title: Simple proteomics data analysis in the object-oriented PowerShell.
abstract: Scripting languages such as Perl and Python are appreciated for solving simple, everyday tasks in bioinformatics. A more recent, object-oriented command shell and scripting language, Windows PowerShell, has many attractive features: an object-oriented interactive command line, fluent navigation and manipulation of XML files, ability to consume Web services from the command line, consistent syntax and grammar, rich regular expressions, and advanced output formatting. The key difference between classical command shells and scripting languages, such as bash, and object-oriented ones, such as PowerShell, is that in the latter the result of a command is a structured object with inherited properties and methods rather than a simple stream of characters. Conveniently, PowerShell is included in all new releases of Microsoft Windows and therefore already installed on most computers in classrooms and teaching labs. In this chapter we demonstrate how PowerShell in particular allows easy interaction with mass spectrometry data in XML formats, connection to Web services for tools such as BLAST, and presentation of results as formatted text or graphics. These features make PowerShell much more than "yet another scripting language."
authors.affiliation: Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands.
authors.forename: Yassene
authors.initials: Y
authors.lastname: Mohammed
authors.forename: Magnus
authors.initials: M
authors.lastname: Palmblad
mesh_terms: D019295:Computational Biology / Q000379:methods*; D020407:Internet; D013058:Mass Spectrometry; D011381:Programming Languages; D040901:Proteomics; D012984:Software