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From 2010.igem.org

Overview

The source code of our project is available now at igame in github.

We use C++ as our programming language, cmake to manage our project, git to reversion control, yacc and lex to build our model file input assistant tool, Qt4 to build the GUI, 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. 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 SBML Ode Solver and Sundials were our main ode solver to produce the simulation data from our sbml model file, because the latest SBML Ode Solver is 1.6.0, developed in 2005, which is out of date and fail to support the newest sbml Level 2 Version 4 standard.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 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.

Prerequisits

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/
• 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, and one can follow 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 Bison site and Flex site.

• git, to download our source code by command

Our source code can be downloaded in github, git is helpful to download.

• • git clone git://github.com/jkdirac/igame.git