[Biopython-dev] Fwd: Abstract

Tiago Antão tiagoantao at gmail.com
Mon May 19 12:49:29 UTC 2008

By the way, the suggested abstract proposal:

Introduction to and news from the Biopython project presenting both
existing modules and current developments including a new Population
Genetics module and XML parsers for the NCBI's Entrez web interface.

An overview of the existing python software ecology will also be
presented in relationship with computational biology. Libraries to do,
among others, plotting, numerical analysis and molecular modeling will
be presented in connection with Biopython and from the point a view of
having a complete platform to do research in computational biology.

Biopython is freely available on http://www.biopython.org under a
liberal "MIT style" open source license,

On Mon, May 19, 2008 at 1:38 PM, Tiago Antão <tiagoantao at gmail.com> wrote:
> In order to address this I am thinking in changing the starting
> paragraph of the "paper" along the following lines:
> In this talk we present the current status of the Biopython project.
> We start by giving a short overview of Biopython - presenting existing
> functionality - and useful software libraries for computational
> biology in the Python development 'ecology' (from plotting libraries
> capable of producing publication quality figures to numerical
> libraries, among others). We then focus on features developed since
> BOSC 2007, future plans for the project and present example usages of
> the new population genetics module.
> I think changing the abstract along these lines might also be good.
> I think I will target most of the presentation to the idea that the
> Python ecology of software development is really good (e.g. putting
> one slide on matplot lib with code and result, to show how concise and
> simple code can produce nice results). "Selling" Biopython in the
> whole python context.
> On Mon, May 19, 2008 at 1:26 PM, Peter Cock <p.j.a.cock at googlemail.com> wrote:
>>>> The point is that most people in the audience are not Biopython users (yet),
>>>> so for them a general introduction is more suitable.
>>> Actually this issue is of a major concern to me... Do you (or anybody)
>>> has a feel of what audience will be there? I think it is important to
>>> tune the message to the audience. I actually was speculating that
>>> people would know about biopython. But if that is not the case, as you
>>> imply, then maybe a something that makes biopython more competitive
>>> for people which might be deciding which system (language and
>>> libraries) might be the best approach...
>> Perhaps I should have given you a broader introduction to BOSC itself.
>>  There will probably be talks from BioPerl, BioJava and BioRuby in the
>> same session, and I would expect almost all the audience to be
>> familiar with at least one of these projects.  However, they may or
>> may not use python, and I would expect that the majority will not be
>> Biopython users.  At least, that was my impression last year at BOSC
>> 2007.  Reading over the talk titles/abstracts from last year should
>> give you a feel for the sort of people there presenting work outside
>> the Bio* projects.  In terms of general impressions, I felt most of
>> the attendees actually did some hands on coding.
>> So yes, as Michiel says, perhaps the current text isn't general
>> enough.  This is a regular opportunity to try raise awareness of the
>> project, although I personally wouldn't give a "hard sell", we should
>> try to give a general overview of Biopython's capabilities.
>> Peter
> --
> http://www.tiago.org


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