<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Dear All-<div><br>Just an update on our activities with OMERO and HCS data.<br><br>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:<br><br><a href="http://jcb.rupress.org/content/194/5/665">http://jcb.rupress.org/content/194/5/665</a><br><br>and the data is at:<br><br>http://jcb-dataviewer.rupress.org/jcb/browse/4608/S1/<br><br>Maybe most useful to click on the "Chart" button.<br><br>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:<br><br>http://jcb.rupress.org/content/194/5/789<br><br>and the data is at:<br><br>http://jcb-dataviewer.rupress.org/jcb/browse/4609/<br><br>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.<br><br>Data download is enabled at the level of wells (and thus individual genes) at the moment. Plate-based data download is coming.<br><br>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.<br><br>Let us know if you have any questions about this resource, the code or our steps going forward.<br><br>Cheers,<br><br>Jason<br></div><br><div>
<span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div style="font-family: Helvetica; "><br class="Apple-interchange-newline"><br class="khtml-block-placeholder"></div><div style="font-family: Helvetica; "><span class="Apple-style-span" style="font-family: Helvetica; ">**************************</span></div><div style="font-family: Helvetica; "><font class="Apple-style-span" face="Arial">Wellcome Trust Centre for Gene Regulation & Expression</font></div><div style="font-family: Helvetica; "><font class="Apple-style-span" face="Arial">College of Life Sciences</font></div><div style="font-family: Helvetica; "><font class="Apple-style-span" face="Arial">MSI/WTB/JBC Complex</font></div><div style="font-family: Helvetica; "><span class="Apple-style-span" style="font-family: Helvetica; ">University of Dundee</span></div><div style="font-family: Helvetica; "><span class="Apple-style-span" style="font-family: Helvetica; ">Dow Street</span></div><div style="font-family: Helvetica; "><span class="Apple-style-span" style="font-family: Helvetica; ">Dundee DD1 5EH</span></div><div style="font-family: Helvetica; "><span class="Apple-style-span" style="font-family: Helvetica; ">United Kingdom</span></div><div style="font-family: Helvetica; "><br style="font-family: Helvetica; "></div><div style="font-family: Helvetica; "><span class="Apple-style-span" style="font-family: Helvetica; ">phone (01382) 385819</span></div><div style="font-family: Helvetica; "><span class="Apple-style-span" style="font-family: Helvetica; ">Intl phone: 44 1382 385819 </span></div><div style="font-family: Helvetica; "><span class="Apple-style-span" style="font-family: Helvetica; ">FAX (01382) 388072 </span></div><div style="font-family: Helvetica; "><span class="Apple-style-span" style="font-family: Helvetica; ">email: <a href="mailto:jason@lifesci.dundee.ac.uk">jason@lifesci.dundee.ac.uk</a></span></div><div style="font-family: Helvetica; "><br style="font-family: Helvetica; "></div><div style="font-family: Helvetica; "><span class="Apple-style-span" style="font-family: Helvetica; ">Lab Page: </span><a href="http://www.lifesci.dundee.ac.uk/gre/staff/jason-swedlow">http://www.lifesci.dundee.ac.uk/gre/staff/jason-swedlow</a></div><div style="font-family: Helvetica; "><span class="Apple-style-span" style="font-family: Helvetica; ">Open Microscopy Environment: <a href="http://openmicroscopy.org">http://openmicroscopy.org</a></span></div><div style="font-family: Helvetica; ">**************************</div><div style="font-family: Helvetica; "><br class="webkit-block-placeholder"></div><div style="font-family: Helvetica; "><div>The University of Dundee is a Scottish Registered Charity, No. SC015096.</div></div><br class="Apple-interchange-newline"></span><br class="Apple-interchange-newline"></div></span></span>
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