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<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt'>Hi
there again,<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt'>Please
forward to user group if you think this group would be a better target…<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt'>I was
wondering a bit on how to actually use OME. To give you an idea of what I am
thinking of, let me describe to you our workflow:<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt'>We
are screening chemical compounds using cell based assays. We want to screen
about 100,000 compounds per screen. The images coming from the INCell Analyzer
comprise the raw data and will usually be analyzed on the fly and the resulting
features (sometime a few dozen) will be written into text files. “Somehow”
those results and images will be imported into OME (see e-mail from yesterday).
<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt'>Then
we want to display a particular feature for all the wells/plates as a heat map
to identify by eye any biases or problems in the data set. For this we envision
right now using Partek’s Screener Solution which could interface with OME
through ODBC. A simple (complex) select statement should bring all the necessary
information into the Screener Solution.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt'>Then
we have to select hits and analyze the screen: <o:p></o:p></span></font></p>
<p class=MsoNormal style='text-indent:.5in'><font size=2 face=Arial><span
style='font-size:10.0pt'>Display a particular feature for all wells and plates.
(This is for quality control). <o:p></o:p></span></font></p>
<p class=MsoNormal style='text-indent:.5in'><font size=2 face=Arial><span
style='font-size:10.0pt'>Select a relevant feature and a threshold.<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-indent:.5in'><font size=2 face=Arial><span
style='font-size:10.0pt'>Write back the results (somehow) to OME. Those results
will eventually group the results in different categories (hit, non-hit,
not-known, positive control, negative control, etc). This actually still has to
be solved.<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-indent:.5in'><font size=2 face=Arial><span
style='font-size:10.0pt'>Then we want to see/ cross-link the results with other
screens: of these hits, which other assays where they active in? Which
compounds where active in a given set of screens? Give me a complete profile of
all the compounds and in which assays they where active, given a specified threshold
etc.<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-indent:.5in'><font size=2 face=Arial><span
style='font-size:10.0pt'>Of course at some point we want to see the compounds
with the results and everything but this will wait a while and needs probably
further discussions on how to integrate all this.<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-indent:.5in'><font size=2 face=Arial><span
style='font-size:10.0pt'>Then we have to push some of the data to PubChem at
the NIH. How could we do this? A simple script with select statements could do
the work, no? Maybe we can write a chain module that automatically propagates
the data to PubChem (they use XML – their own format of course).<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-indent:.5in'><font size=2 face=Arial><span
style='font-size:10.0pt'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt'>At
the moment I believe that the most important part is to improve (or for me to
learn how to do) the grouping features of OME. I don’t think it is good
that you have to know in advance that you want to add something to a data set. From
my experience I would rather play with the data and mark e.g. bad wells along
the way, select images that look interesting in one way or the other and say:
Wow they look cool lets make a new dataset and collect them here, or lets add
them to the list of interesting data. As far as I know this is only possible
once you know the name of the data set, and then you have to search for them
again.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt'>Also
for the sake of better understanding can you please point me to all the
relevant information concerning data sets: how to programmatically do it, how
to do it with ODBC, and the web interface?<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt'>I
would be more than happy to explain in more detail or discuss our strategies as
we are just in the process of getting started…<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt'>Thanks
a lot for all your kind help.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt'>Happy
<st1:country-region w:st="on"><st1:place w:st="on">Turkey</st1:place></st1:country-region>
day (for those of you who don’t care about turkeys, happy weekend…
;-)<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt'>Best<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt'>Bernd<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-indent:.5in'><font size=2 face=Arial><span
style='font-size:10.0pt'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=3 face=Arial><span style='font-size:12.0pt'><o:p> </o:p></span></font></p>
<p><font size=2 face="Times New Roman"><span style='font-size:10.0pt'>Bernd
Jagla, PhD<br>
Associate Research Scientist<br>
<st1:place w:st="on"><st1:PlaceName w:st="on">Columbia</st1:PlaceName> <st1:PlaceType
w:st="on">University</st1:PlaceType></st1:place><br>
<st1:Street w:st="on"><st1:address w:st="on">1150 St. Nicholas Avenue</st1:address></st1:Street><br>
Russ Berrie Medical Pavilion, Room 520<br>
<st1:place w:st="on"><st1:City w:st="on">New York</st1:City>, <st1:State w:st="on">NY</st1:State>
<st1:PostalCode w:st="on">10032</st1:PostalCode></st1:place><br>
Tel: 212 - 851 5560 x16<br>
Fax: 212 - 851 5570<br>
e-mail: baj2107@columbia.edu<br>
</span></font> <o:p></o:p></p>
<p class=MsoNormal><font size=3 face=Arial><span style='font-size:12.0pt'><o:p> </o:p></span></font></p>
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