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 several 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
Understand the concept of systems biology and bio-modeling.
Understand network motifs in systems biology.
Apply bio-modeling tools: Boolean Networks and Petri Nets to model real biological studies.
Evaluate the network created by bio-modeling tools.
Timetable
The most recent timetable can be found at the Computer Science (MSc) student website.
In MyTimetable, you can find all course and programme schedules, allowing you to create your personal timetable. Activities for which you have enrolled via MyStudyMap will automatically appear in your timetable.
Additionally, you can easily link MyTimetable to a calendar app on your phone, and schedule changes will be automatically updated in your calendar. You can also choose to receive email notifications about schedule changes. You can enable notifications in Settings after logging in.
Questions? Watch the video, read the instructions, or contact the ISSC helpdesk.
Note: Joint Degree students from Leiden/Delft need to combine information from both the Leiden and Delft MyTimetables to see a complete schedule. This video explains how to do it.
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%) * kick-off presentation (10%) * final presentation (15%) * final report (65%)
The final mark is the weighted average of the above as indicated.
If an assignment or a presentation is not completed, the resulting grade is a 0. There will be no retakes for the assignments and the presentations. The retake for the final report is an one-time resubmission with an improved version. The final grade can only be sufficient if the weighted average grade is at least a 5.5.
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
As a student, you are responsible for enrolling on time through MyStudyMap.
In this short video, you can see step-by-step how to enrol for courses in MyStudyMap.
Extensive information about the operation of MyStudyMap can be found here.
There are two enrolment periods per year:
Enrolment for the fall opens in July
Enrolment for the spring opens in December
See this page for more information about deadlines and enrolling for courses and exams.
Note:
It is mandatory to enrol for all activities of a course that you are going to follow.
Your enrolment is only complete when you submit your course planning in the ‘Ready for enrolment’ tab by clicking ‘Send’.
Not being enrolled for an exam/resit means that you are not allowed to participate in the exam/resit.
Contact
Lecturer: dr. Lu Cao
Remarks
Software
Starting from the 2024/2025 academic year, the Faculty of Science will use the software distribution platform Academic Software. Through this platform, you can access the software needed for specific courses in your studies. For some software, your laptop must meet certain system requirements, which will be specified with the software. It is important to install the software before the start of the course. More information about the laptop requirements can be found on the student website.