This month's technical meeting will be this coming Tuesday, March 13, at
the offices of Boston.com, starting at 7pm. (Although if it really starts
at 7:30, to allow for people arriving late, that's okay too. ;)
Boston.com is located at 320 Congress St, near South Station. Andrew
will post directions.
James Freeman will be presenting PISE, rescheduled from the previous
meeting. PISE is a system for creating web interfaces to command line
tools via XML. See below for more information on this presentation.
Other topics of discussion may include the DeCSS code that we've been
discussing on the list. Does anyone know how it works?
Pizza and beverages will be provided. If you are planning to attend,
please RSVP to me.
Ronald
---
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.
