http://2010.igem.org/wiki/index.php?title=Team:USTC_Software/resources&feed=atom&action=historyTeam:USTC Software/resources - Revision history2024-03-28T19:44:45ZRevision history for this page on the wikiMediaWiki 1.16.5http://2010.igem.org/wiki/index.php?title=Team:USTC_Software/resources&diff=181016&oldid=prevCfly: /* Prerequisites */2010-10-27T12:27:22Z<p><span class="autocomment">Prerequisites</span></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>* '''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.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>* '''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.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>* '''libsbml''', Version 3.4.1 is required. Not only it is the dependence of '''copasi''', but also the dependence of igame core code.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>* '''libsbml''', Version 3.4.1 is required. Not only it is the dependence of '''copasi''', but also the dependence of igame core code.</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>And libsbml should be built with configure option "./configure --enable-layout=yes --enable-compression=no --with-expat"</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline"> </ins>And libsbml should be built with configure option "./configure --enable-layout=yes --enable-compression=no --with-expat"</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>* '''Bison & Flex'''</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>* '''Bison & Flex'''</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>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].</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>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].</div></td></tr>
</table>Cflyhttp://2010.igem.org/wiki/index.php?title=Team:USTC_Software/resources&diff=181011&oldid=prevCfly: /* Prerequisites */2010-10-27T12:26:58Z<p><span class="autocomment">Prerequisites</span></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>* '''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.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>* '''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.</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline">*</del>*git clone git://github.com/jkdirac/igame.git</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>*git clone git://github.com/jkdirac/igame.git</div></td></tr>
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</table>Cflyhttp://2010.igem.org/wiki/index.php?title=Team:USTC_Software/resources&diff=180961&oldid=prevCfly: /* Prerequisites */2010-10-27T12:24:59Z<p><span class="autocomment">Prerequisites</span></p>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>* '''git''', to download our source code by command </div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>* '''git''', to download our source code by command <ins class="diffchange diffchange-inline">our </ins>source code can be downloaded in [http://github.com/jkdirac/igame github], '''git''' is helpful to download.</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline">Our </del>source code can be downloaded in [http://github.com/jkdirac/igame github], '''git''' is helpful to download.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>**git clone git://github.com/jkdirac/igame.git</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>**git clone git://github.com/jkdirac/igame.git</div></td></tr>
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</table>Cflyhttp://2010.igem.org/wiki/index.php?title=Team:USTC_Software/resources&diff=120487&oldid=prevJkdirac at 15:53, 22 October 20102010-10-22T15:53:43Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>{{Team:USTC_Software/Header}}</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>{{Team:USTC_Software/Header}}</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline">=</del>=Resources<del class="diffchange diffchange-inline">=</del>=</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>=Resources=</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>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.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>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.</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline">=</del>==Downloads<del class="diffchange diffchange-inline">=</del>==</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>==Downloads==</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Executable files can be download at [https://sourceforge.net/projects/ustc-igame/files/ SourcForge] <br/></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Executable files can be download at [https://sourceforge.net/projects/ustc-igame/files/ SourcForge] <br/></div></td></tr>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline">=</del>==Source Code OverView<del class="diffchange diffchange-inline">=</del>==</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>==Source Code OverView==</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>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.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>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.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline">=</del>== Build instruction<del class="diffchange diffchange-inline">=</del>==</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>==Build instruction==</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline">=</del>===Prerequisites<del class="diffchange diffchange-inline">=</del>===</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>===Prerequisites===</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>To sum up, iGame should be complied and run in computers with following tools and libraries:</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>To sum up, iGame should be complied and run in computers with following tools and libraries:</div></td></tr>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline">=</del>===Build<del class="diffchange diffchange-inline">=</del>===</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>===Build===</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>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.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>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.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>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. </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>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. </div></td></tr>
</table>Jkdirachttp://2010.igem.org/wiki/index.php?title=Team:USTC_Software/resources&diff=120478&oldid=prevJkdirac: /* Downloads */2010-10-22T15:49:02Z<p><span class="autocomment">Downloads</span></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>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.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>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.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>===Downloads===</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>===Downloads===</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>Executable files can be download at [https://sourceforge.net/projects/ustc-igame/files/ SourcForge] </div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline"><p></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>Executable files can be download at [https://sourceforge.net/projects/ustc-igame/files/ SourcForge] <ins class="diffchange diffchange-inline"><br/></ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Project source code is available at [http://github.com/jkdirac/igame gitHub]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Project source code is available at [http://github.com/jkdirac/igame gitHub]</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>===Source Code OverView===</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>===Source Code OverView===</div></td></tr>
</table>Jkdirachttp://2010.igem.org/wiki/index.php?title=Team:USTC_Software/resources&diff=120477&oldid=prevJkdirac: /* Source OverView */2010-10-22T15:48:08Z<p><span class="autocomment">Source OverView</span></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Project source code is available at [http://github.com/jkdirac/igame gitHub]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Project source code is available at [http://github.com/jkdirac/igame gitHub]</div></td></tr>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>===Source OverView===</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>===Source <ins class="diffchange diffchange-inline">Code </ins>OverView===</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>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.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>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.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
</table>Jkdirachttp://2010.igem.org/wiki/index.php?title=Team:USTC_Software/resources&diff=120476&oldid=prevJkdirac: /* Build instruction */2010-10-22T15:47:51Z<p><span class="autocomment">Build instruction</span></p>
<table style="background-color: white; color:black;">
<col class='diff-marker' />
<col class='diff-content' />
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<col class='diff-content' />
<tr valign='top'>
<td colspan='2' style="background-color: white; color:black;">← Older revision</td>
<td colspan='2' style="background-color: white; color:black;">Revision as of 15:47, 22 October 2010</td>
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<td colspan="2" class="diff-lineno">Line 29:</td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>**git clone git://github.com/jkdirac/igame.git</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>**git clone git://github.com/jkdirac/igame.git</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></p></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></p></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">====Build====</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">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.</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">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. </ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
</table>Jkdirachttp://2010.igem.org/wiki/index.php?title=Team:USTC_Software/resources&diff=120427&oldid=prevJkdirac: /* Prerequisites */2010-10-22T15:34:14Z<p><span class="autocomment">Prerequisites</span></p>
<table style="background-color: white; color:black;">
<col class='diff-marker' />
<col class='diff-content' />
<col class='diff-marker' />
<col class='diff-content' />
<tr valign='top'>
<td colspan='2' style="background-color: white; color:black;">← Older revision</td>
<td colspan='2' style="background-color: white; color:black;">Revision as of 15:34, 22 October 2010</td>
</tr><tr><td colspan="2" class="diff-lineno">Line 9:</td>
<td colspan="2" class="diff-lineno">Line 9:</td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>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.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>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.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>=== Prerequisites ===</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">=== Build instruction===</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">=</ins>===Prerequisites<ins class="diffchange diffchange-inline">=</ins>===</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>To sum up, iGame should be complied and run in computers with following tools and libraries:</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>To sum up, iGame should be complied and run in computers with following tools and libraries:</div></td></tr>
</table>Jkdirachttp://2010.igem.org/wiki/index.php?title=Team:USTC_Software/resources&diff=120404&oldid=prevJkdirac: /* Downloads */2010-10-22T15:27:02Z<p><span class="autocomment">Downloads</span></p>
<table style="background-color: white; color:black;">
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<col class='diff-marker' />
<col class='diff-content' />
<tr valign='top'>
<td colspan='2' style="background-color: white; color:black;">← Older revision</td>
<td colspan='2' style="background-color: white; color:black;">Revision as of 15:27, 22 October 2010</td>
</tr><tr><td colspan="2" class="diff-lineno">Line 3:</td>
<td colspan="2" class="diff-lineno">Line 3:</td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>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.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>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.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>===Downloads===</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>===Downloads===</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>Executable files can be download at <del class="diffchange diffchange-inline">[</del>[https://sourceforge.net/projects/ustc-igame/files/ SourcForge] </div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>Executable files can be download at [https://sourceforge.net/projects/ustc-igame/files/ SourcForge] </div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>Project source code is available at [http://github.com/jkdirac/igame gitHub]<del class="diffchange diffchange-inline">]</del></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>Project source code is available at [http://github.com/jkdirac/igame gitHub]</div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> </div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>===Source OverView===</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>===Source OverView===</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>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.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>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.</div></td></tr>
</table>Jkdirachttp://2010.igem.org/wiki/index.php?title=Team:USTC_Software/resources&diff=120402&oldid=prevJkdirac at 15:26, 22 October 20102010-10-22T15:26:26Z<p></p>
<table style="background-color: white; color:black;">
<col class='diff-marker' />
<col class='diff-content' />
<col class='diff-marker' />
<col class='diff-content' />
<tr valign='top'>
<td colspan='2' style="background-color: white; color:black;">← Older revision</td>
<td colspan='2' style="background-color: white; color:black;">Revision as of 15:26, 22 October 2010</td>
</tr><tr><td colspan="2" class="diff-lineno">Line 1:</td>
<td colspan="2" class="diff-lineno">Line 1:</td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>{{Team:USTC_Software/Header}}</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>{{Team:USTC_Software/Header}}</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>==Downloads[[https://sourceforge.net/projects/ustc-igame/files/ <del class="diffchange diffchange-inline">Executable</del>] [http://github.com/jkdirac/igame <del class="diffchange diffchange-inline">Code</del>]]<del class="diffchange diffchange-inline">==</del></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">==Resources==</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">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.</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">=</ins>==Downloads<ins class="diffchange diffchange-inline">===</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">Executable files can be download at </ins>[[https://sourceforge.net/projects/ustc-igame/files/ <ins class="diffchange diffchange-inline">SourcForge</ins>] </div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">Project source code is available at </ins>[http://github.com/jkdirac/igame <ins class="diffchange diffchange-inline">gitHub</ins>]]</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>===Source OverView===</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>===Source OverView===</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>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.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>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.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>===<del class="diffchange diffchange-inline">Prerequisits</del>===</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>=== <ins class="diffchange diffchange-inline">Prerequisites </ins>===</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>To sum up, iGame should be complied and run in computers with following tools and libraries:</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>To sum up, iGame should be complied and run in computers with following tools and libraries:</div></td></tr>
</table>Jkdirac