xmlns = "http://www.w3.org/1998/Math/MathML">
+ <apply>
+ <minus/>
+ <apply>
+ <times/>
+ <ci>
+ k3
+ </ci>
+ <ci>
+ S2
+ </ci>
+ </apply>
+ <apply>
+ <times/>
+ <ci>
+ k_3
+ </ci>
+ <ci>
+ S3
+ </ci>
+ </apply>
+ </apply>
+ </math>
+ </kineticLaw>
+ </reaction>
+ <reaction id = "J4" reversible = "false">
+ <listOfReactants>
+ <speciesReference species = "S3" stoichiometry = "1"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species = "X1" stoichiometry = "1"/>
+ </listOfProducts>
+ <kineticLaw>
+ <math xmlns = "http://www.w3.org/1998/Math/MathML">
+ <apply>
+ <minus/>
+ <apply>
+ <times/>
+ <ci>
+ k4
+ </ci>
+ <ci>
+ S3
+ </ci>
+ </apply>
+ <apply>
+ <times/>
+ <ci>
+ k_4
+ </ci>
+ <ci>
+ X1
+ </ci>
+ </apply>
+ </apply>
+ </math>
+ </kineticLaw>
+ </reaction>
+ </listOfReactions>
+ </model>
+</sbml>
diff --git a/models/test_models/reference_data/CMakeLists.txt b/models/test_models/reference_data/CMakeLists.txt
index ed84197..9e97457 100644
--- a/models/test_models/reference_data/CMakeLists.txt
+++ b/models/test_models/reference_data/CMakeLists.txt
@@ -1,13 +1,13 @@
-cmake_minimum_required(VERSION 2.8)
-
-PROJECT(ref_data)
-
-set(ref_data_files
-TestModel_1.dat
-)
-
-install(
-FILES ${ref_data_files}
-DESTINATION models/test_models/reference_data
-COMPONENT testing
-)
+cmake_minimum_required(VERSION 2.8)
+
+PROJECT(ref_data)
+
+set(ref_data_files
+TestModel_1.dat
+)
+
+install(
+FILES ${ref_data_files}
+DESTINATION models/test_models/reference_data
+COMPONENT testing
+)
diff --git a/models/test_models/reference_data/TestModel_1.dat b/models/test_models/reference_data/TestModel_1.dat
index 9058a74..080859a 100644
--- a/models/test_models/reference_data/TestModel_1.dat
+++ b/models/test_models/reference_data/TestModel_1.dat
@@ -1,95 +1,95 @@
-# The following reference data is taken using C# roadrunner version 2.0.1
-# Input model for the data below is TestModel_1.xml. This model file can be found in roadrunners reference_data folder.
-
-[SBML_FILE]
-sbmlFile=Test_1.xml
-
-[STEADY_STATE_CONCENTRATIONS]
-S1 = 0.569694868238558
-S2 = 0.208044382801664
-S3 = 0.13002773925104
-J1 = 0.0715152565880721
-J2 = 0.0715152565880721
-J3 = 0.0715152565880721
-J4 = 0.0715152565880721
-
-[FULL_JACOBIAN]
--0.2 0.067 0
-0.15 -0.467 0.09
- 0 0.4 -0.64
-
-[REDUCED_REORDERED_JACOBIAN]
--0.2 0 0.067
-0 -0.64 0.4
-0.15 0.09 -0.467
-
-
-[FULL_REORDERED_JACOBIAN]
--0.2 0 0.067
-0 -0.64 0.4
-0.15 0.09 -0.467
-
-
-[EIGEN_VALUES]
-eigen_S1 = -0.157263450928358,0
-eigen_S2 = -0.382371338369919,0
-eigen_S3 = -0.157263450928358,0
-
-[STOICHIOMETRY_MATRIX]
-1 -1 0 0
-0 0 1 -1
-0 1 -1 0
-
-[REORDERED_STOICHIOMETRY_MATRIX]
-1 -1 0 0
-0 0 1 -1
-0 1 -1 0
-
-[FULLY_REORDERED_STOICHIOMETRY_MATRIX]
-1 -1 0 0
-0 0 1 -1
-0 1 -1 0
-
-[LINK_MATRIX]
-1 0 0
-0 1 0
-0 0 1
-
-[NR_MATRIX]
-1 -1 0 0
-0 0 1 -1
-0 1 -1 0
-
-[LO_MATRIX]
-
-
-[UNSCALED_ELASTICITY_MATRIX]
--0.0499999999999996 0 0
-0.15 0 -0.0670000000000002
-0 -0.0899999999999976 0.4
-0 0.55 0
-
-
-[SCALED_ELASTICITY_MATRIX]
--0.398303030303028 0 0
-1.19490909090909 0 -0.194909090909091
-0 -0.163636363636359 1.16363636363636
-0 1 0
-
-[UNSCALED_CONCENTRATION_CONTROL_COEFFICIENT_MATRIX]
-5.6969486823856 -4.76768377253816 -0.798587031900144 -0.130677877947294
-1.3002773925104 0.433425797503465 0.0725988210818309 -1.8063020110957
-2.08044382801664 0.693481276005544 -2.38384188626907 -0.390083217753115
-
-[UNSCALED_FLUX_CONTROL_COEFFICIENT_MATRIX]
-0.715152565880722 0.238384188626906 0.0399293515950069 0.00653389389736467
-0.715152565880722 0.238384188626906 0.0399293515950069 0.00653389389736467
-0.715152565880722 0.238384188626906 0.039929351595007 0.00653389389736467
-0.715152565880722 0.238384188626906 0.0399293515950071 0.0065338938973647
-
-[SCALED_FLUX_CONTROL_COEFFICIENT_MATRIX]
-0.715152565880722 0.238384188626906 0.0399293515950069 0.00653389389736468
-0.715152565880722 0.238384188626906 0.0399293515950069 0.00653389389736467
-0.715152565880722 0.238384188626906 0.039929351595007 0.00653389389736467
-0.715152565880722 0.238384188626906 0.0399293515950071 0.0065338938973647
-
+# The following reference data is taken using C# roadrunner version 2.0.1
+# Input model for the data below is TestModel_1.xml. This model file can be found in roadrunners reference_data folder.
+
+[SBML_FILE]
+sbmlFile=Test_1.xml
+
+[STEADY_STATE_CONCENTRATIONS]
+S1 = 0.569694868238558
+S2 = 0.208044382801664
+S3 = 0.13002773925104
+J1 = 0.0715152565880721
+J2 = 0.0715152565880721
+J3 = 0.0715152565880721
+J4 = 0.0715152565880721
+
+[FULL_JACOBIAN]
+-0.2 0.067 0
+0.15 -0.467 0.09
+ 0 0.4 -0.64
+
+[REDUCED_REORDERED_JACOBIAN]
+-0.2 0 0.067
+0 -0.64 0.4
+0.15 0.09 -0.467
+
+
+[FULL_REORDERED_JACOBIAN]
+-0.2 0 0.067
+0 -0.64 0.4
+0.15 0.09 -0.467
+
+
+[EIGEN_VALUES]
+eigen_S1 = -0.157263450928358,0
+eigen_S2 = -0.382371338369919,0
+eigen_S3 = -0.157263450928358,0
+
+[STOICHIOMETRY_MATRIX]
+1 -1 0 0
+0 0 1 -1
+0 1 -1 0
+
+[REORDERED_STOICHIOMETRY_MATRIX]
+1 -1 0 0
+0 0 1 -1
+0 1 -1 0
+
+[FULLY_REORDERED_STOICHIOMETRY_MATRIX]
+1 -1 0 0
+0 0 1 -1
+0 1 -1 0
+
+[LINK_MATRIX]
+1 0 0
+0 1 0
+0 0 1
+
+[NR_MATRIX]
+1 -1 0 0
+0 0 1 -1
+0 1 -1 0
+
+[LO_MATRIX]
+
+
+[UNSCALED_ELASTICITY_MATRIX]
+-0.0499999999999996 0 0
+0.15 0 -0.0670000000000002
+0 -0.0899999999999976 0.4
+0 0.55 0
+
+
+[SCALED_ELASTICITY_MATRIX]
+-0.398303030303028 0 0
+1.19490909090909 0 -0.194909090909091
+0 -0.163636363636359 1.16363636363636
+0 1 0
+
+[UNSCALED_CONCENTRATION_CONTROL_COEFFICIENT_MATRIX]
+5.6969486823856 -4.76768377253816 -0.798587031900144 -0.130677877947294
+1.3002773925104 0.433425797503465 0.0725988210818309 -1.8063020110957
+2.08044382801664 0.693481276005544 -2.38384188626907 -0.390083217753115
+
+[UNSCALED_FLUX_CONTROL_COEFFICIENT_MATRIX]
+0.715152565880722 0.238384188626906 0.0399293515950069 0.00653389389736467
+0.715152565880722 0.238384188626906 0.0399293515950069 0.00653389389736467
+0.715152565880722 0.238384188626906 0.039929351595007 0.00653389389736467
+0.715152565880722 0.238384188626906 0.0399293515950071 0.0065338938973647
+
+[SCALED_FLUX_CONTROL_COEFFICIENT_MATRIX]
+0.715152565880722 0.238384188626906 0.0399293515950069 0.00653389389736468
+0.715152565880722 0.238384188626906 0.0399293515950069 0.00653389389736467
+0.715152565880722 0.238384188626906 0.039929351595007 0.00653389389736467
+0.715152565880722 0.238384188626906 0.0399293515950071 0.0065338938973647
+
diff --git a/rr_support/CMakeLists.txt b/rr_support/CMakeLists.txt
index ca3127e..1b8c8d3 100644
--- a/rr_support/CMakeLists.txt
+++ b/rr_support/CMakeLists.txt
@@ -1,16 +1,16 @@
-cmake_minimum_required(VERSION 2.8)
-project(rr_support)
-set(SUPPORT_FOLDER ${CMAKE_CURRENT_SOURCE_DIR})
-
-#=== Install support code for on the fly compilation
-FILE(GLOB rr_support_headers *.h)
-FILE(GLOB rr_support_source *.c)
-
-install(FILES
- ${rr_support_headers}
- ${rr_support_source}
- gurgle.dat
- DESTINATION rr_support
- COMPONENT rr_core
- )
-
+cmake_minimum_required(VERSION 2.8)
+project(rr_support)
+set(SUPPORT_FOLDER ${CMAKE_CURRENT_SOURCE_DIR})
+
+#=== Install support code for on the fly compilation
+FILE(GLOB rr_support_headers *.h)
+FILE(GLOB rr_support_source *.c)
+
+install(FILES
+ ${rr_support_headers}
+ ${rr_support_source}
+ gurgle.dat
+ DESTINATION rr_support
+ COMPONENT rr_core
+ )
+
diff --git a/rr_support/bcc.cfg b/rr_support/bcc.cfg
index 81a2663..dd6c157 100644
--- a/rr_support/bcc.cfg
+++ b/rr_support/bcc.cfg
@@ -1,7 +1,7 @@
--I"C:\Program Files (x86)\Embarcadero\RAD Studio\8.0\include";"C:\Program Files (x86)\Embarcadero\RAD Studio\8.0\include\windows\crtl";"C:\Program Files (x86)\Embarcadero\RAD Studio\8.0\include\dinkumware";"C:\Program Files (x86)\Embarcadero\RAD Studio\8.0\include\windows\rtl";"C:\Program Files (x86)\Embarcadero\RAD Studio\8.0\include\windows\vcl";"C:\Program Files (x86)\Embarcadero\RAD Studio\8.0\include\windows\sdk"
--L"C:\Program Files (x86)\Embarcadero\RAD Studio\8.0\lib\win32\release";"C:\Program Files (x86)\Embarcadero\RAD Studio\8.0\lib\win32\release\psdk"
--I"R:\roadrunnerwork\trunk\source\rr_support"
--L"R:\roadrunnerwork\trunk\source\rr_support"
-
--D"BUILD_MODEL_DLL";"DEBUG_SPF"
-
+-I"C:\Program Files (x86)\Embarcadero\RAD Studio\8.0\include";"C:\Program Files (x86)\Embarcadero\RAD Studio\8.0\include\windows\crtl";"C:\Program Files (x86)\Embarcadero\RAD Studio\8.0\include\dinkumware";"C:\Program Files (x86)\Embarcadero\RAD Studio\8.0\include\windows\rtl";"C:\Program Files (x86)\Embarcadero\RAD Studio\8.0\include\windows\vcl";"C:\Program Files (x86)\Embarcadero\RAD Studio\8.0\include\windows\sdk"
+-L"C:\Program Files (x86)\Embarcadero\RAD Studio\8.0\lib\win32\release";"C:\Program Files (x86)\Embarcadero\RAD Studio\8.0\lib\win32\release\psdk"
+-I"R:\roadrunnerwork\trunk\source\rr_support"
+-L"R:\roadrunnerwork\trunk\source\rr_support"
+
+-D"BUILD_MODEL_DLL";"DEBUG_SPF"
+
diff --git a/rr_support/rrSupport.c b/rr_support/rrSupport.c
index 5bb680a..5e2fffc 100644
--- a/rr_support/rrSupport.c
+++ b/rr_support/rrSupport.c
@@ -480,49 +480,49 @@ double arctanh(double a)
//First of all sine and cosine tables
-
-double sinTable[] = {
-0.0, //sin(0)
-0.17364817766693034885171662676931 , //sin(10)
-0.34202014332566873304409961468226 , //sin(20)
-0.5 , //sin(30)
-0.64278760968653932632264340990726 , //sin(40)
-0.76604444311897803520239265055542 , //sin(50)
-0.86602540378443864676372317075294 , //sin(60)
-0.93969262078590838405410927732473 , //sin(70)
-0.98480775301220805936674302458952 , //sin(80)
-1.0 //sin(90)
-};
-
-double cosTable[] = {
-1.0 , //cos(0)
-0.99984769515639123915701155881391 , //cos(1)
-0.99939082701909573000624344004393 , //cos(2)
-0.99862953475457387378449205843944 , //cos(3)
-0.99756405025982424761316268064426 , //cos(4)
-0.99619469809174553229501040247389 , //cos(5)
-0.99452189536827333692269194498057 , //cos(6)
-0.99254615164132203498006158933058 , //cos(7)
-0.99026806874157031508377486734485 , //cos(8)
-0.98768834059513772619004024769344 //cos(9)
-};
-// sin (a+b) = sin(a)*cos(b) + sin(b)*cos(a)
-// a = 10*m where m is a natural number and 0<= m <= 90
-// i.e. lets a+b = 18.22
-// then a = 10, b = 8.22
-
-
-double myFastSin(double angle)
-{
-// int aVal;
-// double bVal;
-// static double holyConstant = 0.017453292519943295769236907684886;
-//
-// aVal = angle * 0.1;
-// bVal = angle - (10.0 * aVal);
-//
-// return sinTable[aVal]* cosTable[ spf_ceil(bVal)] + bVal * holyConstant * sinTable[9-aVal];
-// return -1;//sin(angle);//sinTable[aVal]*cosTable[(int)bVal] + bVal*holyConstant*sinTable[9-aVal];
- return 0;
+
+double sinTable[] = {
+0.0, //sin(0)
+0.17364817766693034885171662676931 , //sin(10)
+0.34202014332566873304409961468226 , //sin(20)
+0.5 , //sin(30)
+0.64278760968653932632264340990726 , //sin(40)
+0.76604444311897803520239265055542 , //sin(50)
+0.86602540378443864676372317075294 , //sin(60)
+0.93969262078590838405410927732473 , //sin(70)
+0.98480775301220805936674302458952 , //sin(80)
+1.0 //sin(90)
+};
+
+double cosTable[] = {
+1.0 , //cos(0)
+0.99984769515639123915701155881391 , //cos(1)
+0.99939082701909573000624344004393 , //cos(2)
+0.99862953475457387378449205843944 , //cos(3)
+0.99756405025982424761316268064426 , //cos(4)
+0.99619469809174553229501040247389 , //cos(5)
+0.99452189536827333692269194498057 , //cos(6)
+0.99254615164132203498006158933058 , //cos(7)
+0.99026806874157031508377486734485 , //cos(8)
+0.98768834059513772619004024769344 //cos(9)
+};
+// sin (a+b) = sin(a)*cos(b) + sin(b)*cos(a)
+// a = 10*m where m is a natural number and 0<= m <= 90
+// i.e. lets a+b = 18.22
+// then a = 10, b = 8.22
+
+
+double myFastSin(double angle)
+{
+// int aVal;
+// double bVal;
+// static double holyConstant = 0.017453292519943295769236907684886;
+//
+// aVal = angle * 0.1;
+// bVal = angle - (10.0 * aVal);
+//
+// return sinTable[aVal]* cosTable[ spf_ceil(bVal)] + bVal * holyConstant * sinTable[9-aVal];
+// return -1;//sin(angle);//sinTable[aVal]*cosTable[(int)bVal] + bVal*holyConstant*sinTable[9-aVal];
+ return 0;
}
diff --git a/source/llvm_testing/run_cpp_tests.bat b/source/llvm_testing/run_cpp_tests.bat
index fcd6416..d3774cf 100644
--- a/source/llvm_testing/run_cpp_tests.bat
+++ b/source/llvm_testing/run_cpp_tests.bat
@@ -1,18 +1,18 @@
-
-echo "Running tests..."
- at echo off
-
-REM === Call with three arguments, eg vs 2010 Release..
-set compiler=%1
-set compiler_version=%2
-set build_type=%3
-
-set install_folder=r:\installs\%compiler%\%compiler_version%\%build_type%
-set model_folder=r:\models
-set wc=r:\rrl
-set report_file=%wc%\reports\%compiler%\%compiler_version%\cpp_test_%build_type%.xml
-set temp_folder=r:\rrTemp\%compiler_version%
-
-cxx_api_tests.exe -m%model_folder% -r%report_file% -t%temp_folder%
-
-echo done...
+
+echo "Running tests..."
+ at echo off
+
+REM === Call with three arguments, eg vs 2010 Release..
+set compiler=%1
+set compiler_version=%2
+set build_type=%3
+
+set install_folder=r:\installs\%compiler%\%compiler_version%\%build_type%
+set model_folder=r:\models
+set wc=r:\rrl
+set report_file=%wc%\reports\%compiler%\%compiler_version%\cpp_test_%build_type%.xml
+set temp_folder=r:\rrTemp\%compiler_version%
+
+cxx_api_tests.exe -m%model_folder% -r%report_file% -t%temp_folder%
+
+echo done...
diff --git a/source/testing/CMakeLists.txt b/source/testing/CMakeLists.txt
index aa41204..f0cd30c 100644
--- a/source/testing/CMakeLists.txt
+++ b/source/testing/CMakeLists.txt
@@ -1,122 +1,122 @@
-CMAKE_MINIMUM_REQUIRED(VERSION 2.6.3 FATAL_ERROR)
-PROJECT(RR_CXX_API_TESTS)
-
-set(target cxx_api_tests)
-
-set(tests
-tests/base
-tests/sbml_test_suite
-tests/steady_state
-tests/stoichiometric
-)
-
-add_executable( ${target}
-main
-src/Args
-src/rrTestUtils
-${tests}
-)
-
-set_property(TARGET ${target}
- PROPERTY COMPILE_DEFINITIONS
-LIBSBML_USE_CPP_NAMESPACE
-LIBSBML_STATIC
-STATIC_LIBSTRUCT
-STATIC_PUGI
-STATIC_RR
-STATIC_NLEQ
-)
-
-link_directories(
-${THIRD_PARTY_INSTALL_FOLDER}/lib
-)
-
-include_directories(
-src
-${RR_ROOT}
-${THIRD_PARTY_FOLDER}/unit_test/src
-)
-
-if(UNIX)
-set(staticLibPrefix ".a")
-set(sharedLibPrefix ".so")
-else()
-set(staticLibPrefix "")
-set(sharedLibPrefix "")
-endif()
-
-if(WIN32)
-target_link_libraries (${target}
-roadrunner-static
-unit_test-static${staticLibPrefix}
-)
-endif()
-
-if(UNIX) #Don't know why static roadrunner fails....?
-target_link_libraries (${target}
-roadrunner-static
-libunit_test-static${staticLibPrefix}
-#nleq-static.a
-#rr-libstruct-static
-lapack
-blas
-f2c
-#libsbml-static.a
-#libxml2.so
-#sundials_nvecserial.a
-#sundials_cvode.a
-#pthread
-#poco_foundation-static.a
-#dl
-)
-endif()
-
-#set(resultsDir "${CMAKE_SOURCE_DIR}/reports")
-#
-#if(${BORLAND})
-#set(resultsFile "${resultsDir}/cpp_api_tests-cg_xe1.xml")
-#elseif(${MSVC})
-#set(resultsFile "${resultsDir}/cpp_api_tests-vs_2010.xml")
-#elseif(CMAKE_COMPILER_IS_GNUCC)
-#set(resultsFile "${resultsDir}/cpp_api_tests-gcc.xml")
-#else()
-#set(resultsFile "${resultsDir}/cpp_api_tests_unknown_compiler.xml")
-#endif()
-#
-#set(sbmlModelsDir "${CMAKE_SOURCE_DIR}/models")
-#set(compilerFolder "${CMAKE_SOURCE_DIR}/third_party/compilers/tcc")
-#set(supportCodeFolder "/r/rrl/rr_support")
-#
-#if(UNIX)
-#set(compilerFolder "")
-#endif()
-#
-#Message("SupportCodeFolder is: " ${supportCodeFolder})
-# Call like this -mr:\rrl\models -rr:\rrl\wiki\reports\file -tr:\rrTemp -sSupportCodeFolder -lCompilerFolder
-#add_custom_command(
-# OUTPUT ${resultsFile}
-# COMMAND ${target} -m${sbmlModelsDir} -l${compilerFolder} -s${supportCodeFolder} -r${resultsFile} -v
-# WORKING_DIRECTORY ${PROJECT_SOURCE_DIR}
-# COMMENT "=========== Generating CPP-API Wiki reports =============="
-# VERBATIM
-# )
-#
-#add_custom_target(cppTestingReport ALL DEPENDS ${resulsFile}
-# COMMAND ${target} -m${sbmlModelsDir} -l${compilerFolder} -s"${supportCodeFolder}" -r${resultsFile} -v
-# COMMENT "=========== Generating CPP-API Wiki reports =============="
-# COMMENT "Executing ${target} -m${sbmlModelsDir} -l${compilerFolder} -s${supportCodeFolder} -r${resultsFile} -v"
-#
-#)
-
-install (TARGETS ${target}
-DESTINATION bin
-COMPONENT testing
-)
-
-install(
-FILES run_cpp_tests.bat
-DESTINATION bin
-COMPONENT testing
-)
-
-
+CMAKE_MINIMUM_REQUIRED(VERSION 2.6.3 FATAL_ERROR)
+PROJECT(RR_CXX_API_TESTS)
+
+set(target cxx_api_tests)
+
+set(tests
+tests/base
+tests/sbml_test_suite
+tests/steady_state
+tests/stoichiometric
+)
+
+add_executable( ${target}
+main
+src/Args
+src/rrTestUtils
+${tests}
+)
+
+set_property(TARGET ${target}
+ PROPERTY COMPILE_DEFINITIONS
+LIBSBML_USE_CPP_NAMESPACE
+LIBSBML_STATIC
+STATIC_LIBSTRUCT
+STATIC_PUGI
+STATIC_RR
+STATIC_NLEQ
+)
+
+link_directories(
+${THIRD_PARTY_INSTALL_FOLDER}/lib
+)
+
+include_directories(
+src
+${RR_ROOT}
+${THIRD_PARTY_FOLDER}/unit_test/src
+)
+
+if(UNIX)
+set(staticLibPrefix ".a")
+set(sharedLibPrefix ".so")
+else()
+set(staticLibPrefix "")
+set(sharedLibPrefix "")
+endif()
+
+if(WIN32)
+target_link_libraries (${target}
+roadrunner-static
+unit_test-static${staticLibPrefix}
+)
+endif()
+
+if(UNIX) #Don't know why static roadrunner fails....?
+target_link_libraries (${target}
+roadrunner-static
+libunit_test-static${staticLibPrefix}
+#nleq-static.a
+#rr-libstruct-static
+lapack
+blas
+f2c
+#libsbml-static.a
+#libxml2.so
+#sundials_nvecserial.a
+#sundials_cvode.a
+#pthread
+#poco_foundation-static.a
+#dl
+)
+endif()
+
+#set(resultsDir "${CMAKE_SOURCE_DIR}/reports")
+#
+#if(${BORLAND})
+#set(resultsFile "${resultsDir}/cpp_api_tests-cg_xe1.xml")
+#elseif(${MSVC})
+#set(resultsFile "${resultsDir}/cpp_api_tests-vs_2010.xml")
+#elseif(CMAKE_COMPILER_IS_GNUCC)
+#set(resultsFile "${resultsDir}/cpp_api_tests-gcc.xml")
+#else()
+#set(resultsFile "${resultsDir}/cpp_api_tests_unknown_compiler.xml")
+#endif()
+#
+#set(sbmlModelsDir "${CMAKE_SOURCE_DIR}/models")
+#set(compilerFolder "${CMAKE_SOURCE_DIR}/third_party/compilers/tcc")
+#set(supportCodeFolder "/r/rrl/rr_support")
+#
+#if(UNIX)
+#set(compilerFolder "")
+#endif()
+#
+#Message("SupportCodeFolder is: " ${supportCodeFolder})
+# Call like this -mr:\rrl\models -rr:\rrl\wiki\reports\file -tr:\rrTemp -sSupportCodeFolder -lCompilerFolder
+#add_custom_command(
+# OUTPUT ${resultsFile}
+# COMMAND ${target} -m${sbmlModelsDir} -l${compilerFolder} -s${supportCodeFolder} -r${resultsFile} -v
+# WORKING_DIRECTORY ${PROJECT_SOURCE_DIR}
+# COMMENT "=========== Generating CPP-API Wiki reports =============="
+# VERBATIM
+# )
+#
+#add_custom_target(cppTestingReport ALL DEPENDS ${resulsFile}
+# COMMAND ${target} -m${sbmlModelsDir} -l${compilerFolder} -s"${supportCodeFolder}" -r${resultsFile} -v
+# COMMENT "=========== Generating CPP-API Wiki reports =============="
+# COMMENT "Executing ${target} -m${sbmlModelsDir} -l${compilerFolder} -s${supportCodeFolder} -r${resultsFile} -v"
+#
+#)
+
+install (TARGETS ${target}
+DESTINATION bin
+COMPONENT testing
+)
+
+install(
+FILES run_cpp_tests.bat
+DESTINATION bin
+COMPONENT testing
+)
+
+
diff --git a/source/testing/run_cpp_tests.bat b/source/testing/run_cpp_tests.bat
index fcd6416..d3774cf 100644
--- a/source/testing/run_cpp_tests.bat
+++ b/source/testing/run_cpp_tests.bat
@@ -1,18 +1,18 @@
-
-echo "Running tests..."
- at echo off
-
-REM === Call with three arguments, eg vs 2010 Release..
-set compiler=%1
-set compiler_version=%2
-set build_type=%3
-
-set install_folder=r:\installs\%compiler%\%compiler_version%\%build_type%
-set model_folder=r:\models
-set wc=r:\rrl
-set report_file=%wc%\reports\%compiler%\%compiler_version%\cpp_test_%build_type%.xml
-set temp_folder=r:\rrTemp\%compiler_version%
-
-cxx_api_tests.exe -m%model_folder% -r%report_file% -t%temp_folder%
-
-echo done...
+
+echo "Running tests..."
+ at echo off
+
+REM === Call with three arguments, eg vs 2010 Release..
+set compiler=%1
+set compiler_version=%2
+set build_type=%3
+
+set install_folder=r:\installs\%compiler%\%compiler_version%\%build_type%
+set model_folder=r:\models
+set wc=r:\rrl
+set report_file=%wc%\reports\%compiler%\%compiler_version%\cpp_test_%build_type%.xml
+set temp_folder=r:\rrTemp\%compiler_version%
+
+cxx_api_tests.exe -m%model_folder% -r%report_file% -t%temp_folder%
+
+echo done...
diff --git a/source/testing/run_cpp_tests.sh b/source/testing/run_cpp_tests.sh
index 5a8870b..d382362 100755
--- a/source/testing/run_cpp_tests.sh
+++ b/source/testing/run_cpp_tests.sh
@@ -1,20 +1,20 @@
-
-echo "Running tests..."
-
-# === Call with three arguments!!
-compiler=$1
-compiler_version=$2
-build_type=$3
-
-
-install_folder=/home/sagrada/myhome/downloads/source/roadrunner/install
-model_folder=$install_folder/all/models
-wc=/home/sagrada/myhome/downloads/source/roadrunner/roadrunnerlib
-report_file=$wc/reports/$compiler/$compiler_version/cpp_tests.xml
-temp_folder=/tmp/$compiler_version
-
-echo "cxx_api_tests -m$model_folder -r$report_file -lgcc -s$install_folder/third_party/rr_support -t$temp_folder -d$temp_folder"
-
-./cxx_api_tests -m$model_folder -r$report_file -lgcc -s$install_folder/third_party/rr_support -t$temp_folder -d$temp_folder
-
-echo "done..."
+
+echo "Running tests..."
+
+# === Call with three arguments!!
+compiler=$1
+compiler_version=$2
+build_type=$3
+
+
+install_folder=/home/sagrada/myhome/downloads/source/roadrunner/install
+model_folder=$install_folder/all/models
+wc=/home/sagrada/myhome/downloads/source/roadrunner/roadrunnerlib
+report_file=$wc/reports/$compiler/$compiler_version/cpp_tests.xml
+temp_folder=/tmp/$compiler_version
+
+echo "cxx_api_tests -m$model_folder -r$report_file -lgcc -s$install_folder/third_party/rr_support -t$temp_folder -d$temp_folder"
+
+./cxx_api_tests -m$model_folder -r$report_file -lgcc -s$install_folder/third_party/rr_support -t$temp_folder -d$temp_folder
+
+echo "done..."
--
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