Latest revision as of 12:27, 27 October 2010

Resources

On this page we provide the information of downloading the executable files and source files of our project, and the documentation to introduce the source code build steps and system prerequisites.

Downloads

Executable files can be download at SourcForge
Project source code is available at [http://github.com/jkdirac/igame gitHub]

Source Code OverView

We use [http://en.wikipedia.org/wiki/C%2B%2B C++] as our programming language, [http://www.cmake.org/ cmake] to manage our project, [http://git-scm.com/ git] to [http://en.wikipedia.org/wiki/Revision_control reversion control], [http://dinosaur.compilertools.net/ yacc and lex] to build our model file input assistant tool, [http://qt.nokia.com/ Qt4] to build the GUI, [http://sourceforge.net/projects/dbxml-core/ Oracle dbxml] as our Database manager system. Other wise, several 3-rd party open source software or tools are used in our iGame source code. [http://sbml.org/Software/libSBML Libsbml] is used to deal with sbml file operations. Qwt and Qwtplot3D are used for simulation data visual system. At the early stage of our project [http://www.tbi.univie.ac.at/~raim/odeSolver/ SBML Ode Solver] and Sundials were our main ode solver to produce the simulation data from our sbml model file, because the latest [http://www.tbi.univie.ac.at/~raim/odeSolver/ SBML Ode Solver] is 1.6.0, developed in 2005, which is out of date and fail to support the newest sbml Level 2 Version 4 standard. We succeed in updating the SBML Ode Solver 1.6.0 to support SBML L2V4, but some unfixed bugs was found, so we turn to a better ode solver [http://www.copasi.org/tiki-view_articles.php copasi], which moreover can flexibly display the ode solver output data and modify parameter to adjust the simulation output data curve. Obviously, those open source library and tools convenient to our design and implementation and help us to focus on our core working.

Build instruction

Prerequisites

To sum up, iGame should be complied and run in computers with following tools and libraries:

C++ development environment. In Linux should be GNU C++ Tool Chain And in windows MingW Tool Chain.
Qt4 develop and run-time environment. Qt4.7 is requirement. Editor or IDE like QtCreator or Vim is also needed.
CMake, to configure the project and generate the Makefile. CMake 2.8 or later version is a requirement
dbxml, The Berkeley xml native database, is available at [http://sourceforge.net/projects/dbxml-core/ http://sourceforge.net/projects/dbxml-core/]
copasi, copasi 4.6 is a requirement. the source code and executable binary file can be downloaded at [http://www.copasi.org/tiki-index.php?page=download http://www.copasi.org/tiki-index.php?page=download], and one can follow [http://www.copasi.org/tiki-index.php?page_ref_id=115 those instruction] to build it from source code. What should be noticed is that copasi also has prerequisites, including LAPACK/CLAPACK for Maths, Qwt and Qwtplot3D for plotting, expat to parser xml, raptor The latest version of this RDF parsing library, and libsbml for deal with SBML operations.
libsbml, Version 3.4.1 is required. Not only it is the dependence of copasi, but also the dependence of igame core code.

And libsbml should be built with configure option "./configure --enable-layout=yes --enable-compression=no --with-expat"

Bison & Flex

To compile our code, bison and flex is required. They are used to build a expression parser in igame/core/str_cacu path. To get the those software and more detailed information, please visit [http://www.gnu.org/software/bison/ Bison site] and [http://flex.sourceforge.net/ Flex site].

git, to download our source code by command our source code can be downloaded in [http://github.com/jkdirac/igame github], git is helpful to download.
git clone git://github.com/jkdirac/igame.git

Build

We use cmake to manage the build progress, cmake can generate cross-platform Makefile, we intend to make our project could be built in different operating system. Until now, only Linux operating system is tested. Windows and Mac should be supported soon. Download all source code, run cmake-gui to configure the project. Pay attention to the configure information.There should be "missing ***" messages when Cmake fail to find the dependent libraries. To fix those messages, one need to assign the path of related libraries by Cmake GUI. When Makefiles are successfully generated, execute the Make command to build.

@@ Line 1: / Line 1: @@
+{{Team:USTC_Software/Header}}
+=Resources=
+On this page we provide the information of downloading the executable files and source files of our project, and the documentation to introduce the source code build steps and system prerequisites.
+==Downloads==
+<p>
+Executable files can be download at [https://sourceforge.net/projects/ustc-igame/files/ SourcForge] <br/>
+Project source code is available at [http://github.com/jkdirac/igame gitHub]
+</p>
-==ode solver==
+==Source Code OverView==
+We use [http://en.wikipedia.org/wiki/C%2B%2B C++] as our programming language,  [http://www.cmake.org/ cmake] to manage our project, [http://git-scm.com/ git] to [http://en.wikipedia.org/wiki/Revision_control reversion control], [http://dinosaur.compilertools.net/ yacc and lex] to build our model file input assistant tool, [http://qt.nokia.com/ Qt4] to build the GUI, [http://sourceforge.net/projects/dbxml-core/ Oracle dbxml] as our Database manager system. Other wise, several 3-rd party open source software or tools are used in our iGame source code.  [http://sbml.org/Software/libSBML Libsbml] is used to deal with sbml file operations. Qwt and Qwtplot3D are used for simulation data visual system.  At the early stage of our project [http://www.tbi.univie.ac.at/~raim/odeSolver/ SBML Ode Solver] and [https://computation.llnl.gov/casc/sundials/main.html Sundials] were our main ode solver to produce the simulation data from our sbml model file, because the latest [http://www.tbi.univie.ac.at/~raim/odeSolver/ SBML Ode Solver] is 1.6.0, developed in 2005, which is out of date and fail to support the newest sbml Level 2 Version 4 standard. We succeed in updating the SBML Ode Solver 1.6.0 to support SBML L2V4, but some unfixed bugs was found, so we turn to a better ode solver [http://www.copasi.org/tiki-view_articles.php copasi], which moreover can flexibly display the ode solver output data and modify parameter to adjust the simulation output data curve. Obviously, those open source library and tools convenient to our design and implementation and help us to focus on our  core working.
-==sundials==
+==Build instruction==
+===Prerequisites===
+<p>
+To sum up, iGame should be complied and run in computers with following tools and libraries:
+* '''C++ development environment'''. In Linux should be GNU C++ Tool Chain And in windows MingW Tool Chain.
+* '''Qt4''' develop and run-time environment. '''Qt4.7''' is requirement. Editor or IDE like QtCreator or Vim is also needed.
+* '''CMake''', to configure the project and generate the Makefile. CMake 2.8 or later version is a requirement
+* '''dbxml''', The Berkeley xml native database, is available at [http://sourceforge.net/projects/dbxml-core/ http://sourceforge.net/projects/dbxml-core/]
+* '''copasi''', copasi 4.6 is a requirement. the source code and executable binary file can be downloaded at [http://www.copasi.org/tiki-index.php?page=download http://www.copasi.org/tiki-index.php?page=download], and one can follow [http://www.copasi.org/tiki-index.php?page_ref_id=115 those instruction] to build it from source code. What should be noticed is that '''copasi''' also has prerequisites, including '''LAPACK'''/'''CLAPACK''' for Maths, '''Qwt''' and '''Qwtplot3D''' for plotting, '''expat''' to parser xml, '''raptor''' The latest version of this RDF parsing library, and libsbml for deal with SBML operations.
+* '''libsbml''', Version 3.4.1 is required. Not only it is the dependence of '''copasi''', but also the dependence of igame core code.
+  And libsbml should be built with configure option "./configure --enable-layout=yes --enable-compression=no --with-expat"
+* '''Bison & Flex'''
+To compile our code, bison and flex is required. They are used to build a expression parser in igame/core/str_cacu path. To get the those software and more detailed information, please visit [http://www.gnu.org/software/bison/ Bison site] and [http://flex.sourceforge.net/ Flex site].
+</p>
-==libsbml==
+<p>
+* '''git''', to download our source code by command our source code can be downloaded in [http://github.com/jkdirac/igame github], '''git''' is helpful to download.
+*git clone git://github.com/jkdirac/igame.git
+</p>
-==dbxml==
+===Build===
+We use cmake to manage the build progress, cmake can generate cross-platform Makefile, we intend to make our project could be built in different operating system. Until now, only Linux operating system is tested. Windows and Mac should be supported soon.
+Download all source code, run cmake-gui to configure the project. Pay attention to the configure information.There should be "missing ***" messages when Cmake fail to find the dependent libraries. To fix those messages, one need to assign the path of related libraries by Cmake GUI. When Makefiles are successfully generated, execute the '''Make''' command to build.
-==Qt==
-==Qwt==
+<!-->
+==Libraries==
+Our source code is developed in Linux environment, cross platform is also under consideration. Our project source code can be build in windows with mingw environment. There are many troubles when building in windows, the following article may be helpful.
+===copasi===
-==yacc&lex==
+===libsbml===
-==cmake==
+===dbxml===
+===Qt===
+===Qwt===
+===Qwtplot3D===
+<-->
+<!--> ==Tools==
+===dbparser===
+<p>
+When create a new model file, a simple tool named [http://github.com/jkdirac/igame/tree/master/src/tools/dbparser/ dbparser] may be helpful, It's simple and easy to use, and hope you have fun! More information can be got from it's README.txt file.
+</p>
+Any question please mail jiangkun1@gmail.com
+*Configure
+The dbparser need libsbml to transfer math expressions to MathML string. So libsbml-3.4.1 or
+libsbml 4.0.1 is needed. And modfy those two flags in the Makefile to configure libsbml's header and
+libraries path.
+	CCFLAGS = -g -I../../ExternalCode/sbml -I../../ExternalCode
+	LIBS = libsbml.a libxerces-c.a libxml2.a -lz
+*BUILD
+After configuring, BUILD is very simple. There is only one Makefile in this fold. You can just
+type the command
+	make
+to build the dbparser.
+*How to use, example
+dbparser is kind of a XML editor, to read a data input configure file to generate the needed XML
+formated file. The input file should follow a synatx.
+Take the [http://github.com/jkdirac/igame/blob/master/src/tools/dbparser/test1.in test1.in] as example. Run ./dbparser < test1.in, We can get a XML version file test.xml.
+Description:
+#file = [test.xml]<br/>This is to specify the output file name;
+#module: [helloworld] id = [abcvd];<br/>Define a XML node named module, and value is "helloworld", and with attribute id="abcvd"
+#module id=[a] , name=[b], class=[c], time=[10] { SUBMODULE_STATEMENT };<br/>Define a XML node with a XML node as its value, that is to say, define a composite XML node;
+#math: [a+b];<br/>Define a math expression a+b, and it will be transferred to MathML Node.
+The synatx is simple, have fun!
+<-->
+<!-->
+===git===
+===yacc&lex===
+===cmake===
+'''Cmake''' is a cross platform tool, which can control the compile process, configure file and generate native Makefile. '''CMake''' have a GUI version, it is easy to use, so we prefer '''CMake''' to [http://www.gnu.org/software/automake/ '''AutoMake''']. More information about '''CMake''' is available at [http://www.cmake.org/ http://www.cmake.org/]
+===SBML Ode Solver===
+===Sundials===
+<-->

Team:USTC Software/resources

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