The ParaDiSe Seminar is a working forum for the presentation of ongoing and finished research in the areas related to the specification, modelling, analysis, and verification of software systems.
The meetings are held on Thursday at the Faculty of Informatics, Masaryk University, starting at 12:00.
Seminar Programme — Autumn 2007
Model-Checking of Biological Systems
Systems biology is the study of an organism, viewed as an integrated and interacting network of genes, proteins and biochemical reactions which give rise to life. It integrates experimental and modelling approaches to explain the structure and dynamical properties of biological systems. It aims at building predictive models and simulations of these systems.
The seminar addresses a variety of modelling approaches which have been successfully applied to complex biological systems in the recent years. The seminar will cover, among others, Petri nets, logic-based approaches and model-checking techniques.
Part of the seminar is devoted to original results achieved by the ParaDiSe team under the 6th framework NEST-PATH-COM project EC-MOAN - Scalable Modeling and Analysis Techniques to Study Emergent Cell Behavior.
- September 24, 2007
Systems Biology in a Nutshell
- October 1, 2007
Modelling Biochemical Processes: Deterministic Approach
- October 8, 2007
Discrete Approximation of Gene Regulation
(Sven Dražan / David Šafránek)
- October 15, 2007
Model checking genetic regulatory networks with parameter uncertainty
(Daniel Jakubík / Jakub Chaloupka)
- October 22, 2007
Qualitative networks: a symbolic approach to analyze biological signaling networks
(Petr Ročkai / Pavel Šimeček)
- October 29, 2007
A Unifying Framework for Modelling and Analysing Biochemical Pathways Using Petri Nets (Time Petri Nets for Modelling and Analysis of Biochemical Networks)
(Miroslava Kramáreková / Nikola Beneš)
- November 5, 2007
A Graphical Representation for Biological Processes in the Stochastic pi-Calculus
(Jana Tůmová / Pavel Moravec)
- November 12, 2007
Modeling and querying biomolecular interaction networks (Modelling and Querying Interaction Networks in the Biochemical Abstract Machine BIOCHAM)
(Ondřej Bouda / Pavel Moravec)
- November 19, 2007
On the Analysis of Numerical Data Time Series in Temporal Logic
(Jitka Kudrnáčová / Pavel Šimeček)
- November 26, 2007
Adapting Biochemical Kripke Structures for Distributed Model Checking
(Ondřej Kuzník / Jakub Chaloupka)
- December 3, 2007
Exact Stochastic Simulation of Coupled Chemical Reactions
(Jana Fabriková / Nikola Beneš)
- December 10, 2007
Probabilistic model checking of complex biological pathways
(Milan Češka / David Šafránek)
- December 17, 2007
Parallel Virtual File System.
Abstract: This presentation addresses formal verification of a cluster file system. First, the principle of balanced system is introduced and implications on software complexity are drawn. Next, evolution of file system architecture is given and the cluster file system architecture is discussed in more detail. Then features of a particular cluster file system — Parallel Virtual File System — are presented. Finally, techniques that has been used for PVFS verification are mentioned and directions for future work are discussed.