392106 Algorithms in (Bio)Perl (V) (SoSe 2003)

The lecture will be given in English. It is composed of two parts:

For the first approx. 6 weeks, some advanced topics in Perl programming will be discussed, i.e. selected topics from "Mastering Algorithms in Perl" (http://www.oreilly.com/catalog/maperl/).
For the last approx. 6 weeks, we will explore algorithms implemented in Perl for the Bioperl toolkit.

Although this is a continuation of a course done in the winter, new participants are very welcome as long as they come with some basic
Perl knowledge (E.g. from the first 7-9 chapters of the Tisdall book, http://www.oreilly.com/catalog/begperlbio/).

About Bioperl: Bioperl Release 1.0 has finally come out on March 18, 2002. Bioperl is rapidly becoming the library of choice for many bioinformatics tasks.

Officially organized in 1995 and existing informally for several years prior, The Bioperl Project is an international association of developers of open source Perl tools for bioinformatics, genomics and life science research.

Bioperl is a collection of perl modules that facilitate the development of perl scripts for bioinformatics applications. As such, it does not include ready to use programs in the sense that many commercial packages and free web-based interfaces (eg Entrez, SRS) do. On the other hand, bioperl does provide reusable perl modules that facilitate writing perl scripts for sequence manipulation, accessing of databases using a range of data formats and execution and parsing of the results of various molecular biology programs including Blast, clustalw, TCoffee, genscan, ESTscan and HMMER. Consequently, bioperl enables developing scripts that can analyze large quantities of sequence data in ways that are typically difficult or impossible with web based systems.

About Perl: Perl is a universal scripting and programming language that is used for many applications. It is easy to learn; its elementary constructs are sufficient to write powerful scripts.

Requirements for participation, required level

Prerequisites:
Basic knowledge of Perl.

Bibliography

http://www.oreilly.com/catalog/maperl/
http://www.oreilly.com/catalog/begperlbio/

Kontakt:
Georg Fuellen, M3-118, phone 2904, oder 0251 83-52212. It's best to contact me via email, fuellen@uni-muenster.de

External comments page

http://www.TechFak.Uni-Bielefeld.DE/~fuellen/Lehre/