[ome-users] OMERO with iRODS?

Harri Jäälinoja harri.jaalinoja at helsinki.fi
Wed Oct 20 12:02:23 BST 2010

Dear All,

I want to share with you some ideas. Maybe you can help me figure out if 
they are worth pursuing or not, or even better, help me refine them into 
something useful.

I am evaluating OMERO for use in our microscopy unit, at the moment 
specifically for a Leica HCS confocal microscope. While I have been 
reading about various existing systems, I have somehow developed also an 
interest in the iRODS data management system (http://www.irods.org). 
What I am wondering now is, would it be possible to use OMERO and iRODS 
together and what would be the best way to do it?

iRODS seems to offer proven tools for managing various storage 
resources, with the flexibility to formulate policies about how the data 
is stored and shared, sophisticated authentication systems, data 
integrity checking, even some workflow functionality. This is something 
that a data storage administrator might want to have. For the 
microscopist or biologist that is not very useful, they need the rich 
user interface provided by OMERO. Both aspects are important, and I 
think this is also what DAX is addressing with the OMERO archiving 

iRODS is already being used in the OpenCCDB system 
(http://openccdb.org/index.shtm), and the idea of using it with OMERO 
has been suggested before (http://www.u.arizona.edu/~dcromey/OMX/), so I 
think there might be something to it. The question is, how to do it? I 
can think of three approaches:

1. use an iRODS archive as an external storage to OMERO
- when necessary, move images from the location visible via OMERO.fs to 
the iRODS system, with no concern about OMERO system integrity
- I read in the notes of some OME meeting that somebody said for him it 
would be sufficient if OMERO simply said "Contact your sysadmin..." in 
case an image file is not found.
- sounds trivial
(- a national computing centre will probably soon offer us this service)

2. use OMERO.fs to access data in iRODS
- iRODS stores files in some directory (default <iRODS_install/Vault>). 
- this directory could be made read-only visible to OMERO.fs for input 
into OMERO
- enter data first in iRODS, then automatically in OMERO via OMERO.fs 
- re-organizing data in OMERO would not be possible as this would break 
the iRODS system
- sounds fairly easy

3. create an iRODS extension to OMERO
- iRODS has a Java API (Jargon)
- add features in OMERO for iRODS I/O, work directory synchronization etc.
- when data is entered in OMERO, automatically also in iRODS
- sounds nice but requires coding
- could possibly save OMERO developers the trouble of implementing 
functionality related to data sharing, permissions etc.?

I will soon have an environment where I can install and test OMERO and 
iRODS and other products, so I hope I will have some practical 
experience of approaches 1. and 2. If you think the general idea seems 
worthwhile, maybe the OMERO dev-team could check what number 3. would 
mean in practice and how feasible it is?

Hoping to hear your comments!

Best regards,

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