News:
[01jun2020] Students interested in giving the exam of this course are invited to contact the teacher in advance in order to choose the topic of the seminar/project
[28may2020] First round of student seminars/projects
[06mar2020] Audio/video recordings of lessons form 8 March 2020 onwards will be made available through this new Moodle page available at https://elearning.di.unipi.it/enrol/index.php?id=188. The Moodle page is already active and students can start enrolling. Recordins will be uploaded by following the standard schedule of lessons.
[05mar2020] In accordance with the decisions recently taken at the national level, the lesson of CMCS planned for Friday 06 March 2020 is CANCELED. As regards next week, the plan is to deliver lessons thrugh an eLearning method that has not been defined yet.
[17feb2020] First lesson on Wed 19 February 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: rule-based notations (chemical reaction metaophor), differential equations, Petri nets and agent-based modelling
- Representation of system behavior: transition systems and probabilistic/stochastic models
- Analysis techniques: discrete event simulation, stochastic 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: 4pm-6pm
Office hours:
- See the teacher home page
Lectures:
- Lecture 1 (wed. 19 February 2020, 9am)
- Introduction (slides)
- Lecture 2 (fri. 21 February 2020, 4pm)
- Discrete dynamical systems (slides)
- Lecture 3 (wed. 26 February 2020, 9am)
- Continuous dynamical systems (slides)
- Lecture 4 (fri. 28 February 2020, 4pm)
- Continuous dynamical systems (cont.)
- Lecture 5 (wed. 4 March 2020, 9am)
- The Chemical Reaction Metaphor (slides)
- Lecture 6 (wed. 11 March 2020, 9am)
- Stochastic Simulation of Chemical Reactions (slides)
Video available in the Moodle page - Lecture 7 (fri. 13 March 2020, 4pm)
- Transition Systems (slides)
Video available in the Moodle page - Lecture 8 (wed. 18 March 2020, 9am)
- Probabilistic/Stochastic Transition Systems -- Markov Chains (slides)
Video available in the Moodle page - Lecture 9 (fri. 20 March 2020, 4pm)
- The PRISM model checker (DEMO - PRISM models)
Video available in the Moodle page - Lecture 10 (wed. 25 March 2020, 9am)
- Multiset Rewriting and P Systems (slides)
Video available in the Moodle page - Lecture 11 (fri. 27 March 2020, 4pm)
- Applications of P systems in population biology and ecology (slides)
Video available in the Moodle page - Lecture 12 (wed. 1 April 2020, 9am)
- Petri nets (slides)
Video available in the Moodle page - Lecture 13 (fri. 3 April 2020, 4pm)
- Petri nets (cont.)
Video available in the Moodle page - Lecture 14 (wed. 8 April 2020, 9am)
- Petri nets (cont.)
Tools for Peti nets - Demo (list of tools, CPN Tools, Snoopy and Charlie)
Video available in the Moodle page - Lecture 15 (wed. 15 April 2020, 9am)
- Applications of Petri nets in manufacturing (slides)
Video available in the Moodle page - Lecture 16 (fri. 17 April 2020, 4pm)
- Machine Learning Petri nets: prediction of dynamical properties of biochemical pathways with Graph Neural Networks (slides)
Video available in the Moodle page - Lecture 17 (wed. 22 Apr 2020, 9am)
- Basic notions of Discrete Event Simulation (slides)
Video available in the Moodle page - Lecture 18 (fri. 24 April 2020, 4pm)
- Towards Agent-Based Modeling: Cellular Automata (slides)
Video available in the Moodle page - Lecture 19 (wed. 29 April 2020, 9am)
- Agent-Based Modeling with NetLogo (demo)
Video available in the Moodle page - Lecture 20 (wed. 6 May 2020, 9am)
- Modelling Social Agents - Case Study: Internet addiction (slides)
Video available in the Moodle page - Lecture 21 (fri. 8 May 2020, 4pm)
- Presentation of topics for the final exam (slides)
Topics for a master thesis (slides)
Video available in the Moodle page - Discussion (wed. 13 May 2020, 9am)
- Supervision of student presentations/projects
- Discussion (fri. 15 May 2020, 4pm)
- Supervision of student presentations/projects
- Student presentations (thu. 28 May 2020, 9.30am)
- Gabriele Pisciotta: Cellular Automata, Life and Lenia
Fabio Murgese, Maze Generation with Cellular Automata
Antonio Di Mauro, Endosymbiosis in NetLogo (project)
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
- CPN Tools
- Snoopy and Charlie
- 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!)