[ome-users] OMERO versions

[Jason Swedlow]

Hi All-

On 28 Feb 2008, at 09:47, josh.moore at gmx.de wrote:

>
> (CCing list on reply)
>
> Mikhail Kovtun writes:
>> Josh,
>>
>> As I understood from your reply, the version in the trunk is  
>> workable --
>> in this case, I would like to try it. (Does "yellow" mean that  
>> there is
>> no syntax errors but some tests fail?)
>
> Exactly. Yellow means that there are failing tests, which at the
> moment is no surprise since we are waiting on a new server for our
> integration tests.
>
>> What do you think is better -- do build myself or download binaries?
>> (Are binaries in
>> http://warlock.openmicroscopy.org.uk:5555/job/OMERO/ws/trunk/dist ?)
>
> The binaries are now zipped and archived by Hudson. See
> http://warlock.openmicroscopy.org.uk:5555/job/OMERO/ 
> lastSuccessfulBuild/
>

I'll just reiterate one point (and then reiterate it again below)--  
on the OMERO project, we really place a huge emphasis on testing, and  
docs.  We are not perfect-- by a along shot.  TRUNK is there for you  
to work with, but please realise you are working with tools we are  
still testing.  We never warrant anything anyway, but you're living  
dangerously (we don;t let our users, or their precious data, anywhere  
near TRUNK code til after a code freeze and significant testing).   
Moreover, we can't guarantee that we'll fix anything immediately  
that's in TRUNK-- we've got alot to work on.  We're REALLY excited  
about the facilities going into Beta3, and can understand why you  
are.  Just realise you are on the really dripping bleeding edge. We  
appreciate any and all feedback and we will try to support your needs.

>
>> I would prefer to do build myself -- it gives me more flexibility in
>> rolling back changes and more possibilities to learn OMERO code.  
>> Do you
>> have any document describing build process (what components should be
>> installed on the system, what environmental variables should be  
>> set, etc.)?
>
> Sure. See
> https://trac.openmicroscopy.org.uk/omero/wiki/OmeroContributing
> for information on building from source.
>
>> Who is the best person to address questions regarding OMERO.Editor?
>> After playing a bit with it, I have a number of questions and  
>> comments.
>
> Mikhail meet Will Moore. Will meet Mikhail.
>

OMERO.editor is nearing release, but we're still testing and  
gathering user evaluations internally.  Please do email any comments to:

Will Moore, (will at lifesci.dundee.ac.uk)
Scott Loynton (scottloynton at computing.dundee.ac.uk)
>>

>
>> josh.moore at gmx.de wrote:
>>> Hi Mikhail,
>>>
>>> Mikhail Kovtun writes:
>>>> Jason, Chris, and Josh,
>>>>
>>>> I would like to learn a bit more regarding OMERO development. I  
>>>> am most
>>>> interested in new annotation/search capabilities.
>>>>
>>>> 1) Should new annotation/search capabilities appear in version  
>>>> 3.0 Beta 3?
>>>
>>> Yes. They are both available in the server in trunk.
>>>
>>>> 2) Is the scheduled data (April 15, 2008) realistic? If no, when  
>>>> one may
>>>> expect Beta 3?
>>>
>>> That's a question for the others.

OK, over to me.  In Beta3, we are adding alot of new functionality.   
We are scheduling April 15 for a code freeze.  After that we will  
enter 6 fun-filled weeks of internal testing with our users, driven  
by our Usable Image team (http://www.usableimage.org), docs and  
screencast video generation, and packaging.  We've learned the hard  
way that all this stuff takes time, and must not be neglected.   
Expect solidification by April 15, packaged releases by June 1.  Yep,  
testing, especially iterative user testing,  takes time.


>>>
>>>> 3) What is the role of OMERO.Editor w.r.t. annotation/search?  
>>>> When it is
>>>> expected to be integrated with OMERO?
>>>
>>> One possible use case is that the output of the editor -- the  
>>> protocol
>>> -- can be used to _annotate_ any of number of types (Image, Dataset,
>>> Project, Pixels,...) and then a user could use _search_ to find  
>>> those
>>> Images, Datasets, etc. via the contents of the protocols. But,  
>>> that's
>>> really just the beginning.

What is the role?  OMERO.Editor is a user-centered, standalone tool  
for managing protocols.  It's quite simple to use, and can currently  
do some quite simple things-- just manage my protocols and  
experimental steps, and increasingly some more interesting things:
-- define a template for experimental logging
-- incorporate external specifications (i.e., OME-XML)
-- provide a window into specific ontology terms.
-- enable indexed search through all protocols

See the very nice page Will has made:  http:// 
trac.openmicroscopy.org.uk/shoola/wiki/OmeroEditor (don't miss the  
movie!)

We'd appreciate any and all feedback.

And yes, integration into OMERO is coming-- we are looking at ways to  
do that.  Probably not in Beta3, sorry. But soon thereafter.  We know  
we have to do it, we just want to do it correctly.  We're also very  
excited about collaborating with the NCBO team, fusing Phenote and  
OMERO.Editor (formally named ProtocolEditor; see http:// 
www.bioontology.org/wiki/index.php/Phenote:Main_Page).


>>>
>>>> 4) Does http://cvs.openmicroscopy.org.uk/svn/omero/trunk  
>>>> contains code
>>>> that is going to be version 3.0 Beta 3?
>>>
>>> Yes. Trunk is currently set for 3.0-Beta3. Though it's currently
>>> pretty actively developed, it should be possible to build it and try
>>> out the latest functionality. Take a look at:
>>>
>>> http://warlock.openmicroscopy.org.uk:5555/job/OMERO/
>>>
>>> which shows the current build status of the system.
>>>

Enjoy!

As always, thanks for your support.

Cheers,

Jason

**************************
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