Modeling a spatially distributed signaling pathway in MGS

Principles

This image represents the initial state of a signaling pathway. The model is proposed by A. Bugrim ( A Logic-based Approach for Computational Analysis of Spatially Distributed Biochemical Networks, Andrej Bugrim, ISMB 2000; see also this article) and takes into account the spatial localisation of the molecules. The reaction, diffusion and transport processes described in the Bugrim model are modeled as multiset transformations taking place in a nest of multisets. This is reminiscent of the P system approach. This figure is automatically generated by the MGS simulation program. Each box corresponds to a multiset: the external one represents the universe and contains three elements: the agonist molecule pictured as a thin cone;  the calcium (the thick cone); and the plasma membrane which is represented as a multiset and figured by a translucid box. The various molecules anchored in the plasma membrane are drawn as various solid volumes. The ellipsoidal container represents the cytosol and the solid sphere in the middle of it, the nucleus. Such a figure can be generated at each simulation step to visualize the trajectory of the dynamical system. See below for the first three steps.

The corresponding MGS program

Clément Boin and Nicolas Thibault have developped this program as part of a student project. Thanks for their work !

• The code of the program (without comment) is available here as a text file.
  
• The complete program is described (in french) in this technical report (.ps.gz, 992k) made by Clément Boin and Nicolas Thibault for their TER (a research project done by students). The first part of this report is devoted to an application in Artificial Chemistry. The complete code for these two applications appears in the index.
• The slide presentation of this student project is available as a power-point file (646k).
• An authorware presentation of the Bugrim model is available on-line for netscape and explorer browser under windows (we are sorry but Macromedia does not furnish a plugin for linux).
• And also the same presentation is available as a stand-alone executable (for Windows 9x, NT, XP). Saves this self-extracting archive. Decompress it just by executing it and read the README.txt in the directory just created.
  

this site is under construction.
Pages started: May 2002. Last revision: 24 jully 2003.

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