[Biojava-l] Re: [Bioperl-l] BioInformatics toolbox.

[Robson Francisco de Souza]

	Hi,

On Sun, 7 Apr 2002, autopost wrote:
... snip ...
> It occurs to me that there may be more users than there are 
> programmers.  So, I'm looking to find out if there is a suite of tools that 
> are "ready out of the box" and don't require writing scripts,...  I don't 
> think such a thing exists (correct me if I'm wrong).  So, I'm looking to 
> find people interested in creating such a project.  Or, learn more about 
> what some of the commonalities are among the tasks people are trying to do.

	You will easily find many graphical applications that are commonly
used tools in bioinfomatics (though many in may list may not be
open source): alignment programs like clustax or seaview, GDE (dead?) for
phylogenetic analysis, etc. Web browsers may be accounted as a GUI
commonly used in bioformatics, because so many online servers have easy to
use interfaces to several programs (PFAM is a good example).
	These many programs may give you a feeling of what is needed on an
integrated GUI-based workbench (try Pedro's BioMolecular
Research Tools - http://www.public.iastate.edu/~pedro/research_tools.html
- and the Chemistry, Biology & Related section in SAL (Scientific
Applications on Linux) - http://sal.kachinatech.com/Z/2/. I really think
its not easy to design a good generic GUI to handle so many different
needs/approaches (but see may comment on Piper below).

> When I think of tools, I don't mean scripts - rather something that is GUI 
> based that can be run and is intuitive.  Scripts usually aren't 
> intuitive.  When I hear scripts, I think of many scripts that have to be 
> run one after that other.  Even this is something that would be good in a 
> gui - something to manage the repetitive tasks.

	You should take a look at Piper
(http://www.bioinformatics.org/piper/). It's a framework to allow
GUI-based programming around pre-defined interfaces, much the same way we
do with pipes and command line shell scripts. It's been written in Python
and, the more I think of it, the more I feel it should be tightly
integrated with biopython and other bio-projects as well. It could allow
developing what you are suggesting, as long as the necessary interfaces to
commonly used programs are distributed as complete workflows.
	Unfortunately, this project seems to have lost some of its
momentum (the mailing lists archive was not updated since 2002/Jan). Hope
I'm wrong :).

> As I said, I'm all for the open philosophy.  I just think that having a 
> workbench/toolbox that works out of the box is what's missing.  A 
> Scientist's, BioInformatician's, or Research Assistant's time would be 
> better spent doing research rather than doing (or learning) programming, or 
> learning an API/SDK.

	Hmmmmm... Yes... No? Maybe a good researcher in this field will
always need to know some programming? Specially, unavoidable and useful
tools like bio* libraries!! :)

> If an open-source toolbox (gui based, not script) existed, perhaps those 
> doing research could focus more of their efforts on research, rather than 
> writing scripts around BioPerl, BioJava.

	By the way, implementing (really!) good alignment editors
(e.g. BioEdit - unluckily Windows only!) and integrating the with search
and retrieval routines to access Web databases and phylogenetic analysis
programs would certainly be very, very nice!

> Thoughts?   If anyone wants to contact me directly, I welcome that.  I'm 
> more than interested to hear what people are trying to do with these 
> libraries, what they want to automate, how they want things automated.....

	Again, take a look at Piper, maybe its what you are looking for.
	Hope it helps.
				Robson