The Castle of Hagenberg Algebraic Biology 2008
General Submission Registration Program Location


  • July 30: Arrival - Registration (from 12:00am to 4:00pm in the RISC office)
  • July 31: Registration - Opening - Conference - Welcome Reception
  • August 1: Conference - DentalJazzTrio and Conference Dinner
  • August 2: Conference - Closing
  • August 3: Departure

Detailed Program

July 31, August 1, August 2
Thursday, July 31
08:00-08:45Registration (at the conference desk)
08:45-09:00Opening (Bruno Buchberger)
Session 1. Chair: Katsuhisa Horimoto
09:00-10:00 Invited Talk: Structural Alignments of RNA Sequences
Kiyoshi Asai
10:00-10:30An Improved Algorithm for Detecting a Singleton Attractor in a Boolean Network Consisting of AND/OR Nodes
Takeyuki Tamura and Tatsuya Akutsu
10:30-10:45Coffee break
Session 2. Chair: Ashish Tiwari
10:45-11:15Local Structure and Behavior of Boolean Bioregulatory Networks
Heike Siebert
11:15-11:45Property Preservation Along Embedding of Biological Regulatory Networks
Mbarka Mabrouki, Marc Aiguier, Jean-Paul Comet, Pascale Le Gall
11:45-12:15The Geometry of the Neighbor-Joining Algorithm for Small Trees
Kord Eickmeyer and Ruriko Yoshida
12:15-14:00Lunch break
Session 3. Chair: Luca Cardelli
14:00-14:30The Smallest Multistationary Mass-Preserving Chemical Reaction Network
Anne Shiu
14:30-15:30Tutorial: Algorithms for Inference, Analysis and Control of Boolean Networks
Tatsuya Akutsu, Morihiro Hayashida, Takeyuki Tamura
15:30-15:45Coffee break
Session 4. Chair: Bud Mishra
15:45-16:45Tutorial: Hybrid Systems and Symbolic Computation
Ashish Tiwari
Session 5 (Short Communications). Chair: Bruno Buchberger
16:45-17:00A Biochemical Calculus Based on Strategic Graph Rewriting
Oana Andrei and Helene Kirchner
17:00-17:15Determining Flexibility of Molecules Using Resultants of Polynomial Systems
Robert Lewis and Evangelos Coutsias
17:15-17:30An Algebraic-Numeric Algorithm for the Model Selection in Kinetic Network with Feedback Loop
Masahiko Nakatsui, Hiroshi Yoshida, Masahiro Okamoto, Katsuhisa Horimoto
17:30-17:45Recursive Algebraic Modelling of Gene Signalling, Communication and Switching
Sergiy Pereverzyev jun. and Robert S. Anderssen
17:45-18:00Analysis of Network Dynamics Including Hidden Variables by Symbolic-Numeric Approach
Daisuke Tominaga, Yasuhito Tokumoto, Hiroshi Yoshida, Masahiko Nakatsui, Sachiyo Aburatani, Fuyan Sun, Jun Miyake, Katsuhisa Horimoto
18:00-20:00Welcome Reception

Friday, August 1
Session 6. Chair: Bruno Buchberger
9:15-9:30Neural Algebra and Consciousness: A Theory of Structural Functionality in Neural Nets
Erwin Engeler (summarized by Bruno Buchberger)
9:30-10:00On the Computational Power of Biochemistry
Luca Cardelli and Gianluigi Zavattaro
10:00-10:30Hybrid Semantics for Stochastic pi-calculus
Luca Bortolussi and Alberto Policriti
10:30-10:45Coffee break
Session 7. Chair: Markus Rosenkranz
10:45-11:15Constructing a Knowledge Base for Gene Regulatory Dynamics by Formal Concept Analysis Methods
Johannes Wollbold, Reinhard Guthke, Bernhard Ganter
11:15-12:15 Tutorial: Model Checking: Modelling and Verification in Computer Science
Armin Biere
12:15-14:00Lunch break
Session 8. Chair: Hiroshi Yoshida
14:00-14:30Process Algebra Models of Population Dynamics
Chris McCaig, Rachel Norman, Carron Shankland
14:30-15:30Tutorial: INOH database, declarative description of biological processes
Ken Fukuda
15:30-15:45Coffee break
15:45-16:30Perspectives Meeting
AB'08 Business Meeting and Free Discussion on Symbolic Computation + Biology
17:30Bus departure
18:00DentalJazzTrio and Conference Dinner

Saturday, August 2
Session 9. Chair: Reinhard Laubenbacher
9:00-10:00Invited Talk: Toward Predictive Biology: There is More Mathematics in the Future of Biology
Charles Cantor
10:00-10:30An Algorithm for Qualitative Simulation of Gene Regulatory Networks with Steep Sigmoidal Response Functions
Liliana Ironi, Luigi Panzeri, Erik Plahte
10:30-10:45Coffee break
Session 10. Chair: Dongming Wang
10:45-11:45Tutorial: Differential Algebra and System Modeling in Cellular Biology
François Boulier, François Lemaire
11:45-12:15 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
12:15-14:00Lunch break
Session 11. Chair: Katsuhisa Horimoto
14:00-15:00Tutorial: Systematic Analysis of Protein Interaction Networks Using Mass Spectroscopy
Tohru Natsume
15:00-15:15Coffee break
Session 12. Chair: Manfred Minimair
15:15-15:45Investigating Generic Methods to Solve Hopf Bifurcation Problems in Algebraic Biology
Thomas Sturm and Andreas Weber
15:45-16:15 Algebraic Analysis of Bifurcation and Limit Cycles for Biological Systems
Wei Niu and Dongming Wang