392128 Programming in Perl (V) (WiSe 2002/2003)

This lecture is composed of two parts:

• For the first 8 weeks, some advanced topics in Perl scripting and programming will be discussed. These are data structures, regular expressions,

object-orientation, good programming style, debugging, et al. We will use examples from biology in particular.

• For the last 8 weeks, we will explore the Bioperl set of advanced modules, e.g. Hidden Markov Model support, Phylogeny and comparative genomics

support, Genscan support, et al.

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.

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

Requirements for participation, required level

The lecture will be given in English. Although this is a continuation of a course done in the summer, 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/).

Bibliography

E.g. Tisdall book, http://www.oreilly.com/catalog/begperlbio

External comments page

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