News
25.01.2019: The list of the questions (in addition to the more detailed questions) can be found here : Exam Information
05.11.2018: New Weekly Notes, slides and new articles are online.
24.10.2018: The second mandatory assignment is announced.
22.10.2018: New Weekly Notes are online. Deadline for the first project was finalised to October 31.
11.10.2018: New Weekly Notes, slides and new articles are online.
01.10.2018: New Weekly Notes, slides and new articles are online.
24.09.2018: New Weekly Notes, new slides are online.
17.09.2018: New Weekly Notes, new slides, new notes, and additional material for the first mandatort assignment is online.
10.09.2018: New Weekly Notes, new slides, new notes, new articles online.
29.08.2018: Site Launch.
Schedule
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.
| Date | Topic | Weekly Notes |
|---|---|---|
| Week 36 | Introduction, Course overview, Polya enumeration (teaser), Double Pushout Approach | Week 36 |
| Week 37 | Double Pushout Approach, Graph Grammars, Exploring Chemical Spaces via Graph Grammars, Subgraph Isomorphism (Ullmann algorithm), Introduction to the first mandatory project | Week 37 |
| Week 38 | ILP formulation for autocatalysis, Graph isomorphism, McKay's Canonical Graph Labeling Algorithm, Additional information for the first Mandatory Assignment ("revive" from the strategy framework) | Week 38 |
| Week 39 | Even more on graph canonicalisation (traces), SMILES, starting Ring Perception | Week 39 |
| Week 40 | Ring Perception, MCB, Horton's algorithm, de Pina's algorithm | Week 40 |
| Week 41 | FinishingRing Perception, Starting Petri Nets | Week 41 |
| Week 43 | Petri Nets | Week 43 |
| Week 44 | Petri Nets, Introduction to Mandatory Assignment 2 | Exercises |
| Week 45 | K Shortest Hyperpaths (Synthesis Planning), Introduction to Mandatory Assignment 2 | Week 45 |
| Week 46 | Analytic Combinatorics, Ordinary Generative Functions, Application to Chemistry (Stereochemistry) | |
| Week 47 | Analytic Combinatorics, Exponential Generating Functions, Multivariate Generative Functions | |
| Week 48 | Molecular Descriptors, Principal Component Analysis PCA, Quantitative structure-activity relationship QSAR | |
| Week 49 | (Stochastic) Process Algebras | |
| Week 50 | Polya Counting, Repetition | |
| Week 51 | Repetition |
Office Hours
Just write a short mail, and come by.
- Office: IMADA, Ø14-602b-2 map.
- Phone: 2322
- E-mail: daniel
Literature
- [1] Chemoinformatics, Gasteiger, Johann / Engel, Thomas (eds.), 2003
- [2] Systems Biology - Properties of Reconstructed Networks, Bernhard O. Palsson, 2006
- [3] Handbook of Chemoinformatics Algorithms, Jean-Loup Faulon, Andreas Bender, 2009
- [4] An Introduction to Chemoinformatics, Leach, Andrew R., Gillet, V.J., 2003
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.