[ome-users] Analysis work and Execute chain in OME Java clien t (Shoola) ?

[Josiah Johnston]

This message bounced off the list last time I sent it. Now that is 
fixed, and it can go up for posterity.

You may execute chains that require no user inputs from the Web UI. 
Look for 'Execute Chain' in the menu.
Over the summer, I'm hoping to extend the Web interface to collect 
inputs for any chain. In the meanwhile, you can build custom extensions 
to the web interface to support the needs of your users. Someone 
familiar with perl and web programming would need up to a week to learn 
the core API and build their first extension. After that, it would take 
a few hours per additional extension.

You may execute chains that require user inputs, on the command line. 
type
	ome help execute
for usage information.

I find this inadequate for executing chains needing complex inputs. 
Recently, I have needed to executing complex chains in the course of my 
work, and have written custom scripts to assemble inputs and execute 
complex chains.
This approach is not general purpose, and we hope to build more 
analysis tools in the future.

If you would like to explore OME's functional Analysis System in the 
immediate future, try using OME commander to execute simple chains. If 
you find yourself needing to assemble many user inputs, I'll send you a 
simple example script for executing complex chains.
You can view analysis results in the Web UI. The results aren't 
packaged well for display, but you will have full access to all data.

An update from the Goldberg Lab:
This summer a summer student and I are going to work on the Web UI. We 
are planning to build a framework that greatly simplifies the process 
of extending the Interface to support custom annotation, search, and 
display. I'm also planning to fix any remaining Web UI bugs during the 
summer.

Josiah


On Apr 26, 2005, at 5:12 AM, Jason Swedlow wrote:

> Liang-
>
> Thanks for your email.  Indeed, the Shoola client's don't yet run 
> analyses
> or make analysis results visible.  A few things to note:
>
> 1) OME is a work in progress.  For where we're going in the short to 
> medium
> term, see http://www.openmicroscopy.org/release/
>
> 2) There is alot of other work underway, and support for analyses 
> within
> remote clients is currently being developed by Harry Hochheiser, at 
> NIH.
> Send the list what you'd like to see and we'll work to include it.
>
> 3) If you have some time to dedicate to the project, have a look at 
> the docs
> section of your Shoola distribution (get Shoola from CVS, follow the
> directions for build, and then look in ~/Shoola/OUT/docs/).  There is 
> alot
> there on the system, and if you want to help Harry, Jean-Marie, and 
> Andrea,
> that would be great.
>
> Cheers,
>
> Jason
>
>
> On 26 Apr 2005, at 03:26, Ho Liang Yoong wrote:
>
>
>> Hi,
>>
>> I am able to do some analysis (like Find Spots for example) using the 
>> OME
>> web interface, but I can't seem to find any analysis in the Java 
>> client
>> (Shoola). Please kindly advice. Also, is it possible to execute chain 
>> in
>> shoola? I have built some chains in shoola but I can't find any
>> functionality which allows me to execute them.
>>
>>
>> Thanks.
>>
>>
>> Best regards,
>> Liang Yoong
>> Software Engineer
>> Information Sciences
>> Bioinformatics Institute, BMRC, A-Star
>> Email: lyho at bii.a-star.edu.sg
>> Website: http://www.bii.a-star.edu.sg
>> DID:  +65-64788386
>>
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