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GINsim:a software supporting the definition, the simulation and the analysis of regulatory graphs  

2010-11-09 15:30:12|  分类: R、SVG&GNUPlot画 |  标签: |举报 |字号 订阅

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Introduction

About GINsim

GINsim is a software supporting the definition, the simulation and the analysis of regulatory graphs. The underlying multilevel logical formalism leans on the definition of two types of graphs: regulatory graphs, which model regulatory networks, and state transition graphs, which represent their dynamical behaviour.

Availability

GINsim 2.3 is freely available for academic users, please contact us for other uses. The GINsim website (http://gin.univ-mrs.fr/GINsim) provides the latest official version of the software, documentation, as well as a model library.

Running GINsim

GINsim is a Java application and should thus run on any system offering a Java virtual machine (version 1.4 or later). If Java is not already installed on your computer, it can be downloaded:

Other system requirements depend heavily on model size. To work confortably, a computer with at least 512Mo of RAM is required. A screen resolution of at least 1024x768 is recommended.

GINsim is available in two forms:

  • A single jar file. On a properly configured system, double-click on the file to launch the application, otherwise run it with the command: java -jar GINsim-$version.jar.
  • An archive (zip or tar.gz format). Uncompress it and run the relevant launcher script: runginsim.bat for windows, runginsim.sh for UNIX-like systems, and runginsim.command for Mac OS X. This version includes the documentation (tutorial and user manual) and can be extended through plugins.
[Tip]Tip

Large models may require an increase of the amount of RAM available to the Java virtual machine. This can be done:

  • for the jar file, with the command java -Xmx300M -jar GINsim-$version.jar (replace 300 by the amount of RAM you want, in Mo);
  • for the archive, by changing the value of the JAVAMAXMEM variable in the launcher script.

Overview of the manual

The next section covers the Graphical User Interface of GINsim, mostly through the presentation of the main menu options. Section 3 presents the editing tools dedicated to regulatory graphs. Section 4 is dedicated to simulation (i.e. the generation of state transition graphs). Finally section 5 and 6 present analysis tools.

For a first introduction to GINsim, the GINsim tutorial may be a better starting point. This manual uses as much as possible the same examples and figures.

some results:

Level layout example

GINsim:a software supporting the definition, the simulation and the analysis of regulatory graphs - 喜欢吃桃子 - wangyufeng的博客
 
Ring layout example
GINsim:a software supporting the definition, the simulation and the analysis of regulatory graphs - 喜欢吃桃子 - wangyufeng的博客

Priority Class: example result
GINsim:a software supporting the definition, the simulation and the analysis of regulatory graphs - 喜欢吃桃子 - wangyufeng的博客
more links to:http://gin.univ-mrs.fr/GINsim/doc/2.3/html/userManual.html
 
 
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