[Biojava-l] BioInformatics toolbox.

[Brian Gilman]

Hello,

	There are a few examples of projects that are trying to fill the
void. One that springs to mind is Apollo and my own, OmniGene. However,
without the BioXXX projects, software that is driven through a GUI or
web interface could/would not exist. These software tools are also not
trying to be a biologist swiss army knife. Rather, they are trying to fill
a specific need. Is there a "killer app" for the biology/bioinformatics
domain?? That's a hard question to answer and one that I do not want to
debate on these lists. 

	One thing that you need to do is explicitely define the use
case(s) that you with to solve, as the domain and the people doing the
actual research are not generalists and find it very difficult to define
things in general terms. If you asked a small of biologist for a list of
requirements you would get a whole lot of different answers. It depends on
the part of biology you want to target. If you are looking for money, go
help out the drug discovery/validation/toxicology people...They need an
integrated/interoperable "solution" badly.

	

				Best, 

					-B




-----------------------
Brian Gilman <gilmanb@genome.wi.mit.edu>
Group Leader Medical & Population Genetics Dept.
MIT/Whitehead Inst. Center for Genome Research
One Kendall Square, Bldg. 300 / Cambridge, MA 02139-1561 USA
phone +1 617  252 1069 / fax +1 617 252 1902


On Sun, 7 Apr 2002, autopost wrote:

> All,
> 
> Thanks for responding to my question about open source projects working 
> towards creating tools/applications.
> 
> I'm all for keeping an open philosophy.  BioJava, BioPerl, The Apache 
> projects, SourceForge.net, all great places that help accelerate the 
> development process so we can get the results we need.
> 
> 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.
> 
> 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.
> 
> 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.
> 
> 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.
> 
> HOWEVER, I believe whatever gui tools/workbench is created, BioPerl and 
> BioJava are excellent SDK's/libraries to use as the building blocks.
> 
> 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.....
> 
> m.
> 
> 
> 
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