Tutorials

ICI 2011

Modelling Biological Systems from Molecular Interactions to Population Dynamics

Thomas Anung Basuki Email: thomasanung@gmail.com, anung@unpar.ac.id

Summary This tutorial describes our approaches in modelling biological systems as a way to better understand their complex behaviours. Our approaches are based on the Calculi of Looping Sequences (CLS), a class of formalisms originally developed to model biological systems involving cells and their membrane-based structures. We choose Stochastic CLS and Spatial CLS, two variants of the calculi that support quantitative analysis of the model, and define an approach that supports simulation, statistical model-checking and visualisation as analysis techniques. The approach is implemented in Maude, a rewriting logic-based language that is equipped with tools for simulation and model-checking. A model of budding yeast cell cycle is defined using our approach and a prototype of a visualisation tool based on this model is developed. More recently, we discovered that this class of formalisms is also suitable to model population dynamics of animals, another kind of biological systems that does not involve membrane-based structures. This kind of biological systems is lacking a formal notation for modelling their complex behaviours and we propose one candidate to fulfil the need. We show the applicability of our approach by modelling the population dynamics of Aedes albopictus or Asian tiger mosquito, an important vector of Dengue Fever and many other diseases. Biography Name: Thomas Anung Basuki Address: Griya Bukit Mas II B3/18 Bojong Koneng Bandung Email: thomasanung@gmail.com, anung@unpar.ac.id Phone: +62858 11261960 Education 1. PhD: Computer Science, University of Pisa, Italy, 2010 2. Master: Computer Science, University of Indonesia, 2003 3. Bachelor: Computer Science, Bandung Institute of Technology, 1995 Working Experience 1. Parahyangan Catholic University, Bandung, Indonesia

a. Head of Computer Science Department, (2011) b. Lecturer in the Computer Science Department, (1997 - 2011), teaching at undergraduate

level and supervising undergraduate students in doing their final projects. I have taught the following courses: - Introduction to Information Technology - Algorithm and Data Structures - Formal Logic - Data Base

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- Formal Language and Automata Theory - Human-Computer Interaction - Research Method - Artificial Intelligence - Formal Methods

c. Director of Central Library, (2003 – 2006) d. Vice Dean of Student Affairs, (1998 – 2000)

2. International Institute of Software Technology, United Nations University, Macau.

a. UNU Fellow, (2006 – 2010) 3. PT Aplikanusa Lintasarta, Jakarta, Indonesia, (1996 – 1997)

a. Professional Services and Technical Support Staff, main job was - to support sales officers in giving technical presentation - to support customers during the installation process

4. PT Sigma Cipta Caraka, Jakarta, Indonesia, (1996)

a. Programmer, to customise the smartcard software. Publications 1. Basuki T.A., R. Barbuti, A. Cerone, A. Maggiolo-Schettini, A. Milazzo and E. Rossi. Modelling

Population Dynamics of Aedes Albopictus. In: Proceedings of the First AMCAPOP 2010, 2010. 2. Basuki T.A., A. Cerone, A. Griesmayer and R. Schlatte. Model-Checking User Behaviour Using

Interacting Components. Formal Aspects of Computing, 21:6, 2009. 3. Basuki T.A., A. Cerone and R.V. Carvalho. Modelling Cell Cycle Using different Levels of

Representation. In: Proceedings of MECBIC 2009, 2009 4. Basuki, T.A., A. Cerone and P. Milazzo. Translating Stochastic CLS into Maude. In: Proceedings of

MECBIC 2008, ENTCS 227, 2008. 5. Basuki T.A. Model Checking Interface Design to Reduce User Errors. In: Pre-proceedings of the

Second International Workshop on Formal Methods for Interactive Systems, 2007. 6. Basuki, T.A., A. Cerone and D. Andriana. Formal Specification of Digital Libraries in RSL. UNU-IIST

Technical Report no. 435, June 2010.

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Formal Verification of Reactive Systems Using Predicate Diagrams

Cecilia E. Nugraheni Summary Verification consists of establishing whether a system satisfies some property, that is, whether all possible behaviors of the system are included in the property specified. There are basically two approaches to formal verification, which are the deductive approach and the algorithmic approach. The deductive approach is based on verification rules, which reduces the system validity of a temporal property to the general validity of a set of first-order verification conditions. The most popular algorithmic verification method is model checking. Although this method is fully automatic for finite-state systems, it suffers from the so-called state-explosion problem. The need for a more intuitive approach to verification leads to the use of diagram-based formalisms. Usually, these diagrams are graphs whose vertices are labeled with first-order formulas, representing sets of system states, and whose edges represent possible system transitions. This approach combines some of the advantages of deductive and algorithmic verification: the process is goal-directed, incremental and can handle infinite-state systems. This tutorial will give an overview of the verification process of reactive systems using a class of diagrams called predicate diagrams. We show that the concept of predicate diagrams can be used to verify not only discrete systems, but also some more complex classes of reactive systems such as real-time systems and parameterized systems. Biography Cecilia E. Nugraheni received the B.S. and M.S. degrees in Informatics Engineering from Bandung Institute of Technology in 1993 and 1997, respectively. In 2004 she was awarded the PhD degree from Institut für Informatik, University of Munich, Germany. Her research interest is formal specification and verification of reactive systems. She is now an academic staff at Informatics Dept., Parahyangan Catholic University, Bandung, Indonesia.

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