Lectures content

The schedule of the classes in the Bio-Modeling Spring 2020 course is shown below. Rooms are in the Snellius Building. Slides from the lectures are also provided. They are intended for this 2020 LIACS course only and should be used for that purpose. Please report remarks and/or errors. Thanks in advance.

From the table below lecture notes can be downloaded as PDF files by clicking the relevant links. For some of the slides and materials, you need to be enrolled to the course in Blackboard. If you are not logged in to Blackboard then you are asked for a username and password. Enter your ULCN credentials (connected to student number) in this login field.

The Reading column indicates the material or tasks that we expect you to start to examine from the given lecture, possibly as a form of homework that is due for the next session. A different due date may be given.

# Lecture time Sort descending Room Content Reading Slides and additional material
04 25-02-2020 15.30 - 17.15 408 Extended Petri Nets (Lu Cao) Petri Nets Properties and Extensions [PDF]
Assignment 2 [PDF]
01 04-02-2020 14:15 - 16:00 408 Introduction of Biomodeling (Fons Verbeek; Lu Cao) Course introduction [PDF]
Bio-Modeling & Sytems Biology [PDF]
02 11-02-2020 14:15 - 16:00 408 Basic Petri Nets (Lu Cao) Recommended: Modeling in Systems Biology: The Petri Net Approach chapters 1, (2), 3.
Try the Assignment 1 (Blackboard, 17-02-2020 18:00)
Introduction to Systems Biology, Petri nets [PDF]
Assignment 1 [PDF]
03 18-02-2020 14:15 - 16:00 306 Computer practical 1 Snoopy packages [URL]
Introduction to the Snoopy Environment [PDF]
Practical Exercises 1 [PDF]
05 03-03-2020 14:15 - 16:00 306 Computer practical 2 Manual for Colored Petri Nets in Snoopy, chapters 1-4 Introduction to the Charlie Environment [PDF]
Practical Exercises 2 [PDF]
06 10-03-2020 14:15 - 16:00 408 Bio-model Abstraction (Henning Basold) Sign up for Groups (seminar/case study) in Blackboard before the March 10 lecture!
07 17-03-2020 14:15 - 15:00 Canceled Case study 1: dr. Alireza Mashaghi Tabari (LACDR)
08 17-03-2020 15:30 - 16:15 Canceled Case study 2: prof.dr. Ewa Snaar-Jagalska (IBL)
09 24-03-2020 14:15 - 15:00 Canceled Case study 3: dr. Diederik Kuster (AUMC)
10 24-03-2020 15:15 - 16:00 Canceled Case study 4: TBA