DM832 - Cheminformatics


DM832, Fall 2012

Daniel Merkle


31.10.2012: Two slides were missing in the slide set for Petri Nets, here they are.

23.10.2012: Here you can find details on the oral exam, including the list for a suggestion for exam questions.

10.10.2012: Book chapters and Weekly Notes updated. The document will be updated soon in order to give more details on

02.10.2012: Slides, articles, book chapters, and Weekly Notes updated.

25.09.2012: The final version of the second mandatory assignment is online.

13.09.2012: On Tuesday in week 38 Martin Hanczyc from FKF (see here or here) will introduce us to HCN chemistry.

13.09.2012: Next week (38) lectures will be on Monday and Tuesday, and not Thursday.

13.09.2012: Articles, notes, slides, and Weekly Notes were updated.

06.09.2012: Slighly updated first mandatory assignment: do not use any other constraints methods than using "constrainAdj" for the graph grammar rules.

05.09.2012: The first mandatory assignment is online.

27.08.2012: Weekly notes for 35 and reading material is online.

24.08.2012: Site Launch.


All lectures are in the IMADA seminar room.

Lecture 35 36 37 38 39 40 41
Mon 16-18 Lecture Lecture
Tue 16-18 Lecture Lecture Lecture Lecture Lecture Lecture Lecture
Thu 16-18 Lecture Lecture Lecture Lecture Lecture

Weekly Notes

The slides material presented in the lectures can be found in the Blackboard System.

DateTopicWeekly Notes
Week 35 Introduction, Representation of chemical compounds, SMILES, canoncial SMILES, stereochemistry Week 35
Week 36 Double Pushout Approach, Introduction to the first mandatory project, Graph Grammars, Exploring Chemical Spaces via Graph Grammars, Subgraph Isomorphism (Ullmann algorithm) Week 36
Week 37 More on graph isomorphism, McKay's Canonical Graph Labeling Algorithm, Ring Perception, Hanser Algorithm Week 37
Week 38 More on ring perception, Introduction to the Second Mandatory Assignment, presentation by Martin Hanczyc on HCN chemistry Week 38
Week 39 Finishing ring perception, Petri Nets (in Chemistry and Systems Biology) Week 39
Week 40 Finishing Petri Nets, NPc proof for Petri Nets, Quantitative structure-activity relationship QSAR, Molecular Descriptors, Principal Component Analysis PCA Week 40
Week 41 Mathematical Concepts in Systems Biology, Stoichiometric Models, Flux Balance Analysis, Extreme Pathways Week 41

Office Hours

Just write a short mail, and come by.

  • Office: IMADA, 14-602b-2 map.
  • Phone: 2322
  • E-mail: daniel


In addition to the books we will use original articles as a source of information.

Course Description

The official course description can be found here.

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