News
EXAM UPCOMING: Here you can find details on the oral exam, including the list for a suggestion for exam questions.
21.10.2019: New slides and articles are online, preliminary second (and last) mandatory assignment is online.
07.10.2019: Slide set for Horton's algorithm was improved.
02.10.2019: New Weekly Notes, new slides, new notes online.
26.09.2019: The files for assignment 1 can now also be found in blackboard and on the IMADA webserver. An updated virtual machine was also uploaded (there is no need to use this version, unless you use the default objective function for the ILP solver im mød).
25.09.2019: There was a small update (line 56 and line 84, and some additional comments) in the file doStuff.py provided for the first mandatory assignment. Essentially a default objective function needs to be set via, e.g., objectiveFunction = edge + inFlow. Please update the file yourself if you work with the virtual machine.
23.09.2019: New Weekly Notes online.
16.09.2019: New Weekly Notes, new slides, new notes, and additional material for the first mandatort assignment is online.
09.09.2019: I updated the WEBDAV link in the Weekly Notes of week 36 to https://elearn.sdu.dk/bbcswebdav/courses/N340003101-f-E19/Material. If it still does not work, please use the link that I announced in class.
09.09.2019: New Weekly Notes, new slides, new notes, new articles online.
02.09.2019: Site Launch.
Schedule
The lectures will always start 15 minutes after the full hour.
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, Fun Exercise |
| 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, (Sub-)graph isomorphism, Canonicalization, Additional information for the first Mandatory Assignment ("revive" from the strategy framework) | Week 38 |
| Week 39 | More on graph canonicalisation, SMILES, additional information for the first Mandatory Assignment ("revive" from the strategy framework) | Week 39 |
| Week 40 | starting with Ring Perception, MCB, Horton's algorithm, de Pina's algorithm | Week 40 |
| Week 41 | more on Ring Perception | Week 41 |
| Week 43 | Petri Nets | Week 43 |
| Week 44 | Petri Nets, Introduction to Mandatory Assignment 2 | Week 44Exercises |
| Week 45 | K Shortest Hyperpaths (Synthesis Planning), Analytic Combinatorics | Week 45 |
| Week 46 | Analytic Combinatorics, Exponential Generating Functions, Multivariate Generative Functions | Week 46 |
| Week 47 | Analytic Combinatorics, Boltzmann Sampling, Application to Chemistry (stereoisomers), starting PCA | Week 47 |
| Week 48 | Molecular Descriptors, Principal Component Analysis PCA, Quantitative structure-activity relationship QSAR | |
| Week 49 | (Stochastic) Process Algebras | |
| Week 50 | Polya Counting, Repetition | Week 50 Exercise |
Office Hours
Just write a short mail, and come by.
- Office: IMADA, Ø14-602b-2 map.
- Phone: 2322
- E-mail: daniel
Literature
The course will not be based on a mix of original articles, book chapters, and additional material.- [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.