Boston Perl Mongers is having a technical meeting this Tuesday, February
13, at the offices of Boston.com near South Station, starting at 7pm.
Andrew Langmead will be posting directions.
The topic for the meeting is practical applications of XML. James Freeman
will present the open source software package Pise (Pasteur Institute
Software Environment). An abstract of this talk is included below. Mike
MacHenry will present Any2XML, a set of modules that will allow extraction
of selected data from any text file into one or more XML documents using a
template which is also an XML document.
Pizza and beverages will be provided.
If you have not already RSVPed, please email me if you plan on attending.
Ronald
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Pise (Pasteur Institute Software Environment)
http://www-alt.pasteur.fr/~letondal/Pise/
Abstract of James Freeman's presentation:
There is a growing field called Bioinformatics, that can be defined as
understanding complex biological systems through the use of experiments
tied with computer-based data storage, tracking, and analysis. Software
written in this field is usually written to run on the Unix command
line. Traditional biologists find learning the command line for each
new tool confusing, difficult, and consuming time better spent in the
lab. As a result a local programmer in the lab is tasked to wrap the
command line into a cgi-bin script with the usual html input and html
output pages. PISE (Pasteur Institute Software Environment,
http://www-alt.pasteur.fr/~letondal/Pise/), written by Catherine
Letondal, has been created to automate this process by writing a system
to parse a single XML definition of the command line tool. Parsing this
XML definition the PISE system automatically generates an html form, a
Perl cgi-bin processing script; an html output form and, if necessary,
post processing as well. These features plus automatic defaulting,
specification of simple and complex interface options, and many other
features makes this an extremely valuable system. This system was
developed for Bioinformatics, and the default XML interfaces are for
these kinds of command line tools, but it has been simple to create new
XML interfaces. The PISE system is general enough to handle any program
that runs on the Unix command line. I will present this system at the
next tech meeting.
