Complexe data

Website:website containing additional information
Course code:INFOCD
Credits:7.5 ECTS (=5.25 old credit points)
Period:periode 4 (week 17 t/m 27, dwz 25-4-2005 t/m 8-7-2005; herkansing week 35)
Timeslot:A
Participants:up till now 10 subscriptions
Schedule:Dit is een oud rooster!
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college   ma 11-1317-19,21-26 BBL-430 Hans Philippi
  
wo 11-1317-19,21-26 BBL-430
Nota bene:Er is geen recente vakbeschrijving beschikbaar.
Onderstaande tekst is een oude vakbeschrijving uit collegejaar 2003/2004
Contents:Within the discipline of 'Database systems', the focus is changing. Traditionally, there has been much attention towards fundamental aspects like data models and query languages. Nowadays, we see more interest in different application domains of database systems. Typical domains are geographical information systems, multimedia en bioinformatics. In the Complex Data courses, we will choose one of these domains for further study. The subject for this years course is bioinformatics.

Genetic information is represented bij long sequences of symbols, representing bases (ACGT) or amino acids. So the main datastructure is the string. Typical operations on a genome database are searching for evolutionary related substrings, assembling related families of strings and the reconstruction of evolutionary structures based on genetic patterns. The fact that the matching is non-exact due to evolutionary changes, is the cause of many problems. We will often make use of probabilistic techniques when trying to solve these problems.

Because genetic database are not extremely large, but access methods are often calculation intensive, using a main memory database system might be a good approach. As part of this course, we will do practical exercises with Monet, an extensible main memory DBMS developed at the CWI.

Finally, we will give some attention to the integration problems of several genetic databases.

This course has a lot of topics in common with Computational Biology. We will focus more on datastructures, implementation and database aspects. You should follow the course on Database Architecture before attending this course.

Literature:kan veranderen!
The literature will consist of a reader containing selected articles.
Course form:My intention is to do the course as a seminar. The students will give presentations based on the material. Active participation in discussions is required. The practical exercises will be a major part of this course.
Exam form:The final grade will be calculated is a weighted mean of the grades for the presentation, the participation and the practical exercises.
Minimum effort to qualify for 2nd chance exam:Om aan de aanvullende toets te mogen meedoen is ontbreken van ten hoogte 1 toetsactiviteit toegestaan.
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