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MODELS FOR BIOLOGICAL SYSTEMS

Degree course: 
Corso di Second cycle degree in MATHEMATICS
Academic year when starting the degree: 
2017/2018
Year: 
1
Academic year in which the course will be held: 
2017/2018
Course type: 
Supplementary compulsory subjects
Credits: 
8
Period: 
First Semester
Standard lectures hours: 
80
Detail of lecture’s hours: 
Lesson (80 hours)
Requirements: 

To attend the course of Models for Biological Systems the student is required to have familiarity with the basic notions in the realm of formal languages, algorithms and complexity. This requisite is surely respected by students with a 3-years degree in Mathematics or Computer Science.

Final Examination: 
Orale

An exam is necessary.
The student must agree with the lecturer on a set of papers to be studied. The student has to prepare a presentation and show it to the lecturer.
The student should prove to have a deep knowledge on the content of the papers and the ability to compare the approach of the authors with respect to what treated during lessons.

Assessment: 
Voto Finale

After having attended the course on Models for Biological System, the student will have clear how computer science and biology are related disciplines. On one side, the student will get familiarity with the main features of the languages and formalisms proposed to model and analyse biological systems and with pattern matching algorithms, which are two of the main examples of how computer science can be exploited in the biological setting. On the other side, the student will get familiarity on the main formalisms inspired by biological systems, e.g. systolic automata, Lindenmayer systems and Membrane Systems, and on the basic idea of DNA Computing. The student will be able to tune pattern matching algorithms to new challenges coming from biology, to model simple biologic behaviours by using the proper formalism and to analyse the expressive power of languages inspired by biology.

• DNA computing and application: SAT, TSP.
• Pattern matching, Boyer-Moore algorithm, Aho-Corasick algorithm, Apostolico-Giancarlo algorithm, Knuth-Morris-Pratt algorithm, with particular analysis on how they perform on DNA streams.
• Formal methods for biologic systems, Gillespie approach, Calculus of Looping Sequences.
• Cellular automata, Lindenmayer systems, Membrane systems, Process Algebras.

The official material consists in the slides and the scientific papers delivered by the lecturer.

The course consists in 72 hours of front teaching, with the help of slides which will be available on the e-learning website. Exercises will be proposed and solved interactively with the lecturer.

Professors

TINI SIMONE

Borrowers