Admission requirements
This course is open to all students that have been admitted to the minor ‘Quantitative Biology’. Students have to select either this course or the course ‘Elementary practical biology and methods for non-biologists’, depending on their background. Please consult the course or minor coordinator when there is uncertainty about which course is the most appropriate.
Description
In the course the students will become acquainted with mathematical concepts and methods involved in the modeling of dynamical processes in terms of ordinary differential equations (ODEs). These type of equations have been used successfully in various branches of Science, after their invention by Isaac Newton. The modeling approach will be explained by means of application motivated examples: e.g. from chemical reaction networks, electrophysiology, membrane transport. It is discussed what is the meaning of solving such equations. The concept of ‘state’ of the modeled system is introduced. Typically, a model in terms of ODEs cannot be solved explicitly, i.e. there does not exist an easy functional expression that describes the state of the system at any point of time. Instead, the students will be introduced to the technique of ‘phase plane analysis’: a graphical method that allows one to gain insight into the dynamics represented by the model. It is particularly handy in analyzing models when no explicit solution is available. Basic concepts like steady state, stability of steady states and periodic solutions are introduced. The freely available software tool for phase plane analysis, XPPAUT by Bart Ermentrout, will be demonstrated by which one can examine moderately complicated mathematical models.
Course objectives
Students with a Life Science background will learn fundamental concepts and methods from mathematics needed in other courses in the minor to enable effective communication with mathematicians. They will get acquainted with the type of research questions considered in applied mathematics, in particular within the context of analysis of dynamic mathematical models using ordinary differential equations. Attention is given to interpreting the mathematical expressions in a model as representing particular physical, chemical or biological processes. Moreover, in exercise sessions the students will increase their practical skills in manipulating with mathematical expressions and work with various concepts. The use of particular software tools in the analysis of models will be demonstrated and examined in exercise sessions.
Final qualifications:
Ability to effectively communicate about mathematical models.
Ability to interpret mathematical models in terms of underlying processes.
Skilled in manipulating with a selection of types of mathematical expressions and concepts.
Ability to analyze basic mathematical models, combining explicit elementary computations with the use of software tools for more complicated problems.
Understanding what type of information can be obtained from mathematical analysis and simulation of the discussed types of mathematical models.
Timetable
The time table is provisional and provided times are indicative. A detailed final schedule will become available before the start of the minor. It is foreseen that he course starts intensively in the first two weeks of September, then less intensively in the next two weeks. In week 5 the course is closed by a written exam.
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 and exercise sessions. Instruction in the use of computational software tools is provided.
Assessment method
Written exam (100%). The retake is also a written exam.
Reading list
Will be announced.
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.
Exchange and Study Abroad students: please see the Prospective students website for information on the application procedure.
Contact
Course coordinator: Dr. S.C. Hille
Email: shille@math.leidenuniv.nl
Remarks
Brightspace will be used for communication and provision of course material.
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.