Algebraic Biology: Second International Conference, Ab 2007, Castle Of Hagenberg, Austria, July 2-4, 2007, Proceedings (lecture Notes In Computer Science)

This volume constitutes the refereed proceedings of the Second International Conference on Algebraic Biology, held at the Castle of Hagenberg, Austria in July 2007. The conference was run as part of the Research Institute for Symbolic Computation (RISC) Summer 2007. Nineteen full papers are presented, together with three invited papers and four tutorials. Each paper has been carefully reviewed by the book’s team of expert editors to ensure each one meets the highest standards of research and scholarship. The conference served as an interdisciplinary forum for the presentation of research on all aspects of the application of symbolic computation in biology, including computer algebra, computational logic, and related methods. Papers also examine solutions to problems in biology using symbolic methods. Readers learn new, innovative approaches to solving problems in biology. Front Matter....Pages - Algebraic Systems Biology: Theses and Hypotheses....Pages 1-14 Discrete Models of Biochemical Networks: The Toric Variety of Nested Canalyzing Functions....Pages 15-22 Membrane Computing as a Framework for Bio-modeling (An Informal Glimpse)....Pages 23-35 Relating Attractors and Singular Steady States in the Logical Analysis of Bioregulatory Networks....Pages 36-50 Translating Time-Course Gene Expression Profiles into Semi-algebraic Hybrid Automata Via Dimensionality Reduction....Pages 51-65 On Proving the Absence of Oscillations in Models of Genetic Circuits....Pages 66-80 Attenuation Regulation as a Term Rewriting System....Pages 81-94 Glucose-Insulin Control of Type1 Diabetic Patients in H 2 /H ∞ Space Via Computer Algebra....Pages 95-109 Exact Parameter Determination for Parkinson’s Disease Diagnosis with PET Using an Algebraic Approach....Pages 110-124 Efficient Haplotype Inference with Pseudo-boolean Optimization....Pages 125-139 An Algebraic Algorithm for the Identification of Glass Networks with Periodic Orbits Along Cyclic Attractors....Pages 140-154 Analyzing Pathways Using SAT-Based Approaches....Pages 155-169 Algorithmic Algebraic Model Checking IV: Characterization of Metabolic Networks....Pages 170-184 Cascaded Games....Pages 185-201 On Differential Algebraic Decision Methods for the Estimation of Anaerobic Digestion Models....Pages 202-216 Protein Structure Prediction Using Residual Dipolar Couplings....Pages 217-231 A Stochastic Pi Calculus for Concurrent Objects....Pages 232-246 Modeling Static Biological Compartments with Beta-binders....Pages 247-261 Deducing Interactions in Partially Unspecified Biological Systems....Pages 262-276 Reduction of Algebraic Parametric Systems by Rectification of Their Affine Expanded Lie Symmetries....Pages 277-291 Prefix Reversals on Binary and Ternary Strings....Pages 292-306 Toric Ideals of Phylogenetic Invariants for the General Group-Based Model on Claw Trees K 1,n ....Pages 307-321 Inference of Protein-Protein Interactions by Using Co-evolutionary Information....Pages 322-333 A Short Survey of Automated Reasoning....Pages 334-349 Inference of Complex Regulatory Network for the Cell Cycle System in Saccharomyces Cerevisiae ....Pages 350-364 Manifestation and Exploitation of Invariants in Bioinformatics....Pages 365-377 Back Matter....Pages - This volume contains the proceedings of the 2nd International Conference on Algebraic Biology (AB2007). It was held during July 2-4, 2007 in the Castle of Hagenberg, Austria, and was organized by the Research Institute for Symbolic Computation (RISC) of the Johannes Kepler University, Linz. Algebraic biology is the interdisciplinary forum for the presentation of - search on all aspects of applications of symbolic computation (computer al- bra, computational logic, and related methods) in biology. The?rst conference onalgebraicbiology(AB 2005)washeldduring November28-30,2005inTokyo, Japan. The initiation of the series of algebraicbiology conferences was motivated by therecenttrendsinsymboliccomputationandbiology:Insymboliccomputation, the recent advances in computer performance and algorithmic methods have - celeratedthe extensionofthe scienti?c?elds to whichsymboliccomputationcan be applied. In biology, the determinationof complete genomicsequencesandthe subsequentimprovementsofexperimentaltechniqueshaveyieldedlargeamounts of information about the biological molecules underlying various biological p- nomena. Under these circumstances, the marriage of symbolic computation and biology is expected to generate new algebraic models for biological phenomena and new symbolic techniques for biological data analysis. Thisremainstheintendedpro?leoftheseriesofalgebraicbiologyconferences, andit?guredinthemanuscriptspublishedinAB2007. Thepapersinthepresent volume are evidence of the healthy growth in the?eld of algebraic biology This Volume Constitutes The Refereed Proceedings Of The Second International Conference On Algebraic Biology, Held At The Castle Of Hagenberg, Austria In July 2007. The Conference Was Run As Part Of The Research Institute For Symbolic Computation (risc) Summer 2007. Nineteen Full Papers Are Presented, Together With Three Invited Papers And Four Tutorials. Each Paper Has Been Carefully Reviewed By The Book's Team Of Expert Editors To Ensure Each One Meets The Highest Standards Of Research And Scholarship. The Conference Served As An Interdisciplinary Forum For The Presentation Of Research On All Aspects Of The Application Of Symbolic Computation In Biology, Including Computer Algebra, Computational Logic, And Related Methods. Papers Also Examine Solutions To Problems In Biology Using Symbolic Methods.--publisher's Website. Hirokazu Anai, Katsuhisa Horimoto, Temur Kutsia (eds.). Includes Bibliographical References And Index. This book constitutes the refereed proceedings of the Second International Conference on Algebraic Biology, AB 2007, held at the Castle of Hagenberg, Austria in July 2007 as part of the RISC Summer 2007, organized by the Research Institute for Symbolic Computation. The 19 revised full papers presented together with 3 invited papers and 4 tutorials were carefully reviewed and selected from 40 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) in biology as well as other problems in biology being approached with symbolic methods