DM840 - Algorithms in Cheminformatics

Algorithms in Cheminformatics

DM840, Spring 2016

Daniel Merkle


26.05.2016: Here you can find details on the oral exam, including the list for a suggestion for exam questions.

25.04.2016: The lecture on Tuesday Apr. 26th is in U107 at 10.15.

29.03.2016: News slides online, new articles online, exercises for "Petri Nets" are online, the second mandatory assignment will be presented on Friday this week.

09.03.2016: News slides online, new articles online, source code for graph canonicalisation online.

03.03.2016: The Friday lecture of this week (04.03.) is moved to U10.

11.02.2016: The first mandatory assignment is online.

09.02.2016: Weekly notes for week 06 and reading material is online.

02.02.2016: First lecture: Friday 05.02.2016, 8:15am

01.02.2016: Site Launch.


The lectures will always start 15 minutes after the full hour.

All lectures, unless stated explicitly, are in the IMADA seminar room.

Weekly Notes

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

DateTopicWeekly Notes
Week 05 Introduction, Course overview, Polya enumeration (teaser), Double Pushout Approach Week 05
Week 06 Double Pushout Approach, Graph Grammars, Exploring Chemical Spaces via Graph Grammars, Subgraph Isomorphism (Ullmann algorithm), Introduction to the first mandatory project Week 06
Week 09 More on graph isomorphism, McKay's Canonical Graph Labeling Algorithm, Introduction to the first Mandatory Assignment, Week 09
Week 10 Even more on graph isomorphism (traces), SMILES, starting Ring Perception Week 10
Week 11 Even more on Ring Perception, MCB, Horton's algorithm, de Pina's algorithm Week 11
Week 13 Petri Nets Week 13, Exercises
Week 14 Petri Nets, Analytic Combinatorics
Week 15 Analytic Combinatorics, Generative Functions, Polya Counting
Week 16 Quantitative structure-activity relationship QSAR, Molecular Descriptors, Principal Component Analysis PCA
Week 17 more on Quantitative structure-activity relationship QSAR, Molecular Descriptors, Principal Component Analysis PCA, why not to use SMILES
Week 18 Chemical Organizations
Week 19 (Stochastic) Process Algebras
Week 20 Mathematical Concepts in Systems Biology, Stoichiometric Models, Flux Balance Analysis, Extreme Pathways, Repetition of topics
Week 20 Repetition of topics

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

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