The Castle of Hagenberg Algebraic Biology 2007
General Submission Registration Program Location
  • July 1: Arrival, registration.
  • July 2: Conference opening. Plenary sessions. Tutorial sessions.
  • July 3: Plenary sessions. Tutorial sessions.
  • July 4: Plenary sessions. Tutorial session. Conference dinner. Closing.
  • July 5: Departure.

Program: July 2, July 3, July 4.


Monday, July 2.
07:30The AB bus leaves from Sommerhaus Linz to Arcotel.
07:45The AB bus leaves from Arcotel to Hagenberg.
Session 1. Chair: Bruno Buchberger
08:30-09:30 Invited Talk. Algebraic Systems Biology: Theses and Hypotheses.
Bud Mishra
09:30-10:00Algorithmic Algebraic Model Checking IV: Characterization of Metabolic Networks.
Venkatesh Mysore and Bud Mishra.
10:00-10:15Coffee break.
Session 2.Chair: René Vestergaard
10:15-10:45Translating Time-course Gene Expression Profiles into Semi-Algebraic Hybrid Automata via Dimension Reduction.
Alberto Casagrande, Kevin Casey, Rachele Falchi, Carla Piazza, Benedetto Ruperti, Giannina Vizzotto, Bud Mishra.
10:45-11:15On Proving the Absence of Oscillations in Models of Genetic Circuits.
François Boulier, Marc Lefranc, François Lemaire, Pierre-Emmanuel Morant, Asli Ürgüplü.
11:15-11:45Attenuation Regulation as a Term Rewriting System.
Eugene Asarin, Thierry Cachat, Alexander Seliverstov, Tayssir Touili, Vassily Lyubetsky.
11:45-13:15Lunch break.
Session 3. Chair: Manfred Minimair
13:15-13:45Glucose-Insulin Control of Type1 Diabetic Patients in H2/H Space via Computer Algebra.
Levente Kovács, Belá Paláncz.
13:45-14:15Exact Parameter Determination for Parkinson's Disease Diagnosis with PET Using an Algebraic Approach.
Hiroshi Yoshida, Koji Nakagawa, Hirokazu Anai, Katsuhisa Horimoto.
14:15-14:30Coffee break.
Session 4 (Tutorials). Chair: Bruno Buchberger
14:30-15:10Quantified Constraint Solving and Biology.
Hoon Hong.
15:10-15:50Inference of Protein-Protein Interactions by Using Co-evolutionary Information.
Tetsuya Sato, Yoshihiro Yamanishi, Katsuhisa Horimoto, Minoru Kanehisa, Hiroyuki Toh.
15:50-16:05Coffee break.
Session 5 (Tutorials). Chair: Carolyn Talcott
16:05-16:45A Short Survey of Automated Reasoning.
John Harrison.
16:45-17:25Inference of Complex Regulatory Network for the Cell Cycle System in Saccharomyces cerevisiae.
Sachiyo Aburatani.
20:15The school/AB bus leaves from Hagenberg to Linz

Tuesday, July 3.
07:45The AB bus leaves from Sommerhaus Linz to Arcotel.
08:00The AB bus leaves from Arcotel to Hagenberg.
Session 6. Chair: Katsuhisa Horimoto.
08:30-09:30 Invited Talk. Discrete Models of Biochemical Networks: The Toric Variety of Nested Canalyzing Functions. (Slides)
Abdul S. Jarrah, Reinhard Laubenbacher.
09:30-10:00Efficient Haplotype Inference with Pseudo-Boolean Optimization.
Ana Graça, João Marques-Silva, Inês Lynce, Arlindo L. Oliveira.
10:00-10:15Coffee break.
Session 7. Chair: Hiroshi Yoshida
10:15-10:45An Algebraic Algorithm for the Identification of Glass Networks with Periodic Orbits along Cyclic Attractors.
Igor Zinovik, Daniel Kroening and Yury Chebiryak.
10:45-11:15Analyzing Biological Pathways using SAT-based Approaches.
Ashish Tiwari, Carolyn Talcott, Merrill Knapp, Patrick Lincoln, Keith Laderoute.
11:15-11:45Relating Attractors and Singular Steady States in the Logical Analysis of Bioregulatory Networks
Heike Siebert, Alexander Bockmayr.
11:45-13:15Lunch break.
Session 8. Chair: François Boulier
13:15-13:45Cascaded Games.
Jittisak Senachak, Mun'delanji Vestergaard, René Vestergaard.
13:45-14:15On Differential Algebraic Decision Methods for the Estimation of Anaerobic Digestion Models.
Elena Chorukova, Sette Diop, Ivan Simeonov.
14:15-14:30Coffee break.
Session 9 (Tutorials). Chair: Hiroyuki Toh
14:30-15:10Manifestation and Exploitation of Invariants in Bioinformatics.
Limsoon Wong.
15:10-15:50Towards a Statistical Definition of a Species in Terms of Probabilities of Conspecificity, with Examples Drawn from the Study of African Plio-Pleistocene Hominids. (Slides)
Francis Thackeray.
15:50-16:05Coffee break.
Session 10 (Tutorials). Chair: Hoon Hong
16:05-16:45New combinatorial results for words over four letters.
Veikko Keränen.
17:00The AB bus leaves from Hagenberg to Linz.

Wednesday, July 4.
07:45The AB bus leaves from Sommerhaus Linz to Arcotel.
08:00The AB bus leaves from Arcotel to Hagenberg.
Session 11. Chair: Hoon Hong
08:30-09:30 Invited Talk. Membrane Computing as a Framework for Bio-Modeling (An Informal Glimpse).
Gheorghe Păun.
09:30-10:00Protein Structure Prediction using Residual Dipolar Couplings.
Ioannis Z. Emiris, Sotirios I. Pantos.
10:00-10:15Coffee break.
Session 12. Chair: Thierry Cachat
10:15-10:45A Stochastic Pi-Calculus for Concurrent Objects.
Céline Kuttler, Cédric Lhoussaine, Joachim Niehren.
10:45-11:15Modeling Static Biological Compartments with Beta-Binders. (Slides)
Maria Luisa Guerriero, Corrado Priami, Alessandro Romanel.
11:15-11:45Deducing Interactions in Partially Unspecified Biological Systems. (Slides)
Paolo Baldan, Andrea Bracciali, Linda Brodo, Roberto Bruni.
11:45-13:15Lunch break.
Session 13. Chair: Ruriko Yoshida
13:15-13:45Reduction of Algebraic Parametric Systems by Rectification of their Affine Expanded Lie Symmetries.
Alexandre Sedoglavic.
13:45-14:15Prefix Reversals on Binary and Ternary Strings.
Cor Hurkens, Leo van Iersel, Judith Keijsper, Leen Stougie, John Tromp, Steven Kelk.
14:15-14:45Toric Ideals of Phylogenetic Invariants for the General Group-Based Model on Claw Trees K1,n. (Slides)
Sonja Petrović, Julia Chifman.
14:45-15:00Coffee break.
Session 14 (Tutorials). Chair: Katsuhisa Horimoto
15:00-15:40A Systematic Treatment of Growth Terms Appearing in Continuum Mechanics Formulations for Biological Materials. (Slides)
Hans Irschik.
15:40-16:20Harmonicity vs. Frustration in Protein Folding and Function.
Nobuhiro Go.
16:20-17:00Concavity in Biological Morphometric. (Slides, program)
Gautam Dasgupta.
17:30The school/AB bus leaves from Hagenberg to Linz.
19:00-22:00Conference dinner.