Lectures content

The schedule of the classes in the Bio-Modeling and Petri Nets Spring 2019 course is shown below. Rooms are in the Snellius Building. Slides from the lectures are also provided. They are intended for this 2019 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.

# Sort ascending Lecture time Room Content Reading Slides and additional material
18 14-06-2019 14:00 - 16:30 403 Case study discussion moments (per-team) Schedule
17 14-05-2019 15:45 - 17:30 401 Presentation session (moved from 07-05) Schedule
16 30-04-2019 15.30 - 17.15 401 Per-team feedback session
15 23-04-2019 15.30 - 17.15 401 Plenary/Brainstorm + Team-lecturer grouping session (case study discussion on current status)
14 16-04-2019 15.30 - 17.15 --- No lecture
13 09-04-2019 15.30 - 17.15 401 Kick-off of case studies: Talk about what you have done so far
12 02-04-2019 15.30 - 17.15 401 Seminar session 2: Presentations on implemented Petri nets Check the Blackboard page for details! Blaetke. 4.4 Examples: 4.1, 4.2 (pp.34-41) [PDF]
Heiner et al. Figs. 2, 4, 5 + explanation for Example 4.1 [PDF]
Heiner et al. Figs. 3, 6, 10 + explanation for Example 4.2 [PDF]
Rodriguez et al. [PDF]
11 26-03-2019 15:30 - 17:15 401 Seminar session 1: Presentations on implemented Petri nets Bonzanni et al. [PDF]
Bonzanni et al. Erratum [PDF]
Koch, Junker and Heiner [PDF]
10 19-03-2019 16:30 - 17:15 401 Case study: prof. Charles McLean Press Case study preferences: mail us by 26-03-2019
Read Seminar 2 papers for 02-04-2019
Bacterial infection in Atlantic slamon [PDF]
09 19-03-2019 15:30 - 16:15 303 Computer practical 2 Practical Assigment exercises [PDF]
08 12-03-2019 16:30 - 17:15 401 Case study: dr. Astrid van der Sar (VUmc) Read the Seminar 1 papers for 26-03-2019 Mycobacterium tuberculosis host-pathogen interactions [PDF]
07 12-03-2019 15:30 - 16:15 401 Case study: dr. Christian Tudorache (IBL) Coping with the clock [PDF]
06 05-03-2019 16:30 - 17:15 401 Coloured Petri Nets Coloured Petri Nets, ch. 2, 4 (slides)
Computer practical exercises for 19-03-2019
Coloured Petri Nets [URL]
05 05-03-2018 15:30 - 16:15 401 Case study: dr. Paul van Heusden (IBL) Regulatory networks in yeast phosphate homeostasis [PDF]
04 26-02-2019 15:30 - 17:15 303 Computer practical 1 Try the Take Home Exercise Practical Assigment exercises [PDF]
Snoopy packages [URL]
03 19-02-2019 15.30 - 17.15 401 Petri Nets continuation Snoopy-related literature BMPN2019-Membranes [PDF]
BMPN2019-Gradient [PDF]
BMPN2019-Tools and Extensions [PDF]
02 12-02-2019 15:30 - 17:15 401 Introduction to Petri Nets Recommended: Modeling in Systems Biology: The Petri Net Approach [PDF] chapters 1, (2), 3 BMPN2019-PN [PDF]
01 05-02-2019 16:30 - 17:15 401 Introduction to Bio-Modelling & Systems Biology bmpn2019-lecture01 [PDF]
00 05-02-2019 15:30 - 16:15 401 Introduction to Course/Logistics 2019-BMPN-INTRO [PDF]