[Biojava-l] Re: [Bioperl-l] Re: Biojava-l digest, Vol 1 #611 - 2 msgs

[jong]

Hi,

The suggestion you made is because you did not know the
broad band philosophy of BioXXX.

Bioperl and some other sister projects have originally been based on
'open' philosophy. Object oriented Bioperl is a very
significant part of it, however, the general Bioperl encompasses it.
(Bioperl is a much broader concept than object oriented
Bioerl 1.0.)
So, James Tisdall's early 1990's perl libraraies and
workbenches were in fact bioperl (his codes were shared
and integrated in other bioperl libraries including early
version of Bio OO module). Also, intrinsically a lot of people's
utilities are part of bioperl. If you create a new way
of sharing bio resources, it will be a new aspect of BioXXX,
as long as you like the open and free (and not egoistic) idea of
BioXXX.

The toolset idea is exactly as old as Bioperl OO module and library.
For example, one of the first aim of Bioperl project was
to always create programs that correspond to each subroutine.
For example, if there is a Bio::Blast::Parse., we intended to
have an equivalent stand alone tool (such as parse_blast_output.pl)
generated automatically and subsequently adjusted for both testing
and actual use as a quick tool.

This was because when first bioperl developers made OO Bioperl,
their working colleagues did not necessarily understand
OO concept or the structure of OO Bioperl.

There are several sources for such utilies (Script central in
www.bioperl.org??).

One available (albeit not maintained properly due to lack of time) is at:
http://interaction.mrc-dunn.cam.ac.uk/Bioperl/Bioinf.html
or http://bio.cc/Bioperl/Bioinf.html

There used to be a SQL based tools/algorithm/subroutine server called
Persus,
but I did not have time to keep maintaining it. If anyone is interested
in that, let me know.

Cheers,

Jong

> Are there any open source projects that are working towards creating tools
> or a suite of applications for BioInformatics rather than creating a
> library/SDK?  We want to find a group that is interested (or is already)
> creating pre-built tools
>
> BioPerl and BioJava are great libraries.  I would think the next step is
> using them to create a toolset that allows "users" to get up and running
> without having to know how to program.
>
> Anyone intersted?  Or, is anyone already doing this?
>
> m.
>
>
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