first commit contd..

CMakeLists.txt

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+PROJECT( LIBCOPASI )
+CMAKE_MINIMUM_REQUIRED( VERSION 2.6 )
+
+#--------------------------------------------------------------------------
+#    just some setup for compilers etc.
+#--------------------------------------------------------------------------
+#just a few linker frags needed for Linux
+IF (UNIX AND NOT APPLE)
+	SET(CMAKE_SHARED_LINKER_FLAGS "${CMAKE_SHARED_LINKER_FLAGS} -lrt")
+	SET(CMAKE_MODULE_LINKER_FLAGS "${CMAKE_MODULE_LINKER_FLAGS} -lrt")
+	SET(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -lrt")
+    SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fPIC")
+    SET(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -fPIC")
+ENDIF(UNIX AND NOT APPLE)
+
+# CMake not supporting Win32 MinGW?
+
+IF( WIN32 AND MINGW)
+  ADD_DEFINITIONS(-DMINGW)
+  SET(CMAKE_RC_COMPILER_INIT windres)
+  ENABLE_LANGUAGE(RC)
+  SET(CMAKE_RC_COMPILE_OBJECT
+    "<CMAKE_RC_COMPILER> <FLAGS> -O coff <DEFINES> -i <SOURCE> -o <OBJECT>")
+ENDIF( WIN32 AND MINGW)
+
+#Build type
+OPTION( USE_DEBUG_MODE "Release vs Debug mode" OFF)
+IF (USE_DEBUG_MODE)
+	SET(CMAKE_BUILD_TYPE "Release" CACHE STRING "Build type")
+	SET(CMAKE_RC_COMPILE_OBJECT Debug)
+ELSE(USE_DEBUG_MODE)
+	SET(CMAKE_BUILD_TYPE "Debug" CACHE STRING "Build type")
+	SET(CMAKE_RC_COMPILE_OBJECT Release)
+ENDIF(USE_DEBUG_MODE)
+#--------------------------------------------------------------------------
+
+#include folders
+INCLUDE_DIRECTORIES( BEFORE
+    ${LIBCOPASI_SOURCE_DIR}
+    ${LIBCOPASI_SOURCE_DIR}/curl/include
+    ${LIBCOPASI_SOURCE_DIR}/expat
+	${LIBCOPASI_SOURCE_DIR}/expat/lib
+    ${LIBCOPASI_SOURCE_DIR}/muparser
+    ${LIBCOPASI_SOURCE_DIR}/lapack/INCLUDE
+)
+
+#output folder for libraries same as exe's
+SET(LIBRARY_OUTPUT_PATH ${EXECUTABLE_OUTPUT_PATH})
+
+#build individual subdirectories using CMakeLists.txt in each directory
+
+#if the system already has lapack, then don't build it
+OPTION( BUILD_LAPACK "check this if your system does not have lapack library" ON ) #use cmake gui to set this
+IF (BUILD_LAPACK)
+	ADD_SUBDIRECTORY( lapack )     #linear algebra
+ENDIF(BUILD_LAPACK)
+
+ADD_SUBDIRECTORY( muparser )  #math parser
+ADD_SUBDIRECTORY( curl )      #needed by raptor
+ADD_SUBDIRECTORY( raptor )    #RDF parser
+ADD_SUBDIRECTORY( libSBML )    #systems biology markup language parser
+ADD_SUBDIRECTORY( antimony )   #human-readable test-based reaction networks
+ADD_SUBDIRECTORY( boost )      #regular expressions
+ADD_SUBDIRECTORY( copasi )     #simulation and analysis package
+ADD_SUBDIRECTORY( libstructural )   #network structural analysis based on stoichiometry matrix
+ADD_SUBDIRECTORY( galib )   #genetic algorithms library
+

README.txt

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+==================
+     ABOUT
+==================
+This is a simplified C API to the Copasi C++ library. The API uses 
+a few data structures that wrap Copasi's C++ classes as well as 
+provide some additional features, such as being able to use simple
+names, e.g. "A", instead of Copasi's complete names, e.g. <model1.compartmentX.A>
+
+==================
+  DEPENDENCIES
+==================
+
+lapack -- linear algebra package, used by Copasi C++ code
+libSBML -- Systems Biology Markup Language parser, used by Copasi C++ code
+expat -- XML parser used by libSBML and Copasi C++
+curl -- required by Raptor library
+raptor -- RDF parser required by Copasi C++
+muparser -- used within the C API for parsing mathematical expressions and getting the tokens
+boost -- the boost regex library is used by the C API to substitute strings inside formulas
+
+===============================
+  GETTING THE SOURCE CODE
+===============================
+First install Subversion. In Linux and Mac, just use apt-get svn.
+In Windows, download TortoiseSVN (graphical version) or SilkSVN (command-line version)
+
+Once Subversion is installed, use the following command to get the source:
+svn checkout https://copasi-simple-api.googlecode.com/svn/trunk/ copasi-simple-api
+
+If you are using TortoiseSVN, first create an empty folder called copasi-api. Then
+right-click on that newly created folder and select "SVN Checkout". Enter 
+https://copasi-simple-api.googlecode.com/svn/trunk/ as the source URL
+
+==========================
+  BUILDING THE LIBRARY
+==========================
+
+Lets assume that the source code is located in a folder named "copasi-simple-api"
+
+1) Install Cmake from cmake.org
+    for Linux, just type 'apt-get cmake cmake-gui'
+
+2) Run cmake-gui
+    In the Cmake program, find two text boxes labeled, "where is the source code" and "where to build"
+
+3) Type the full copasi-simple-api/ folder path for the line that says "where is the source code"
+
+4) Type copasi-simple-api/BUILD folder path for the line that says "where to build"
+
+5) Click the "Configure" button
+
+6) Cmake will create the BUILD folder and then ask you to select the compiler. 
+    It is recommended that you use standard compilers, e.g. gcc for Unix and 
+    Visual Studio or MinGW for MS Windows.
+
+7) Once configuration is done, click the "Generate" button
+
+8) Go to the copasi-simple-api/BUILD folder. 
+    If you used Visual Studio as the compiler, you will find a project file (.sln) -- open it and build all
+    If you used GCC, you will find a makefile. cd into this folder and run "make"
+
+==========================
+  USING THE LIBRARY
+==========================
+
+See test_copasi_api.c for example
+
+
+
+
+