[Biopython-dev] BOSC biopython outline

Thomas Sicheritz-Ponten thomas at cbs.dtu.dk
Tue May 8 04:01:22 EDT 2001

Hej Andrew,

>   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
> given,
> 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
>    http://www.biopython.org/wiki/html/BioPython/BoscOhOne.html

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
> antagonistic.

* 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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