[ome-devel] IDR Demos-- First Public Release

[Jason Swedlow (Staff)]

Dear All-

Just as a follow-up to this.

Data loading has been completed for several studies (including Tara Oceans and Mitocheck), and a new study, data from Breinig et al<http://msb.embopress.org/content/11/12/846> has been added at http://idr-demo.openmicroscopy.org/pgpc.

In total, there are:
* 12 studies, 16 screens
* 2500 plates
* 29M frames
* 37TB of image data

We are continuing to add more datasets to this resource.

Comments, ideas or usage welcome.

Cheers,

Jason

--------------------
Centre for Gene Regulation & Expression | Open Microscopy Environment | University of Dundee

Phone:  +44 (0) 1382 385819
email: j.swedlow at dundee.ac.uk<mailto:j.swedlow at dundee.ac.uk>

Web: http://www.lifesci.dundee.ac.uk/people/jason-swedlow
Open Microscopy Environment: http://openmicroscopy.org<http://openmicroscopy.org/>


From: Jason Swedlow <j.r.swedlow at dundee.ac.uk<mailto:j.r.swedlow at dundee.ac.uk>>
Date: Tuesday, 20 October 2015 15:21
To: OME Users <ome-users at lists.openmicroscopy.org.uk<mailto:ome-users at lists.openmicroscopy.org.uk>>, OME Development <ome-devel at lists.openmicroscopy.org.uk<mailto:ome-devel at lists.openmicroscopy.org.uk>>
Subject: IDR Demos-- First Public Release

Dear All-

We've previously mentioned the BBSRC-funded IDR project on these lists.  The aim is to develop next proof-of-concepts for large-scale data publication.  In particular we want to demonstrate the value of aggregating several large imaging studies into one resource and drawing as many links as possible between them- at the level of perturbations, ontological annotations and quantitative features.  Finally, we want to test the feasibility of making these data available in a virtual resource that users can use to test their own algorithms and datasets.

These are obviously quite ambitious goals, but we are making some progress.  We'd like to show you all where we are, ask for comments or ideas,  and maybe stimulate your own ideas how you can contribute the project or use these resources- both data and software-- for your own work.

The IDR resources are now up and available at:

http://idr-demo.openmicroscopy.org Data from eleven genetic or siRNA screens from a series of published papers.  All metadata submitted by authors is included in the resource.

http://idr-demo.openmicroscopy.org/mito Data from the Mitocheck screen (http://mitosys.org) (as of this writing, about 10% of the data loaded, more coming)

http://idr-demo.openmicroscopy.org/tara Data (images and metadata) from the Tara Oceans study (http://oceans.taraexpeditions.org/en/) (as of this writing, about 45% of the data loaded, more coming)

These studies are available from different URLs as this helped us during the data loading phase.

All of these are available via the "vanilla" OMERO web interface.  There is no question that this interface isn't customised for this type of use case, and the datasets "stretch" and in some cases break the design of this UI.  We'll be doing work on the UI in due course.  Our goal was to get the data integration done and have a foundation for designing  about a virtual analysis resource.

Again, any thoughts or comments welcome.  Obviously if you know of datasets that would be candidates for this resource, please do let us know.  The principles for datasets we want to include are written up in the Euro-BioImaging/Elixir Data Strategy<http://www.eurobioimaging.eu/content-news/euro-bioimaging-elixir-image-data-strategy>.

Thanks again for your support and comments.

Cheers,

Jason

--------------------
Centre for Gene Regulation & Expression | Open Microscopy Environment | University of Dundee

Phone:  +44 (0) 1382 385819
email: j.swedlow at dundee.ac.uk<mailto:j.swedlow at dundee.ac.uk>

Web: http://www.lifesci.dundee.ac.uk/people/jason-swedlow
Open Microscopy Environment: http://openmicroscopy.org<http://openmicroscopy.org/>



The University of Dundee is a registered Scottish Charity, No: SC015096
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