[Biopython-dev] Software demonstration at GIW 2003 in Japan

Iddo Friedberg idoerg at burnham.org
Thu Oct 16 12:23:56 EDT 2003

Michiel Jan Laurens de Hoon wrote:
> Dear Biopython developers,
> I am volunteering to give a software demonstration of Biopython at the 
> International Conference on Genome Informatics (GIW) in Tokyo/Yokohama 
> this December. GIW is the largest annual conference on bioinformatics in 
> Asia: see http://giw.ims.u-tokyo.ac.jp/giw2003 for more information.
> The software demonstrations are set up like a poster session (instead of 
> an oral presentation such as at BOSC), allowing easy communication with 
> potential users. Such a software demonstration comes with a two-page 
> paper describing the software. This paper is not medline-indexed and 
> there is no rigorous refereeing involved for such short papers. However, 
> it appears together with the full-length papers in the proceedings, so 
> there will be a permanent record. The proceedings will be publicly 
> available on the web after the conference. 
> (http://www.jsbi.org/journal/GIW02/GIW02SS05.pdf is the paper for the 
> software demonstration by our Bioruby colleagues last year at GIW).

Fantastic! I'm reminded of the "Made in" albums by Deep Purple:
"Biopython: Made in Japan".

> The deadline for submissions has already passed, however since my lab is 
> organizing this conference we have some leeway. I'll be happy to write 
> the paper, but I will need some help:

Nothing like having friends in high places... or being in one yourself.

> 1) Are there any other papers on Biopython from which I can plagiarize 
> the parts of Biopython that I am not very familiar with?

Jeff & Brad wrote something, but back in 2000. A lot has changed since.


> 2) Would somebody be willing to have a look at the paper before I submit 
> it, in case I write something wrong?

I can.

> 3) Who should I include as co-authors? Anybody is welcome, as far as I 
> am concerned.

Ummm.. definitely the triumvirate: Jeff, Brad & Andrew.

Here's what I would do: take the top N posters to biopython-dev, N being
the number of people you want on the paper.

> 4) Does anybody have any cool scripts that make use of Biopython that I 
> can show off at the conference?

I have two websites:



Which use the FASTA parsing, GenBank parsing, PDB parsing, GO module,
and some other stuff. Nothing really cool in the source codes though. If
you want to show code, I would suggest using something basic, like the
manual. However, those are biopython powered sites, which is always good
for PR.

> Thanks in advance,
> --Michiel, U Tokyo.

Iddo Friedberg, Ph.D.
The Burnham Institute
10901 N. Torrey Pines Rd.
La Jolla, CA 92037
Tel: +1 (858) 646 3100 x3516
Fax: +1 (858) 646 3171

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