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Bio-modeling and Petri Nets

Vak 2013-2014

Admission requirements

Bachelor degree in Computer Science, Biology, Biomedical Science, LST or Pharmaceutical Science, or currently enrolled in the Master Bio-Informatics. Note that knowledge of both biological processes and Petri Nets is not a prerequisite for taking the course.

Description

To systematically investigate biological systems experimental and computational approaches can be combined. To understand a biological system, structural and dynamic properties can be represented in a computational model describing the entities involved and their interaction. This course aims at making students aware of formal, mathematically precise, approaches to the faithful modelling of biological processes. In an interdisciplinary approach we will investigate how to construct and analyse such models using the framework of the modelling technique Petri nets and related tools. Biological case studies will be used as a guide to the modelling of biological phenomena.

This course is a combination of lectures, seminar sessions with student presentations, practical assignments and project work. After a few introductory lectures and two practical sessions on using Petri Net tools, groups will be formed to work on small projects to model aspects of a given biological process using Petri nets. Knowledge of Biology (the case studies) or Computer Science (Petri Nets) is not a prerequisite.
Presence at all meetings is mandatory.
The students’ projects may serve as a stepping stone to a computer science master project. All information on the course can be found at www.liacs.nl/~csbpn/

Course objectives

  • becoming acquainted with uses of modelling techniques for biological research
  • gaining theoretical knowledge of the modelling framework of Petri nets
  • critically presenting and discussing academic papers
  • being able to use the Petri net modelling tool to construct, simulate and analyse Petri net models
  • translating a biological case study (a process) into a formal and executable model
  • presenting the approach followed

Timetable

The most recent timetable can be found at the LIACS website

Mode of instruction

  • Lectures
  • Computer practical
  • Seminar sessions
  • Presentation of own work (including a written report following a template)

Assessment method

Grading is based on

  • participation in seminar discussions (10%)
  • practical exercises (10%)
  • individual presentation of a journal paper (20%)
  • contribution to a group project, modeling, presentation and report (60%)

The final mark is the weighted average of the above as indicated, but under the addional condition that both

  • the result for the first 40% (three bullets)
  • and the result for the last 60% (bullet) mentioned
    should be sufficient (at least 5.5).

Reading list

Literature will be provided during the course.

Registration

You have to sign up for classes and examinations (including resits) in uSis. Check this link for more information and activity codes.

There is a limited capacity for students from outside the master Computer Science programme. Please contact the study advisor.

Contact information

Study coordinator Computer Science, Riet Derogee

Website

For more details and a description in English, see the website