[ome-users] Manual about OME server

[Ilya Goldberg]

On Apr 6, 2007, at 3:37 AM, WANG Juhui wrote:

> Hi, Ilya,
>
> Thank you for answering  so quickly. I make a quick test about OME  
> now, so  just have some simple questions for beginners such as
> 1) How to add a new user with the Web UI?
> 2) How to delete a registred project with the Web UI?

These can only be done on the command-line for now.  Maybe somebody  
can contribute a Web-based version of the command-line admin tool?   
It would be pretty easy.

> 3) It seems that ImageJ can communicate with OME server, how about  
> OMERO?

So far, no.  But we're working on it.

> 4) Do OMERO and OME use the same data model?

Close, but not compatible.  They can't use the same database either.

> 5) May we get the data model implemented in OME?

Not sure what you mean.
There's a datamodel for microscopy image data, which is what's  
specified in the OME-XML Schema (ome.xsd).  Is this the one you mean?

The datamodel described in ome.xsd is implemented using  
SemanticTypes.  The collection of SemanticTypes used to define  
everything in ome.xsd are in src/xml/OME/Core/
There are many extensions implemented in the OME Server to make it a  
useful piece of software.  Those datamodels are defined in other  
subdirectories of src/xml/OME/.  The Analysis subdirectory contains  
many data models used for image analysis that are not defined by  
ome.xsd.
These files are all OME-XML documents following the STD.xsd and/or  
AML.xsd sub-schemas.

Unlike many other systems, the datamodels for the OME Server are  
specified in XML only - there is no code that implements them other  
than the XML specification.  There is of course code that uses  
specific datamodels to do things with, but the implementation of the  
datamodels (making DB tables, generic views, searches, displays, etc)  
is all handled by generic code using the XML specification.  This  
way, the datamodel(s) can be extended at runtime just by importing  
more OME-XML files.

Does that help?
-Ilya


>
> Best!
>
> Juhui
>
>
>
>
>
> Ilya Goldberg a écrit :
>
>> Hi Juhui
>> There's quite a bit of documentation on our website, including  
>> some  HowTo's to get started with "canned" tasks.  Have you been  
>> able to  connect to it with the web UI? (try http://localhost/  
>> from the local  machine, or connect to it from another machine  
>> using its IP address  or hostname).
>> Probably the first thing you'd want to do is import some images.    
>> There are quite a few different formats here:
>> http://openmicroscopy.org/TestImages/
>>
>> Clicking on the [?] next to menu items in the Web UI will send you  
>> to  the appropriate documentation on openmicroscopy.org
>>
>> If you have specific questions about particular usages, ask away.
>> -Ilya
>>
>> On Apr 5, 2007, at 9:49 AM, WANG Juhui wrote:
>>
>>
>>> HI,
>>>
>>> I just installed the OME server on  Mandriva 2006. Every thing   
>>> seems to
>>> work..., except I don't know how to use it.  Is there any user's  
>>> guide
>>> for this outstanding system?  I promise here that I will publish my
>>> installation experience soon.
>>>
>>> Best!
>>>
>>> -- 
>>> Juhui WANG						Email:	juhui.wang at jouy.inra.fr	
>>> INRA - Mathématiques et Informatique Appliquées		Tel:	+(33) 01  
>>> 34  65 22 29	
>>> Domaine de Vilvert					Fax: 	+(33) 01 34 65 22 17	
>>> F-78352 Jouy-en-Josas		
>>>
>>>
>>> _______________________________________________
>>> ome-users mailing list
>>> ome-users at lists.openmicroscopy.org.uk
>>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>>>
>>>
>>
>> _______________________________________________
>> ome-users mailing list
>> ome-users at lists.openmicroscopy.org.uk
>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>>
>>
>
>
> -- 
> Juhui WANG						Email:	juhui.wang at jouy.inra.fr	
> INRA - Mathématiques et Informatique Appliquées		Tel:	+(33) 01 34  
> 65 22 29	
> Domaine de Vilvert					Fax: 	+(33) 01 34 65 22 17	
> F-78352 Jouy-en-Josas		
>