Algebraic Biology

1. Front Matter

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2. Algorithms for Inference, Analysis and Control of Boolean Networks

   • Tatsuya Akutsu, Morihiro Hayashida, Takeyuki Tamura

   Pages 1-15

3. Tutorial on Model Checking: Modelling and Verification in Computer Science

   • Armin Biere

   Pages 16-21

4. Differential Algebra and System Modeling in Cellular Biology

   • François Boulier, François Lemaire

   Pages 22-39

5. Hybrid Semantics for Stochastic π-Calculus

   • Luca Bortolussi, Alberto Policriti

   Pages 40-55

6. Applying a Rigorous Quasi-Steady State Approximation Method for Proving the Absence of Oscillations in Models of Genetic Circuits

   • François Boulier, Marc Lefranc, François Lemaire, Pierre-Emmanuel Morant

   Pages 56-64

7. On the Computational Power of Biochemistry

   • Luca Cardelli, Gianluigi Zavattaro

   Pages 65-80

8. The Geometry of the Neighbor-Joining Algorithm for Small Trees

   • Kord Eickmeyer, Ruriko Yoshida

   Pages 81-95

9. Neural Algebra and Consciousness: A Theory of Structural Functionality in Neural Nets

   • Erwin Engeler

   Pages 96-109

10. An Algorithm for Qualitative Simulation of Gene Regulatory Networks with Steep Sigmoidal Response Functions

    • Liliana Ironi, Luigi Panzeri, Erik Plahte

    Pages 110-124

11. Property Preservation along Embedding of Biological Regulatory Networks

    • Mbarka Mabrouki, Marc Aiguier, Jean-Paul Comet, Pascale Le Gall

    Pages 125-138

12. Process Algebra Models of Population Dynamics

    • Chris McCaig, Rachel Norman, Carron Shankland

    Pages 139-155

13. Algebraic Analysis of Bifurcation and Limit Cycles for Biological Systems

    • Wei Niu, Dongming Wang

    Pages 156-171

14. The Smallest Multistationary Mass-Preserving Chemical Reaction Network

    • Anne Shiu

    Pages 172-184

15. Local Structure and Behavior of Boolean Bioregulatory Networks

    • Heike Siebert

    Pages 185-199

16. Investigating Generic Methods to Solve Hopf Bifurcation Problems in Algebraic Biology

    • Thomas Sturm, Andreas Weber

    Pages 200-215

17. An Improved Algorithm for Detecting a Singleton Attractor in a Boolean Network Consisting of AND/OR Nodes

    • Takeyuki Tamura, Tatsuya Akutsu

    Pages 216-229

18. Constructing a Knowledge Base for Gene Regulatory Dynamics by Formal Concept Analysis Methods

    • Johannes Wollbold, Reinhard Guthke, Bernhard Ganter

    Pages 230-244

19. Back Matter

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This volume contains the proceedings of the Third International Conference on Algebraic Biology (AB 2008). Jointly organized by the National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, and the Research Institute for Symbolic Computation (RISC), Hagenberg, Austria, it was held from July 31 to August 2, 2008 in the Castle of Hagenberg. Algebraic biology is an interdisciplinary forum for research on all aspects of applying symbolic computation in biology. The ?rst conference on algebraic biology (AB 2005) was held November 28–30, 2005 in Tokyo, the second during July 2–4, 2007 in Hagenberg. The AB conference series is intended as a bridge between life sciences and symbolic computation: On the one hand, new insights inbiologyarefoundbypowerfulsymbolicmethods;ontheotherhand,biological problems suggestnew algebraicstructures andalgorithms.While this pro?le has been established in the previous proceedings, the papers in the present volume demonstrate the continuous growth of algebraic biology. We received 27 submissions from 14 countries (Australia, Austria, Canada, China, Colombia, France, Germany, Italy, Japan, Norway, Russia, Switzerland, UK, USA), and 14 papers were accepted for publication. Each submission was assigned to at least three ProgramCommittee members, who carefully reviewed the papers, in many cases with the help of external referees. The reviews were discussedby the ProgramCommittee for oneweekvia the EasyChairconference management system.

• algebraic methods
• artificial intelligence
• automata
• biology
• calculi
• combinatorics
• computer
• computer algebra
• differential algebra
• distributed computing
• dynamic systems
• formal methods
• gene expression
• life sciences
• logic

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