Algebraic Biology

This book constitutes the refereed proceedings of the Third International Conference on Algebraic Biology, AB 2008, held at the Castle of Hagenberg, Austria in July 2008 as part of the RISC Summer 2008, organized by the Research Institute for Symbolic Computation.

The 14 revised full papers presented together with 3 tutorial lectures were carefully reviewed and selected from 27 submissions. The conference is the interdisciplinary forum for the presentation of research on all aspects of applications of symbolic computation (computer algebra, computational logic, and related methods) to various issues in biology and life sciences as well as other problems in biology being approached with symbolic methods.

Klappentext

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.

Inhalt

Algorithms for Inference, Analysis and Control of Boolean Networks.- Tutorial on Model Checking: Modelling and Verification in Computer Science.- Differential Algebra and System Modeling in Cellular Biology.- Hybrid Semantics for Stochastic ?-Calculus.- Applying a Rigorous Quasi-Steady State Approximation Method for Proving the Absence of Oscillations in Models of Genetic Circuits.- On the Computational Power of Biochemistry.- The Geometry of the Neighbor-Joining Algorithm for Small Trees.- Neural Algebra and Consciousness: A Theory of Structural Functionality in Neural Nets.- An Algorithm for Qualitative Simulation of Gene Regulatory Networks with Steep Sigmoidal Response Functions.- Property Preservation along Embedding of Biological Regulatory Networks.- Process Algebra Models of Population Dynamics.- Algebraic Analysis of Bifurcation and Limit Cycles for Biological Systems.- The Smallest Multistationary Mass-Preserving Chemical Reaction Network.- Local Structure and Behavior of Boolean Bioregulatory Networks.- Investigating Generic Methods to Solve Hopf Bifurcation Problems in Algebraic Biology.- An Improved Algorithm for Detecting a Singleton Attractor in a Boolean Network Consisting of AND/OR Nodes.- Constructing a Knowledge Base for Gene Regulatory Dynamics by Formal Concept Analysis Methods.