News
21.01.2015: Exam Information online (including final question list).
04.01.2015: Exam Information online.
20.10.2014: The second mandatory assignment including both options is online.
29.09.2014: New articles and Weekly Notes online.
16.09.2012: The first mandatory assignment is online.
08.09.2014: Weekly notes for 36 and week 37 and reading material is online.
29.08.2014: Site Launch.
Schedule
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 | More on graph isomorphism, McKay's Canonical Graph Labeling Algorithm, Introduction to the first Mandatory Assignment, | Week 38 |
Week 40 | Even more on graph isomorphism (traces), Ring Perception | Week 40 |
Week 41 | Even more on Ring Perception, MCB, Horton's algorithm, de Pina's algorithm, Introduction to the 2nd mandatory project | Week 40 |
Week 43 | Petri Nets (in Chemistry and Systems Biology) | t.b.a. |
Week 44 | More on Petri Nets, NPc proof for a reachability problem, more on Graph Isomorphism | |
Week 46 | Quantitative structure-activity relationship QSAR, Molecular Descriptors, Principal Component Analysis PCA | |
Week 47 | more on Quantitative structure-activity relationship QSAR, Molecular Descriptors, Principal Component Analysis PCA, why not to use SMILES | |
Week 48 | Mathematical Concepts in Systems Biology, Stoichiometric Models, Flux Balance Analysis, Extreme Pathways | |
Week 49 | Analytic Combinatorics, Generative Functions | |
Week 50 | Polya Counting, Counting in Chemistry, Exercises | Exercises |
Week 51 | Process Algebras | Exercises |
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.