[ome-users] Update on OMERO and HCS

[Jason Swedlow]

Dear All-

Just an update on our activities with OMERO and HCS data.

At the beginning of September, the Journal of Cell Biology published four HCS screens on the JCB DataViewer (a custom version of OMERO, built and maintained by Glencoe Software), totalling about 300 GB of data.  The first was a genome wide screen of the S. cerevisiae non-essential collection, looking for modifiers of the DNA repair pathway.  This was essentially a "re-publishing" of a previously published paper.  The new paper is at:

http://jcb.rupress.org/content/194/5/665

and the data is at:

http://jcb-dataviewer.rupress.org/jcb/browse/4608/S1/

Maybe most useful to click on the "Chart" button.

A second paper, which looked for modifiers of actin structure in cells, used one screen in Drosophila cells and two targetted screens in human cells:  The paper is at:

http://jcb.rupress.org/content/194/5/789

and the data is at:

http://jcb-dataviewer.rupress.org/jcb/browse/4609/

The presentation of the data there can be debated-- there are advantages and disadvantages to what was done, and the decisions were made by many people.  For example, we think we can do a better job at visualising the plates and their content.  However, as a scientist, I do like the browser-based view of the screen results, that shows what the authors scored as hits, and allows me to browse their interpretation of the results.

Data download is enabled at the level of wells (and thus individual genes) at the moment.  Plate-based data download is coming.

This custom UI was built by Glencoe Software, under contract to Rockefeller University Press.  As always, this code is being rolled into the GPL-released version of OMERO.  We have some versioning issues to reconcile, but getting these facilities into the open source codebase is a major priority.  We'll send updates on this list as the code becomes available.

Let us know if you have any questions about this resource, the code or our steps going forward.

Cheers,

Jason



**************************
Wellcome Trust Centre for Gene Regulation & Expression
College of Life Sciences
MSI/WTB/JBC Complex
University of Dundee
Dow Street
Dundee  DD1 5EH
United Kingdom

phone (01382) 385819
Intl phone:  44 1382 385819 
FAX   (01382) 388072 
email: jason at lifesci.dundee.ac.uk

Lab Page: http://www.lifesci.dundee.ac.uk/gre/staff/jason-swedlow
Open Microscopy Environment: http://openmicroscopy.org
**************************

The University of Dundee is a Scottish Registered Charity, No. SC015096.



-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.openmicroscopy.org.uk/pipermail/ome-users/attachments/20111002/37ebef6c/attachment.html>