| Website: | website containing additional information |
| Course code: | INFOMACB |
| Credits: | 7.5 ECTS |
| Period: | periode 4 (week 17 t/m 27, dwz 23-4-2012 t/m 6-7-2012; herkansing week 34)
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| Timeslot: | C |
| Participants: | up till now 15 subscriptions |
| Schedule: | Note: from now on the schedule is to be found in Osiris |
| Teachers: | Dit is een oud rooster!
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| Contents: | The Life Sciences are an exciting field for computer scientists. The field is heavily reliant on algorithmic models and computational techniques, and is in great need of efficient and highly scalable algorithms e.g. for the analysis and understanding of biological systems. Many problems involve massive data sets and discrete algorithmic questions of great complexity: sequence comparison, alignment of multiple sequences, genome rearrangements, and so on, questions that are being studied by computer scientists everywhere. The long-term goal is to develop realistic simulation models of cells, organisms and the principles of their development. The insights would make it possible to test new hypotheses, new developmental models, and even new drugs by computer simulation. Before that goal is achieved, many fundamental computer science problems must be solved. In this course we will study the typical algorithmic challenges and complexities that must be overcome.
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| Literature: | The seminar will be based on the following book:
H-J. Böckenhauer, D. Bongartz, Algorithmic Aspects of Bioinformatics, Springer-Verlag, Berlin, 2007.
See e.g. here for some details about the book. The book is required and should be at your disposal from the beginning, to study the weekly readings of the seminar.
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| Course form: | Seminar. After a few introductory lectures by the lecturer, students are expected to give presentations on (specific parts of) the book chapters and related material. Students are challenged to explore their topics in an active way. In the second part of the seminar every participant must also write a term paper (in English) on a special topic from the seminar. (Note: If there is considerable interest for the seminar, students may be grouped in two for the presentations part of the seminar requirement. Due to the seminar format, the total number of participants is strictly limited to 20.) |
| Exam form: | The grade depends on the given presentations (50%), the term paper (40%) and active participation (10%). |
| Minimum effort to qualify for 2nd chance exam: | Om aan de aanvullende toets te mogen meedoen moet de oorspronkelijke uitslag minstens 4 zijn. |
| Description: | After an introduction the seminar will follow the chapters of the book:
- Introduction
- Basics of Molecular Biology.
- Basic Concepts: Strings, Graphs, and Algorithms.
- String Algorithms.
- Alignment Methods.
- Introduction and Overview.
- Physical Mapping.
- DNA Sequencing.
- Finding Signals in DNA Sequences.
- Genome Rearrangements.
- Phylogenetic Trees.
- Haplotyping.
- Molecular Structures.
- References.
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