Admission requirements
Not applicable.
Description
In order 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 interactions.
This course aims at making students aware of formal and mathematically precise approaches to the faithful modeling of biological processes. In an interdisciplinary approach we will investigate how to construct and analyze such formal models using the frameworks of Boolean Networks and Petri nets. Biological case studies will be used as a guide to the modelling of biological phenomena.
This course is a combination of lectures and project work. After the introductory lectures and some practical sessions on using Boolean Network and Petri Net tools, groups will be formed to work on a project to model aspects of a given biological process. Knowledge of Biology (the case studies) or Computer Science (Boolean Network and Petri Nets) is not a prerequisite. Presence at all meetings is mandatory.
Course objectives
becoming acquainted with uses of modelling techniques for biological research
gaining theoretical knowledge of the modelling framework of Boolean Networks and Petri nets
Timetable
The most recent timetable can be found at the Computer Science (MSc) student website.
You will find the timetables for all courses and degree programmes of Leiden University in the tool MyTimetable (login). Any teaching activities that you have sucessfully registered for in MyStudyMap will automatically be displayed in MyTimeTable. Any timetables that you add manually, will be saved and automatically displayed the next time you sign in.
MyTimetable allows you to integrate your timetable with your calendar apps such as Outlook, Google Calendar, Apple Calendar and other calendar apps on your smartphone. Any timetable changes will be automatically synced with your calendar. If you wish, you can also receive an email notification of the change. You can turn notifications on in ‘Settings’ (after login).
For more information, watch the video or go the the 'help-page' in MyTimetable. Please note: Joint Degree students Leiden/Delft have to merge their two different timetables into one. This video explains how to do this.
Mode of instruction
Lectures
Case study sessions
Presentation of own work (including a written report following a template)
Course load
Hours of study: 168 (= 6 EC)
Lectures: 48
Presentation and preparations: 30
Practical work: 30
Report: 60
Assessment method
Grading is based on:
presence, assignments completion and active participation in discussion (10%)
contribution to a project: modeling, presentation, report (90%)
The final mark is the weighted average of the above as indicated.
Reading list
Systems biology - a textbook.
An Introduction to Systems Biology--Design Principles of Biological Circuits.
Modeling in Systems Biology – The Petri Net Approach.
Additional Materials that will be announced during the course.
Registration
From the academic year 2022-2023 on every student has to register for courses with the new enrollment tool MyStudyMap. There are two registration periods per year: registration for the fall semester opens in July and registration for the spring semester opens in December. Please see this page for more information.
Please note that it is compulsory to both preregister and confirm your participation for every exam and retake. Not being registered for a course means that you are not allowed to participate in the final exam of the course. Confirming your exam participation is possible until ten days before the exam.
Extensive FAQ's on MyStudymap can be found here.
Contact
Lecturer: dr. Lu Cao