<div dir="ltr">Just another short note - I tried downloading the pipeline file (data file 1) which looked OK and the reproduce.zip file which was definitely not. All I got was an empty file (0KB download size).</div><div class="gmail_extra">
<br><br><div class="gmail_quote">On Tue, Nov 12, 2013 at 7:51 AM, Lee Kamentsky <span dir="ltr"><<a href="mailto:leek@broadinstitute.org" target="_blank">leek@broadinstitute.org</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr">Hi Vebjorn,<div>Simon is trying to download the AZ dataset from JBS and found it to be corrupted. I'd rather not start a 700gb download just to test. Did you check to see if the files are accessible?</div>
<div><br></div><div>Simon, if you need the data, the most straightforward approach may be for me to burn a CD and mail it. I think it would be a good dataset to test what you do at scale.</div><div><br></div><div>--Lee</div>
</div><div class="gmail_extra"><br><br><div class="gmail_quote">On Mon, Nov 11, 2013 at 12:51 PM, Simon Li <span dir="ltr"><<a href="mailto:s.p.li@dundee.ac.uk" target="_blank">s.p.li@dundee.ac.uk</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div style="word-wrap:break-word">
<div>Thanks Lee.</div>
<div><br>
</div>
<div>The features set you calculated for that screen sounds like a good test of our infrastructure. However I'm having trouble downloading the supplementary data from:</div>
<div><a href="http://jbx.sagepub.com/content/early/2013/09/09/1087057113503553/suppl/DC2" target="_blank">http://jbx.sagepub.com/content/early/2013/09/09/1087057113503553/suppl/DC2</a></div>
<div><br>
</div>
<div>Data_S3_reproduce.zip is empty</div>
<div>Data_S2_database.zip seems to be corrupt</div>
<div><br>
</div>
<div>Does it look correct from your end?</div>
<div><br>
</div>
<div>Thanks</div>
<div><br>
</div>
<div>Simon</div>
<div><br>
</div>
<div><br>
</div>
<br>
<div>
<div>On 7 Nov 2013, at 20:55, Lee Kamentsky <<a href="mailto:leek@broadinstitute.org" target="_blank">leek@broadinstitute.org</a>> wrote:</div>
<br>
<blockquote type="cite">
<div dir="ltr">I promised to roughly describe the CellProfiler use case - we recently published a paper whose data should be available on-line, so I based it on that. Enclosed is what I wrote up as well as the paper and the supplement. The supplement is actually
more important because it has more details about the analysis (and the features).
<div><br>
</div>
<div><br>
<div class="gmail_drive_chip" style="width:396px;min-height:18px;max-height:18px;background-color:#f5f5f5;padding:5px;color:#222;font-family:arial;font-style:normal;font-weight:bold;font-size:13px;border:1px solid #ddd">
<a href="https://docs.google.com/a/broadinstitute.org/file/d/0Bzg4PoGEku2FTFFBS0ZsZTFoSXc/edit?usp=drive_web" style="display:inline-block;overflow:hidden;text-overflow:ellipsis;white-space:nowrap;text-decoration:none;padding:1px 0px;border:none;width:100%" target="_blank"><img src="https://ssl.gstatic.com/docs/doclist/images/icon_10_generic_list.png" style="vertical-align:bottom;border:none"> <span dir="ltr" style="color:#15c;text-decoration:none;vertical-align:bottom">Ljosa_JBiomolScreen_2013.pdf</span></a></div>
<br>
<div class="gmail_drive_chip" style="width:396px;min-height:18px;max-height:18px;background-color:#f5f5f5;padding:5px;color:#222;font-family:arial;font-style:normal;font-weight:bold;font-size:13px;border:1px solid #ddd">
<a href="https://docs.google.com/a/broadinstitute.org/file/d/0Bzg4PoGEku2FLVZkTEZqUDJ5X1k/edit?usp=drive_web" style="display:inline-block;overflow:hidden;text-overflow:ellipsis;white-space:nowrap;text-decoration:none;padding:1px 0px;border:none;width:100%" target="_blank"><img src="https://ssl.gstatic.com/docs/doclist/images/icon_10_generic_list.png" style="vertical-align:bottom;border:none"> <span dir="ltr" style="color:#15c;text-decoration:none;vertical-align:bottom">Ljosa_JBiomolScreen_2013_supplement.pdf</span></a></div>
<br>
</div>
</div>
<div class="gmail_extra"><br>
<br>
<div class="gmail_quote">On Thu, Nov 7, 2013 at 9:20 AM, Simon Li <span dir="ltr">
<<a href="mailto:s.p.li@dundee.ac.uk" target="_blank">s.p.li@dundee.ac.uk</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Some notes from our meeting yesterday:<br>
<a href="http://www.openmicroscopy.org/site/community/minutes/minigroup/omero-features-meetings/2013-11-06-omero-features-google-hangout" target="_blank">http://www.openmicroscopy.org/site/community/minutes/minigroup/omero-features-meetings/2013-11-06-omero-features-google-hangout</a><br>
<br>
Summary:<br>
We're thinking of representing features as a 2D array, with metadata stored as key-value maps attached to the array, or individual columns or rows. These keys could describe things such as the feature name (column), sample metadata (row), algorithm parameters,
calculation pipelines, etc.<br>
<br>
This should work as an OMERO API- in order to retrieve features you'd pass in a set of key-value pairs, for instance to specify which features you want and which images/ROIs etc, and OMERO would handle the logic and return the feature table(s) matching those
parameters. Since everyone has different requirements the keys could be anything, however we're trying to define a small set of standard keys- any suggestions are very welcome.<br>
<br>
Outside of OMERO we still need a format for transporting features, so we're thinking some form of HDF5.<br>
<br>
Simon<br>
<br>
<br>
The University of Dundee is a registered Scottish Charity, No: SC015096<br>
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</blockquote>
</div>
<br>
</div>
<span><AZ_use_case.docx></span></blockquote>
</div>
<br>
<br>
<span style="font-size:10pt">The University of Dundee is a registered Scottish Charity, No: SC015096</span>
</div>
</blockquote></div><br></div>
</blockquote></div><br></div>