[Biopython-dev] BOSC biopython outline
thomas at cbs.dtu.dk
Tue May 8 04:01:22 EDT 2001
> As most of you know, I'm presenting the Biopython talk at BOSC 2001,
> which is in Copenhagen. Unlike almost every other presentation I've
> I'm starting to work on this one with time to spare. And unlike every
> other one, I'm going to try a collaborative development through Wiki.
> Take a look at
Ok - brainstorming !
> Written in Python, which some people prefer (warning, down this path lies
> language wars). Lots of libraries. Batteries included. Portable. I
> (AndrewDalke) personally believe Python code scales better for large
> projects than most other languages, but that can be perceived as overly
* We probably have to be carefull about not raising a flame war. If you are the
first speaker or if the previous (probably perl) speakers haven't mentioned
anything - it might be wise to start with some diplomatic words about "use
the language you are comfortable with" etc.
* There are a lot of perl people there but probably few from the others (tcl,
java ...). How do you want to compare python ?
- this and that etc. is better than perl ?
I can back you up at "Python code scales better for large projects than
most other languages":
I used biotcl (hardly usable at all) and developed biowish (bio+ tcl +
graphics) and used it of course for a lot of research .... until my
little brother asked me to look into python. After 2 days I started to
rewrite the tcl code for my last (and biggest) PhD project, which was a
#$%#$% to write in tcl, mainly because it was to big and tcl's OO solutions
sucked. After one week, I hade rewritten all code and expanded the amount of
features/codeby a factor of 10 (and was 3 month ahead of my schedule :-)
And its still easy to navigate through the code and add new features ....
!!! I have seen the light !!!
* Our Vision:
one of my visions - because of python's (almost standard) graphical modules (Tk,
wx, GTK++ etc.) its very easy to integrate graphics which makes biopython
VERY easy and fast to build tools for graphical comparisons (e.g. genomes)
* to mention:
* one of the strongest features of biopython (IMHO) are the parsers and how
easy it is to make new parsers ...
I don't know what perl has to offer - but perl people I meet were
definitely interested in biopython's Swiss and Blast parser's.
* we have two graphical sequence editor's in the standard distribution
* SeqGui, a wx application by Cayte ???
* xbbtools, a Tkinter application by me (Thomas Sicheritz-Ponten)
Mybe more after lunch
Sicheritz-Ponten Thomas, Ph.D CBS, Department of Biotechnology
thomas at biopython.org The Technical University of Denmark
CBS: +45 45 252489 Building 208, DK-2800 Lyngby
Fax +45 45 931585 http://www.cbs.dtu.dk/thomas
De Chelonian Mobile ... The Turtle Moves ...
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