News
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.
Schedule
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.
| Date | Topic | Weekly 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, 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.