By Tatsuya Akutsu, Morihiro Hayashida, Takeyuki Tamura (auth.), Katsuhisa Horimoto, Georg Regensburger, Markus Rosenkranz, Hiroshi Yoshida (eds.)
This publication constitutes the refereed court cases of the 3rd overseas convention on Algebraic Biology, AB 2008, held on the citadel of Hagenberg, Austria in July 2008 as a part of the RISC summer time 2008, geared up through the learn Institute for Symbolic Computation.
The 14 revised complete papers provided including three educational lectures have been rigorously reviewed and chosen from 27 submissions. The convention is the interdisciplinary discussion board for the presentation of study on all elements of purposes of symbolic computation (computer algebra, computational good judgment, and similar equipment) to varied matters in biology and lifestyles sciences in addition to different difficulties in biology being approached with symbolic methods.
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Extra info for Algebraic Biology: Third International Conference, AB 2008, Castle of Hagenberg, Austria, July 31-August 2, 2008 Proceedings
Pn . Greek letters and ki− , ki+ (1 ≤ i ≤ n − 1) represent parameters: Differential Algebra and System Modeling in Cellular Biology α −−−→ G + Pn − ←−−−− H, ρf G −−−−→ G + M, θ β M −−−−→ M + P, δ −−−→ Pi + P − ←−−−− Pi+1 ρb H −−−−→ H + M, M −−−M−→ ∅, ki+ 33 δ P −−−P−→ ∅, (28) (1 ≤ i ≤ n − 1). ki− This generalized chemical reactions system can now be canonically translated as a system of parametric ordinary differential equations, denoting Ai = (ki− Pi+1 − ki+ Pi P ). Variables G, H, M, P = P1 , .
A single gene regulated by a polymer of its own protein One considers the genetic circuit depicted in Figure 1. The single gene is regulated by an order n polymer of its own protein. The integer number n is a parameter of the system. This study was motivated by the activity of a working group aiming at modeling the circadian clock of the green alga ostreococcus tauri. The addressed question was: does there exist biologically meaningful parameters values which make this circuit oscillate? More technically: does there exist biologically meaningful parameters values which make a Poincar´e-Andronov-Hopf bifurcation occur?
For instance, proteins are described by variables, while genes are modeled as agents, with different internal states depending on which transcription factors are bound to them (see  for further details). Therefore, the discrete dynamics of the hybrid automata associated with an sCCP program comes from the different inner states of agents, while the continuous dynamics describes the time evolution of sCCP variables. In  it is shown that the hybrid semantics of sCCP is more adherent to the stochastic dynamics than the continuous one.