diff -ruN /usr/ports//biology/libsbml/Makefile ./Makefile
--- /usr/ports//biology/libsbml/Makefile	2014-03-07 21:52:40.000000000 +0600
+++ ./Makefile	2014-04-13 18:18:28.850648524 +0600
@@ -2,27 +2,26 @@
 # $FreeBSD: head/biology/libsbml/Makefile 347402 2014-03-07 15:52:40Z bapt $
 
 PORTNAME=	libsbml
-PORTVERSION=	4.2.0
+PORTVERSION=	5.9.0
 CATEGORIES=	biology devel
 MASTER_SITES=	SF
-MASTER_SITE_SUBDIR=	sbml/${PORTNAME}/${PORTVERSION}
-DISTNAME=	${PORTNAME}-${PORTVERSION}-src
+MASTER_SITE_SUBDIR=	sbml/${PORTNAME}/${PORTVERSION}/stable
+DISTNAME=	libSBML-${PORTVERSION}-core-src
 
 MAINTAINER=	wen@FreeBSD.org
 COMMENT=	API Library for Working with SBML File
 
+LICENSE=	LGPL21
+
 LIB_DEPENDS=	libxml2.so:${PORTSDIR}/textproc/libxml2
 
-OPTIONS_DEFINE=	PYTHON RUBY
+OPTIONS_DEFINE=	PYTHON RUBY EXAMPLES
 
-USES=		gmake zip
-USE_GCC=	any
+USES=	gmake
 GNU_CONFIGURE=	yes
 USE_LDCONFIG=	yes
 WRKSRC=		${WRKDIR}/${PORTNAME}-${PORTVERSION}
-MAKE_JOBS_UNSAFE=	yes
 
-NO_STAGE=	yes
 .include <bsd.port.options.mk>
 
 .if ${PORT_OPTIONS:MPYTHON}
@@ -45,14 +44,15 @@
 .endif
 
 post-patch:
-	${REINPLACE_CMD} -e 's#%%PREFIX%%#${PREFIX}#' \
+	${REINPLACE_CMD} -e 's#%%PREFIX%%#${STAGEDIR}${PREFIX}#' \
 		${WRKSRC}/Makefile.in
 
 post-install:
 .if ${PORT_OPTIONS:MEXAMPLES}
-	${MKDIR} ${EXAMPLESDIR}
+	${MKDIR} ${STAGEDIR}${EXAMPLESDIR}
 	cd ${WRKSRC}/examples \
-		&& ${FIND} . -type d -exec ${MKDIR} ${EXAMPLESDIR}/\{} \; \
-		&& ${FIND} . -type f -exec ${INSTALL_DATA} \{} ${EXAMPLESDIR}/\{} \;
+		&& ${FIND} . -type f -name "._Makefile.in" -exec ${RM} -f {} \; \
+		&& ${FIND} . -type d -exec ${MKDIR} ${STAGEDIR}${EXAMPLESDIR}/\{} \; \
+		&& ${FIND} . -type f -exec ${INSTALL_DATA} \{} ${STAGEDIR}${EXAMPLESDIR}/\{} \;
 .endif
 .include <bsd.port.mk>
diff -ruN /usr/ports//biology/libsbml/distinfo ./distinfo
--- /usr/ports//biology/libsbml/distinfo	2014-01-22 21:30:13.000000000 +0600
+++ ./distinfo	2014-04-10 01:28:57.412678100 +0600
@@ -1,2 +1,2 @@
-SHA256 (libsbml-4.2.0-src.zip) = 31f4c63adc2bdd2ef7093dc206b4eb940a0c9cc0b98366f27316635fc44472ba
-SIZE (libsbml-4.2.0-src.zip) = 9469890
+SHA256 (libSBML-5.9.0-core-src.tar.gz) = 8991e4a6876721999433495b747b790af7981ae57b485e6c92b7fbb105bd7e96
+SIZE (libSBML-5.9.0-core-src.tar.gz) = 11478158
diff -ruN /usr/ports//biology/libsbml/pkg-plist ./pkg-plist
--- /usr/ports//biology/libsbml/pkg-plist	2014-01-22 21:16:56.000000000 +0600
+++ ./pkg-plist	2014-04-13 17:41:12.416799772 +0600
@@ -42,8 +42,6 @@
 include/sbml/annotation/RDFAnnotation.h
 include/sbml/common/common.h
 include/sbml/common/extern.h
-include/sbml/common/libsbml-config-unix.h
-include/sbml/common/libsbml-config-win.h
 include/sbml/common/libsbml-config.h
 include/sbml/common/libsbml-namespace.h
 include/sbml/common/libsbml-version.h
@@ -91,7 +89,6 @@
 include/sbml/validator/VConstraint.h
 include/sbml/validator/Validator.h
 include/sbml/validator/constraints/IdBase.h
-include/sbml/validator/constraints/IdList.h
 include/sbml/validator/constraints/MathMLBase.h
 include/sbml/validator/constraints/OverDeterminedCheck.h
 include/sbml/validator/constraints/UniqueIdBase.h
@@ -118,27 +115,68 @@
 include/sbml/xml/XMLToken.h
 include/sbml/xml/XMLTokenizer.h
 include/sbml/xml/XMLTriple.h
-lib/libsbml.so.6
+include/sbml/AlgebraicRule.h
+include/sbml/AssignmentRule.h
+include/sbml/ExpectedAttributes.h
+include/sbml/ModifierSpeciesReference.h
+include/sbml/RateRule.h
+include/sbml/SBMLConstructorException.h
+include/sbml/SimpleSpeciesReference.h
+include/sbml/annotation/Date.h
+include/sbml/annotation/ModelCreator.h
+include/sbml/annotation/RDFAnnotationParser.h
+include/sbml/common/libsbml-config-common.h
+include/sbml/conversion/ConversionOption.h
+include/sbml/conversion/ConversionProperties.h
+include/sbml/conversion/SBMLConverter.h
+include/sbml/conversion/SBMLConverterRegister.h
+include/sbml/conversion/SBMLConverterRegistry.h
+include/sbml/conversion/SBMLFunctionDefinitionConverter.h
+include/sbml/conversion/SBMLIdConverter.h
+include/sbml/conversion/SBMLInferUnitsConverter.h
+include/sbml/conversion/SBMLInitialAssignmentConverter.h
+include/sbml/conversion/SBMLLevelVersionConverter.h
+include/sbml/conversion/SBMLLocalParameterConverter.h
+include/sbml/conversion/SBMLRuleConverter.h
+include/sbml/conversion/SBMLStripPackageConverter.h
+include/sbml/conversion/SBMLUnitsConverter.h
+include/sbml/extension/ISBMLExtensionNamespaces.h
+include/sbml/extension/SBMLDocumentPlugin.h
+include/sbml/extension/SBMLDocumentPluginNotRequired.h
+include/sbml/extension/SBMLExtension.h
+include/sbml/extension/SBMLExtensionException.h
+include/sbml/extension/SBMLExtensionNamespaces.h
+include/sbml/extension/SBMLExtensionRegister.h
+include/sbml/extension/SBMLExtensionRegistry.h
+include/sbml/extension/SBaseExtensionPoint.h
+include/sbml/extension/SBasePlugin.h
+include/sbml/extension/SBasePluginCreator.h
+include/sbml/extension/SBasePluginCreatorBase.h
+include/sbml/math/L3FormulaFormatter.h
+include/sbml/math/L3Parser.h
+include/sbml/math/L3ParserSettings.h
+include/sbml/util/ElementFilter.h
+include/sbml/util/IdFilter.h
+include/sbml/util/IdList.h
+include/sbml/util/IdentifierTransformer.h
+include/sbml/util/MetaIdFilter.h
+include/sbml/validator/SBMLExternalValidator.h
+include/sbml/validator/SBMLInternalValidator.h
+include/sbml/validator/SBMLValidator.h
+include/sbml/xml/XMLConstructorException.h
+include/sbml/xml/XMLLogOverride.h
+lib/libsbml.so.14
 lib/libsbml.so
 lib/libsbml.la
 lib/libsbml.a
-@dirrm include/sbml/annotation
-@dirrm include/sbml/common
-@dirrm include/sbml/compress
-@dirrm include/sbml/math
-@dirrm include/sbml/units
-@dirrm include/sbml/util
-@dirrm include/sbml/validator/constraints
-@dirrm include/sbml/validator
-@dirrm include/sbml/xml
-@dirrm include/sbml/
 %%WITH_PYTHON%%%%PYTHON_SITELIBDIR%%/libsbml/_libsbml.so
-%%WITH_PYTHON%%%%PYTHON_SITELIBDIR%%/libsbml/libsbml.py
-%%WITH_PYTHON%%%%PYTHON_SITELIBDIR%%/libsbml/libsbml.pyc
 %%WITH_PYTHON%%%%PYTHON_SITELIBDIR%%/libsbml.pth
 %%WITH_PYTHON%%%%PYTHON_SITELIBDIR%%/%%SBML_EGGINFO%%
+%%WITH_PYTHON%%%%PYTHON_SITELIBDIR%%/libsbml/__init__.py
+%%WITH_PYTHON%%%%PYTHON_SITELIBDIR%%/libsbml/__init__.pyc
 %%WITH_PYTHON%%@dirrm %%PYTHON_SITELIBDIR%%/libsbml
-%%WITH_RUBY%%%%RUBY_SITEARCHLIBDIR%%/libSBML.so
+%%WITH_RUBY%%%%RUBY_SITELIBDIR%%/%%RUBY_ARCH%%/libSBML.so
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/CMakeLists.txt
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/README.txt
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/FormulaGraphvizFormatter.h
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/Makefile
@@ -153,6 +191,23 @@
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/translateMath.c
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/util.c
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/util.h
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/CMakeLists.txt
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/addCVTerms.c
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/addModelHistory.c
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/addingEvidenceCodes_1.c
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/addingEvidenceCodes_2.c
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/appendAnnotation.c
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/createExampleSBML.c
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/printAnnotation.c
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/printNotes.c
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/printRegisteredPackages.c
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/printSupported.c
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/printUnits.c
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/promoteParameters.c
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/stripPackage.c
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/translateL3Math.c
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/unsetAnnotation.c
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/unsetNotes.c
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/validateSBML.c
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/Makefile
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/Makefile.in
@@ -176,10 +231,60 @@
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/util.c
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/util.h
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/validateSBML.cpp
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/CMakeLists.txt
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/addCustomValidator.cpp
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/callExternalValidator.cpp
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/getAllElementsWithNotes.cpp
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/inferUnits.cpp
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/inlineFunctionDefintions.cpp
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/layout/Makefile.in
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/layout/addLayout.cpp
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/layout/convertLayout.cpp
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/layout/example1-L3.cpp
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/layout/example1.cpp
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/layout/example2-L3.cpp
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/layout/example2.cpp
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/layout/example3-L3.cpp
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/layout/example3.cpp
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/printRegisteredPackages.cpp
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/printSupported.cpp
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/promoteParameters.cpp
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/renameSId.cpp
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/rngvalidator.cpp
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/setIdFromNames.cpp
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/setNamesFromIds.cpp
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/stripPackage.cpp
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/translateL3Math.cpp
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/csharp/Makefile
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/csharp/Makefile.in
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/csharp/echoSBML.cs
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/csharp/validateSBML.cs
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/csharp/CMakeLists.txt
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/csharp/GetAllElementsWithNotes.cs
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/csharp/SetIdFromNames.cs
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/csharp/addCVTerms.cs
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/csharp/addCustomValidator.cs
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/csharp/addModelHistory.cs
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/csharp/addingEvidenceCodes_1.cs
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/csharp/addingEvidenceCodes_2.cs
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/csharp/appendAnnotation.cs
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/csharp/callExternalValidator.cs
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/csharp/convertSBML.cs
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/csharp/createExampleSBML.cs
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/csharp/layout/example1-L3.cs
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/csharp/printAnnotation.cs
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/csharp/printMath.cs
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/csharp/printNotes.cs
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/csharp/printRegisteredPackages.cs
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/csharp/printSBML.cs
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/csharp/printUnits.cs
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/csharp/printsupported.cs
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/csharp/promoteParameters.cs
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/csharp/readSBML.cs
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/csharp/stripPackage.cs
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/csharp/translateMath.cs
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/csharp/unsetAnnotation.cs
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/csharp/unsetNotes.cs
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/Makefile
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/Makefile.in
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/README.txt
@@ -199,13 +304,21 @@
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/unsetAnnotation.java
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/unsetNotes.java
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/validateSBML.java
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/layout/Makefile.in
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/layout/example1.cpp
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/layout/example1.java
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/layout/example1.py
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/layout/example2.cpp
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/layout/example3.cpp
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/layout/layout2svg.xsl
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/CMakeLists.txt
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/addCustomValidator.java
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/addingEvidenceCodes_1.java
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/addingEvidenceCodes_2.java
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/callExternalValidator.java
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/createExampleSBML.java
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/getAllElementsWithNotes.java
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/layout/layout_example1.java
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/layout/layout_example1_L3.java
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/printRegisteredPackages.java
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/printsupported.java
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/promoteParameters.java
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/setIdFromNames.java
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/stripPackage.java
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/layout/README.txt
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/perl/convertSBML.pl
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/perl/evaluateMath.pl
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/perl/extractReactionInfo.pl
@@ -215,12 +328,101 @@
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/perl/readSBML.pl
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/perl/translateMath.pl
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/perl/validateSBML.pl
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/perl/addCVTerms.pl
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/perl/addCustomValidator.pl
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/perl/addModelHistory.pl
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/perl/addingEvidenceCodes_1.pl
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/perl/addingEvidenceCodes_2.pl
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/perl/appendAnnotation.pl
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/perl/callExternalValidator.pl
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/perl/createExampleSBML.pl
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/perl/echoSBML.pl
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/perl/layout/example1-L3.pl
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/perl/printAnnotation.pl
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/perl/printNotes.pl
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/perl/printRegisteredPackages.pl
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/perl/printUnits.pl
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/perl/printsupported.pl
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/perl/promoteParameters.pl
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/perl/stripPackage.pl
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/perl/unsetAnnotation.pl
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/perl/unsetNotes.pl
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/echoSBML.py
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/validateSBML.py
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/addCVTerms.py
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/addCustomValidator.py
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/addModelHistory.py
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/addingEvidenceCodes_1.py
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/addingEvidenceCodes_2.py
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/appendAnnotation.py
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/callExternalValidator.py
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/convertSBML.py
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/createExampleSBML.py
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/getAllElementsWithNotes.py
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/layout/example1-L3.py
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/layout/example1.py
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/printAnnotation.py
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/printMath.py
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/printNotes.py
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/printRegisteredPackages.py
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/printSBML.py
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/printUnits.py
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/printsupported.py
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/promoteParameters.py
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/readSBML.py
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/setIdFromNames.py
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/stripPackage.py
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/translateMath.py
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/unsetAnnotation.py
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/unsetNotes.py
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/r/addCVTerms.R
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/r/addModelHistory.R
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/r/addingEvidenceCodes_1.R
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/r/addingEvidenceCodes_2.R
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/r/appendAnnotation.R
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/r/convertSBML.R
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/r/createExampleSBML.R
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/r/echoSBML.R
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/r/evaluateMath.R
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/r/printAnnotation.R
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/r/printMath.R
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/r/printNotes.R
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/r/printRegisteredPackages.R
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/r/printSBML.R
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/r/printSupported.R
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/r/printUnits.R
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/r/promoteParameters.R
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/r/readSBML.R
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/r/stripPackage.R
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/r/translateMath.R
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/r/unsetAnnotation.R
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/r/unsetNotes.R
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/r/validateSBML.R
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/ruby/convertSBML.rb
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/ruby/echoSBML.rb
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/ruby/printMath.rb
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/ruby/validateSBML.rb
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ruby/addCVTerms.rb
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ruby/addCustomValidator.rb
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ruby/addModelHistory.rb
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ruby/addingEvidenceCodes_1.rb
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ruby/addingEvidenceCodes_2.rb
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ruby/appendAnnotation.rb
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ruby/callExternalValidator.rb
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ruby/createExampleSBML.rb
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ruby/printAnnotation.rb
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ruby/printNotes.rb
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ruby/printRegisteredPackages.rb
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ruby/printSBML.rb
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ruby/printUnits.rb
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ruby/printsupported.rb
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ruby/promoteParameters.rb
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ruby/readSBML.rb
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ruby/stripPackage.rb
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ruby/translateMath.rb
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ruby/unsetAnnotation.rb
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ruby/unsetNotes.rb
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ruby/layout/example1-L3.rb
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample-models/README.txt
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample-models/from-spec/level-2/README.txt
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample-models/from-spec/level-2/algebraicrules.xml
@@ -252,16 +454,38 @@
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample-models/from-spec/level-3/README.txt
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample-models/from-spec/level-3/twoalgebraicrules.xml
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample-models/from-spec/level-3/twodimensional.xml
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/xslt/layout/layout2svg.xsl
 %%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/c
+%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/c++/layout
 %%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/c++
+%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/csharp/layout
 %%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/csharp
+%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/java/layout
 %%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/java
+%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/perl/layout
 %%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/layout
 %%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/perl
+%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/python/layout
 %%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/python
+%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/r
+%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/ruby/layout
 %%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/ruby
 %%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/sample-models/from-spec/level-3
 %%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/sample-models/from-spec/level-2
 %%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/sample-models/from-spec
 %%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/sample-models
+%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/xslt/layout
+%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/xslt
 %%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%
+@dirrm include/sbml/annotation
+@dirrm include/sbml/common
+@dirrm include/sbml/compress
+@dirrm include/sbml/conversion
+@dirrm include/sbml/extension
+@dirrm include/sbml/math
+@dirrm include/sbml/units
+@dirrm include/sbml/util
+@dirrm include/sbml/validator/constraints
+@dirrm include/sbml/validator
+@dirrm include/sbml/xml
+@dirrm include/sbml/