Admission requirements
Elementary calculus, some basic knowledge of linear algebra is useful (e.g. matrix addition, matrix multiplication, Gaussian elimination method).
Description
This course is a primer in methods for mathematical modelling of metabolism, the ensemble of biochemical reactions that are essential for life.
After introducing classical kinetic models, the course will delve deeper into the concept of graph-based modelling of metabolic networks. The course will illustrate how network topology alone gives important biological insights. To this end, we will introduce the fundamentals of convex sets and how they relate back to the biology of the metabolic network being modelled. Concepts from the research literature such as extreme currents, extreme pathways, and elementary modes will be discussed. These concepts are applied to the problem of optimal metabolite production in industrial microbes, the Warburg effect in tumor cells, metabolic regulation of multicellular organisms, and the dynamics of microbial ecosystems. The lectures will include demonstrations of the software packages COPASI and COBRApy, as well as worked examples for algorithms for linear optimization and for finding generating vectors in the steady state solution space.
Course objectives
Learn to work with differential equation-based models and graph representation of (bio)chemical reaction networks, analysis methods and algorithms for computing flux balance analysis, elementary flux modes and extreme currents.
Understand the approaches and limitations of the modelling methods, read and understand current research on the topic.
Learn to approach biological questions on metabolism using differential equation-based modelling and flux-balance analysis.
Timetable
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
The class is taught primarily via lectures. Some lectures include step-by-step demonstrations of the software. Practical homework exercises ask students to use the presented software on new problems, and include also pen-and-paper exercises.
An individually written essay on a research paper will enable students to learn to read and interpret the literature hands-on.
Assessment Method
The final grade consists of two constituent examinations (30% + 30%), practical homework assignments (30%), and a practical team presentation (10%).
The constituent examinations are an individually written essay with subsequent oral presentation, and a written exam. The retakes for the essay is also written with subsequent oral presentation, and the written exam retake is written.
No minimum grade is required to take part for either exam. The homework and team presentation count as a practical and there is no retake for them.
To pass the course, the weighted average of all partial grades must be at least 5.5
Reading list
The course is based on materials collected from various sources and internal notes. Lecture slides will be made available for self-study. Various research papers will be distributed during the course.
Optional further reading:
Kremling, Andreas. Systems biology: mathematical modeling and model analysis. CRC Press, 2013. ISBN 9781466567894
Palsson, Bernhard Ø. Systems biology: properties of reconstructed networks. Cambridge university press, 2006. ISBN 9780521859035
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
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.