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Re: Mashup browser compatibility - and use of Mashup for Mouse BIRN contribution to future demo

From: William Bug <William.Bug@DrexelMed.edu>
Date: Sun, 13 May 2007 01:31:08 -0400
Message-Id: <2BE4591C-676E-4AA8-A502-9DED6462DEAD@DrexelMed.edu>
Cc: public-semweb-lifesci hcls <public-semweb-lifesci@w3.org>
To: Alan Ruttenberg <alanruttenberg@gmail.com>
Works for me now (MacTel running OS X v10.4.9 & Firefox v2.0.0.3 with  
a ridiculous number of plugins installed).

This is great, Alan.

So if I understand the changes you've made, we are now looking at a  
side-by-side comparison of the pseudo-colored, gene-specific  
immunohisto. sections from two different brains - (the brains 'gene  
painted' for Kcnip3 & Kcnd1) - presenting the roughly equivalent  
sagittal sections (Kcnip3@2850 and Kcnd1@2800) from those two brains?

Work has begun on the Mouse BIRN Atlasing Tool project to link this  
into our framework.  The idea would be, when viewing atlas-registered  
images or spatially-mapped gene expressions results overlaid onto an  
MBAT atlas view, a user would be able to right click on a an image  
and would be presented with a very simple way to query against your  
neurocommons ABA RDF store.  If they click on a spatially mapped gene- 
expression pattern, they'd be presented with a very simple option:
	1) view Nissl & immuno-stain for the ABA brain stained for that gene  
- constrained to the set of sections from that ABA brain known to  
intersect with the selected brain region
	2) view this side-by-side comparison by providing a user the ability  
to select from a list of other genes (preferably two lists - one  
constrained to genes we can relate to the current expressed gene  
pattern they just clicked on via www.genenetwork.org or via a  
pathways ontology; the other way to select a gene would be through a  
text query box - just give any string and we'd return all gene names  
that match via a regex either to the full gene name or gene name  
abbrev. tag)

If they just click on an image with segmented brain regions (no gene  
expression), they'd provided with a way to again act on those two  
options above (Nissl + immuno for 1 ABA brain OR immuno comparison  
view for 2 brains) - selecting genes based on some combination of  
string matching and ontology constraints based on gene networks,  
pathways, genes related to a specific GO MF or GO CC.

The results from the SPARQL query would then dynamically populate  
your Google Map HTML+JS template which would be presented in a JFrame  
(MBAT is a Java app).  Our developers are also spec'ing out how to  
add an additional "slicing" widget to the Google Map widgets, so a  
user could process through one of these constrained image sets  
(constrained based on their 'cutting' through a given brain region)  
from a given ABA gene-painted brain.

I don't see any reason why most of this functionality wouldn't be  
ready to include in the SfN presentation (possibly even in alpha for  
ISMB in July, pending our access to MBAT programmer resources for  
whom this may not be the top priority).


On May 13, 2007, at 12:45 AM, Alan Ruttenberg wrote:

> Hi Don,
> When you or someone else gets a chance, give a try again. I think  
> it will work now, thanks to:
> Brian Gilman (use a modern Ajax framework) and
> Mike Travers( wrap parentheses around the expression to be evaluated).
> Much appreciated!!
> -Alan
> On May 12, 2007, at 8:26 AM, Donald Doherty, Ph.D. wrote:
>> Alan,
>> I'm getting the same errors in Firefox 2.0 and IE 6.0 on the  
>> Windows XP
>> platform.
>> Don
>>> On the demo page there is a link to the Google Maps/Allen Brain
>>> Institute/SPARQL mashup. It works properly on Safari. However it  
>>> gets
>>> an error in Firefox after retrieving the results and doesn't display
>>> an image. In IE7, it retrieves the results but then doesn't seem to
>>> to update the images shown properly. The firefox test is on the Mac,
>>> the IE7 test is under XP.
>>> I suspect that this has to do with details of the XMLHTTPRequest. If
>>> there is someone knowledgeable about such issues I'd appreciate if
>>> you could have a look and see if you can figure out what the problem
>>> is. Also testing on other browsers/OS would be appreciated.
>>> The URL to test is http://hcls1.csail.mit.edu:8890/map/
>>> #Kcnip3@2850,Kcnd1@2800
>>> Thanks!
>>> -Alan
>> -- 
>> Donald Doherty, Ph.D.
>> Brainstage Research, Inc.
>> www.brainstage.com
>> donald.doherty@brainstage.com
>> 412-683-1410
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Bill Bug
Senior Research Analyst/Ontological Engineer

Laboratory for Bioimaging  & Anatomical Informatics
Department of Neurobiology & Anatomy
Drexel University College of Medicine
2900 Queen Lane
Philadelphia, PA    19129
215 991 8430 (ph)
610 457 0443 (mobile)
215 843 9367 (fax)

Please Note: I now have a new email - William.Bug@DrexelMed.edu

Received on Sunday, 13 May 2007 05:28:49 UTC

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