[ome-users] question re OME XML semantic types for biological material + OME command line interface question/request

[Ilya Goldberg]

I can try and have a go at the second question.  The first question  
may be better answered by people who've actually used the SPW (screen  
plate well) datamodel to process a screen.  Bernd Jagla at Columbia  
is one such.  Maybe he'll chime in.

As for running command-line programs from the AE, the reason we let  
support for this slide was that it was getting really complicated to  
try and deal with all possible ways of executing something from the  
command line.  What's desperately needed is a simplification or an  
80/20 solution.
Having a use-case (or several) for contrast is a key requirement for  
coming up with an 80/20 solution.
So, can you describe the kinds of things you would need in an  
interface to deal with your scripts?  There are many options open, so  
I realize its kind of an open-ended question, but I think there will  
be some significant demand for this, and your use-cases can be the  
drivers for implementing such an API.

What do you think?

The fall-back is to write a little-bitty perl wrapper for your  
scripts and declare the perl wrapper as your "Handler".  This is how  
we deal with FindSpots, which is a 3-D global-threshold segmentation  
algorithm written in C, and executed on the command-line.  It reads a  
set of pixels and produces a table of "spots" with various measured  
parameters (centroid, dispersion, form-factor, etc).

-Ilya


On Feb 9, 2007, at 9:06 AM, <Keith.Neil at sanofi-aventis.com>  
<Keith.Neil at sanofi-aventis.com> wrote:

> Hi - First I am trying to see how I would best store in OME XML the
> results of a phenotypic screen, and I'm not sure how to describe the
> compound treatment and dose information and the positive and negative
> control information in the XML correctly so that I can create  
> templates
> to display things nicely from OME.
>
> What I want is to be able to properly annotate the compounds +
> concentrations tested in each well of plates in a screen, and to flag
> the wells that are control wells, and then to be able to use this
> semantic information in querying, and creating a table view of the
> screen.  I can create a category group called treatment, and then  
> add my
> treatments, but how to associate dose to the treatment?  Also if I use
> category group, this is tied to each image, when I would rather it be
> tied to the 'sample' in the well?
>
> Did I read somewhere that you plan to re-use from the MGED ontology/ 
> xml
> the biomaterials element ?
>
> Second, I saw that in an older version there was the possibility to  
> run
> command line scripts from the analysis engine but that it broke in
> recent versions.  I'd be interested to have this working to  
> incorporate
> some non mathlab scripts, or scilab scripts.
>
> Thanks for your help!
>
> Keith
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