PISE is a framework that, given an abstract definition of a program's parameters, can generate differents interfaces to run it (provided there is a configuration module for it). Available interfaces are WWW (the most popular and best maintained), conversational, SeqLab, Tcl/Tk and X11 interfaces. What is considered a parameter is very general and includes command line parameters, web forms, simple interaction on STDIN, and parameter files.
About 300 molecular biology programs have been defined and run under Pise, including various sequence analysis, phylogeny, alignment, structural analysis (RNA, secondary and tertiary structure) and gene prediction programs. Pise has been in production for more than 4 years at the Pasteur Institute, with about 1000 submitted jobs a day during the last year (http://bioweb.pasteur.fr/). The whole system, e.g generators and the complete set of already defined interfaces is also installed in several other sites, namely for interfacing EMBOSS programs. Other users have developed new programs' interfaces (in genetic analysis, primer design, and imaging analysis). We are also aware of projects for building a new GUI generator.
More information at http://www.pasteur.fr/recherche/unites/sis/Pise/