Jong's Email to Bioperl mailing list on Steve Chervitz's email

From Bioperl

From - Thu Aug 19 11:17:02 1999
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Date: Mon, 26 Jul 1999 14:32:15 +0100
From: "J.H.P" <jong@ebi.ac.uk>
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CC: Ewan Birney <birney@sanger.ac.uk>, bioperl-99@bio.perl.org
Subject: The past/ and future of bioperl?: Re: First draft of the booklet:
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Hi,

On the bioperl project's past/present/future written in the introduction by Steve Chervitz, I think the past and
future part are not accurate in two ways.
The first thing is that the vision of one person Steve Brenner is not historically true.
Secondly, the defining someone's 'vision' etc is not to the original concept of Bioperl.

We should not concentrate on who started on what etc to make Bioperl to be truly open, practically useful and philosophically and scientifically sound.

Bioperl's authors not only the people who are in the past, present but also the future. There is no one who created 'vision' :-) or anything like
that. Everybody who agrees and like the idea of Perl and more open attitude in exchanging idea
has the real 'vision'.

It is not a vision of Steve Brenner or anybody. So, I suggest a modification of the part by Steve Chervitz to accommodate an open attitude which
was prevalent from the start of it.

The first concept of bioperl is written in late 1994 and early 1995 served from a machine
installed in Gonville and Caius college of Cambridge university called 'sonja'.

I do not know how exactly Steve Chervitz attribute it to Steve Brenner, even though I can guess.
but I will describe the past of it as I know what happened.

In the Centre for Protein Engineering MRC, Tim Hubbard was making a perl library called th_lib.pl.

It was the acumulation of years of perl quick hacks. You could call it by using 'require th_lib.pl' in
your perl code. It was very useful to use especially if you were in CPE network working with Tim. In other words,
the subroutines were not insulated and there were small humber of absolute directories etc. However, essentially
it had many small utilities to let you do some bioinformatics tasks rapidly. Tim is an excellent
programmer. However, he did not have any systematic programming background as I as I could see.

Jong Park (me), as his first PhD student was forced to abandon his arragance as a 'C' programmer and learn
Perl (with reluctance even though I was not a good C programmer at all). Within a week, I saw the 'philosophy'
of Perl. It was more than just a clever language or an efficient utility or lang. I realized Perl has the most
suitable language for bioinformatics.

So, I started use perl and build up a library 'jong_lib.pl'.
However, soon it was clear that codes were not general and modular enough. So, I decided to use perl module
rather than lib to make it more portable. As I became more fluent the lib became more modularized. Then
Bio.pl was born which had a description as a headbox with well insulated subroutines (which you could easily
take and put in your own programs). This time, I was actively collecting any useful general algorithms from
Tim Hubbard, James Tisdall, Sean Eddy, Alex Bateman, Tom Christiasen,
Mike Stoke, Larry Wall, and many many people who taught me and gave me codes over comp.lang.perl (later
this became comp.lang.perl.misc etc).

By this time, Steve Brenner came to visit MRC CPE( where Protein Engineering Research Language was
being used actively) office to see Tim and his supervisor Cyrus Chothia (who was sitting right
next to me). I told him about a perl module for all the biological community which is totally
free and open (CopyLeft).

http://cyrah.ebi.ac.uk:1111/Proj/Bio/Bioperl/copyleft.html

He was sceptic on using Perl. So, we had exchanged very long emails on why perl is better or worse than
C, C++ etc in developing a module like that (which I had again later with Ewan at some point. I
call it 'techno arragance' :-) which I had when Tim threw Learning Perl on my desk with a kind of
blushed face.

However, Steve eventually agreed to the idea of a biological perl module. One afternoon, he came
to CPE room and sat down beside me and asked what name we should put for such a module. So, something
like protperl, etc etc were discussed and he suggested bioperl as it is shorter but longer than
Bio(.pl) which I was using. I was agreeing to most of his suggestions and we chose Bioperl.
Until this time Bio.pm was just a direct translation of Bio.pl by using pl2pm program of Larry Wall.

Sometime after, Steve established a mailing list for bioperl. Steve did most of the administrative
work in setting up and also we agreed to have a lunch (or whatever) meeting in ISMB 95. He advertised
it a little bit in ISMB95, however, just before the planned meeting he told me he cancelled it, so it
the first informal meeting on bioperl did not happen in 95. By this time I was trying to convert
my Bio.pm to a fully object oriented version however it was not that straightforward as I did not understand
perl OO completely. Until then, the mailing list was full ofabstract design level talk. Personally, I wanted to
see some real codes were made. Anyway, if I skip small details, George Fuellen suggested a design
with much more detail and enthusiasm when the list became quiet. This revitalized the communal
activity of bioperl. Then, Richard Resnick started to do some real work which I always
thank. By this time, I fully understood OO and could read the module etc. However, interestingly,
I found that most of my colleagues did not understand OO and did not bother to know what it is like etc.
It was always quicker for them to copy and paste some useful subroutine from my library (which some
of them still do).

(At this point, with some other personal reasons, I started to see bioperl in two or more ways of achieving
the goal which caused me never translate or code specifically for Bioperl OO module)

Throughout the period and (in the future) bioperl was a natural consequence of many people
who had the vision of sharing (a honest and true sharing rather than some empty echos with
selfish interest to enhance their fame, influence etc, as I have seen in some). Bioperl should remain
that way. If we have to say about 'vision', bioperl is the vision of the result of connected
network of minds including the future generation.

Cheers,

Jong


> > guys - first attempt at throwing this together. I'd like to have
> > it done in a couple of days. It is available at
> >
> > ftp://ftp.sanger.ac.uk/pub/birney/libs/booklet.ps
>
> Nice-- and a very nice intro. I'd clearly mark the date of the
> workshop-- the title page says ``June 25, 1999 ;-)
> I may be able to proofread the final booklet on short notice;
> you can probably reach me easily every day until
> Wednesday July 4, except Fri noon -> Mon morning.
>
> -re- Contact for questions on facilities,
> I'd suggest to list all three locals (Marc, Tim and myself.)
>
> > I am aware of a number of typos and problems to the tex formatting (though
> > feel free to point them out to me as well), but more importantly:
> >
> > a) I need to where *precisely* we are having the workshop (like, which
> > room, what building etc) and where in DKFZ that is
> >
> > b) What buses run from Bizmark Platz to DKFZ
>
> I'd like to leave these q's to Marc or Tim, but I can
> find out if you need this information very urgently.
>
> > c) Any other information we can add to the "location" section.
>
> I think http://bio.perl.org/bioperl-99/location.html
> is fine; I've improved a bit on that ``big black blob ;-)
>
> > In addition - Chris - can you send me a tab delimited dump of
> > your database so I can make up an attendee list?
> >
> > What else do we need?
>
> what do we do w/ ppl who just come there w/o having paid ?
> (if it's just a 2-3 cases, I could let them pay me in
> dollars or DM, and write US bank checks for chris.)
>
> > Finally - when are people going to around? - I'll be there from the
> > wednesday late afternoon. Which hotels are we all booked into?
>
> I'm staying at the IBIS -- I'll solicit input from
> Marc and Tim later this week -re- when I should arrive
> (wednesday late afternoon would be the latest for me I guess).
>
> Are we going to have a pre-meeting in the early evening ?
>
> > I am sure we are missing something crucial -
> >
> > Chris - do we need to write anything about finances?
> >
> > Tim/Mark/Georg - are we all ok for the food in particular. Should I make
> > out "food tickets" saying "lunch for one person" to be distributed?
> >
> > What do people think about little badges?
>
> that would be nice-- at least we should have empty badges
> where ppl can write their names on.
>
> > hey-ho. Looking forward to it/dreading something going wrong <grin>
>
> Looks like everything is getting along nicely:) nevertheless,
> I'd hope David States is listening, etc, since he seems to be most experienced
> w/ organizing ...
>
> > Ewan Birney
> > <birney@sanger.ac.uk>
> > http://www.sanger.ac.uk/Users/birney/
>
> best wishes,
> georg

-- Jong Park : a Biology student -- Tel work: +44 1223 49-4613

BioPerl Conference with ISMB 99 in Heidelberg ==>

http://bio.perl.org/bioperl-99/