News:
[5mar2019] The class of Friday, 8 March 2019 is CANCELED!
[20feb2019] First class in Aula Fib L1!
Brief description of the course:
The course will deal with methods for the modeling, simulation and formal analysis of complex systems such as populations, biological systems, social networks, and so on.
Draft syllabus:
- Complex systems: basic concepts and the relationships between component interaction and population dynamics
- Modelling methodologies: agent-based modelling, Petri nets and rule-based notations
- Representation of system behavior: transition systems and probabilistic/stochastic models
- Analysis techniques: discrete event simulation, model checking and statistical model checking
- Applications: selected case studies from social sciences, life sciences (biology and biomedicine) and others
Timetables:
Lectures schedule (second semester, room Fib L1)
- Wednesday: 9am-11am
- Friday: 9am-11am
Office hours:
- Should be on Tuesday: 2pm-4pm
- but it is better to fix an appointment (via email)
Lectures:
- Lecture 1 (wed. 20 February 2019, 9am)
- Introduction (slides)
- Lecture 2 (fri. 22 February 2019, 9am)
- Discrete dynamical systems (slides)
- Lecture 3 (wed. 26 February 2019, 9am)
- Continuous dynamical systems (slides)
- Lecture 4 (fri. 1 March 2019, 9am)
- Continuous dynamical systems (cont.)
- Lecture 5 (wed. 6 March 2019, 9am)
- The Chemical Reaction Metaphor (slides)
- Lecture 6 (wed. 12 March 2019, 9am)
- Stochastic Simulation of Chemical Reactions (slides)
- Lecture 7 (fri. 15 March 2019, 9am)
- Transition Systems (slides)
- Lecture 8 (wed. 20 March 2019, 9am)
- Probabilistic/Stochastic Transition Systems -- Markov Chains (slides)
- Lecture 9 (fri. 22 March 2019, 9am)
- The PRISM model checker (DEMO - PRISM models)
- Lecture 10 (wed. 27 March 2019, 9am)
- Multiset Rewriting and P Systems (slides)
- Lecture 11 (fri. 29 March 2019, 9am)
- Applications of P systems in population biology and ecology (slides)
- Lecture 12 (wed. 10 April 2019, 9am)
- Petri nets (slides)
- Lecture 13 (fri. 12 April 2019, 9am)
- Petri nets (cont.)
- Lecture 14 (wed. 17 April 2019, 9am)
- Applications of Petri nets in manufactoring (slides)
- Lecture 15 (fri. 3 May 2019, 9am)
- Basic notions of Discrete Event Simulation (slides)
Discussion about student presentations/projects - Lecture 16 (wed. 8 May 2019, 9am)
- Cellular Automata and Agent Based Modeling NetLogo
- Lecture 17 (wed. 15 May 2019, 9am)
- Computational modelling of Internet addiction slides
Proposal of topics for theses slides - Student presentations (wed. 5 June 2019, 9am)
- Flavio Ascari: Prism Games
Andrea Cossu: Modeling Internet addiction in NetLogo - Student presentations (fri. 7 June 2019, 9am)
- Selman Alpdundar: Petri nets modeling of hospital procedures
Alessandro di Giorgio: Agent-based modeling of Music Group Playing - Student presentations (fri. 14 June 2019, 9am)
- Nicolas Mannini: An approach to computational complexity with P systems
Teaching material:
Slides of the lectures are available above.
Lecture notes:
- Notes on a Short Course and Introduction to Dynamical Systems in Biomathematics by Urszula Forys
- Chapter 2 of A Guide to Numerical Modelling in Systems Biology by Peter Deuflhard and Susanna Roblitz (free download from the UniPi subnet)
- Mathematical and Computer Modelling of Nonlinear Biosystems by Urszula Fory's
- Stochastic Simulation of Chemical Kinetics by Daniel T. Gillepie (free download from the UniPi subnet)
- Dave Parker's Lectures on Probabilistic Model Checking
- G. Geeraerts' Slides on Petri nets
- A Petri net based deadlock prevention policy for flexible manufacturing systems by J. Ezpeleta, J.M. Colom and J. Martinez (free download from the UniPi subnet)
Software:
These are the software tools that will be used in the context of the course:
- Any spreadsheet
- GNU Octave
- Dizzy stochastic simulator (old version)
- The PRISM model checker
- NetLogo
- Java (or any other programming language...)
Exams:
It may consist in either a presentation of a scientific paper, a small project (to be done in groups of 1-3 students), or a standard oral exam.
Proposals of scientific papers and projects ideas will be made available close to the end of the course (proposals from students are also welcome!)