[Bioperl-pipeline] Re: biopipe questions

[J.W. Bizzaro]

[e-mail] And then access management would be done by a set of 
hosts.allow and hosts.deny files.  Easy.

BTW, I was looking into BioMOBY a bit more (and I'm on the mailing 
list).  I think the original plan for Piper was something like 
BioPipe+BioMOBY.  It would be nice to see the two work together, maybe 
have BioPipe and BioMOBY XML combined into a single XML file that would 
be submitted to the "system" (I don't know yet how BioPipe and BioMOBY 
will work together).  On the front-end, I think I can handle doing that, 
as long as it is one file that is submitted (minimal interaction between 
front and back).

Right now, I'm thinking that I'd have an imagemap drawn out with active 
areas for components and connections.  When the user clicks on a 
component, a BioMOBY interface is brought up (pop up browser window) so 
that program parameters/options can be set.  When the user clicks on the 
connections, a pop up browser window shows the BioPipe connection 
options.  And then when finished, the XML gets sent to the "system".

Returning to the topic of "the user has too many options".  Recall that 
I told you of the idea of having "hidden components"?  It simply works 
like this: any parameter/option that has been *preset* (already set) 
will not show up in the graphical view of the pipeline.  This would 
apply to nested piplines too (where a pipline can be described and 
"packaged" into a single component (node or whatever--do you have a 
glossary of the terms you use?).  The short of it, and the good news, is 
that I think these are purely front-end problems (even the nested 
pipeline problem) that won't have to be addressed by changes in your XML 
or be given any other consideration.

Cheers.
Jeff

Elia Stupka wrote:
>>I wonder if it may be simplest to handle pipeline XML submission (from 
>>the front-end to BioPipe) via e-mail.  The front-end (or any user) would 
>>simply mail in the XML.  And on BioPipe's end, users can be identified 
>>by their e-mail address, which is where the results are sent.  Most 
>>CGI-based bioinformatic programs that I know of handle jobs this way.
>>
>>It's not fancy but it would work.
> 
> 
> Good idea actually, will test it out for sure!
> 
> Elia
> 
-- 
J.W. Bizzaro                                jeff at bioinformatics.org
President, Bioinformatics.Org       http://bioinformatics.org/~jeff
"As we enjoy great advantages from the inventions of others, we
should be glad of an opportunity to serve others by any invention
of ours; and this we should do freely and generously."
                    -- Benjamin Franklin
--