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Models for biological systems

Models for Biological Systems
Corso di laurea magistrale in Informatica F008

Instructor: Simone Tini

Syllabus in Italian

6 INF/01 48 I o II English

Course Objectives and Expected Outcomes
The main target is to show that 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 analyze 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, Lindamayer systems and Membrane Systems, and on the basic ideas of DNA Computing.

A 3-years graduated student in Computer Science or Mathematics does not need any other prerequisite.
Course Topics

  • 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.

Course Format
Classical lessons delivered by the lecturer merged with some exercises solved interactively with the students.
Textbooks and suggested materials
All slides will be on the website e-learning.
Evaluation procedure
The optimal evaluation procedure consists on a seminar given by the student.
Office hours
The lecturer will be available to meet interested students, and to interact with them by email. At least one meeting at week will be organized.

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