13th International Conference on Membrane Computing - MTA Sztaki

T. Hinze, B. Schell, M. Schumann, C. Bodenstein
The corresponding experimental setup can be captured by the P meta framework
assuming the non-probabilistic P module n = (X, Y, F) from [3] to act as
unique neuronal core oscillator from which up to 14 instances are employed:
5 Conclusions
Π SCN =(M,P) with
M = {(n, 14)}
P = {0 :ModuleConnect(n[1] → n[3], {(Y,X)}),
0:ModuleConnect(n[1] → n[4], {(Y,X)}),...,
0:ModuleConnect(n[10] → n[14], {(Y,X)})
300 : ModuleConnect(n[2] → n[4], {(Y,X)}),...,
300 : ModuleConnect(n[6] → n[10], {(Y,X)})}
Assembly and reassembly as well as composition and decomposition of predefined
reaction network modules on the fly appears to be a promising strategy
in order to achieve complex systems capable of new or extended functionality.
Inspired by biological evolution at a granularity of highly conserved genetic
ensembles, our P meta framework provides a tool for control and systematic
conduction of corresponding studies. Within two application cases, we demonstrated
the descriptive capacity behind this approach. Particularly at the edge
of straight-forward lines for complex network inference in reverse engineering, a
strict utilisation of previously identified modules and their reuse can contribute
to explore the abilities of resulting systems in a more effective and efficient way.
Further studies will address technical aspects of module integration from different
specification platforms. It seems that modules based on ODEs on the one
hand and discrete forms along with rewriting rules on the other, needs to interact
with each other via appropriate interfaces. To this end, the Infobiotics
workbench offers an extensive functionality [5]. A fruitful combination of the
universe of P systems featured by their ability to manage dynamical structures
with the universe of ODEs featured by a profound toolbox for analytical examination
could be an innovative clue. In all simulation studies carried out for this
paper, we consistently utilised the Complex Pathway Simulator software CoPaSi
(version 4.7) along with the Gepasi Model Extractor for generation of several
instances from a common module specification. Corresponding source files are
available from the authors upon request.
References
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2003
3. S. Bernard, D. Gonze, B. Cajavec, H. Herzel, A. Kramer. Synchronization-induced
rhythmicity of circadian oscillators in the suprachiasmatic nucleus. PLoS Comput
Biol 3(4):e68, 2007
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