<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Jerome-<div><br></div><div>This is hugely useful feedback. </div><div><br></div><div>Responses in line.</div><div><br><div><div>On 22 Jul 2009, at 12:19, Jerome Avondo wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div><br>Hi,<br><br>I had a long meeting with our users, here at the John Innes Centre, about the OMERO platform and specifically the OMERO.insight and OMERO.importer.<br><br>This was to give them a good overview of the system, and try and identify how it would fit with our use cases, with the ultimate goal to get them to start using it.<br><br>A couple points came up which I thought I would report back,<br><br>Firstly, let me say overall impression is that it looks great, and is something we want/will to adopt for the whole lab. :)</div></blockquote><div><br></div><div>Ok, that is great. Please keep all feedback coming-- we love it!</div><br><blockquote type="cite"><div><br><br>Three main issues did however come up...<br><br>1) Project, Dataset...<br><br>The Project, Dataset hierarchy was something people found quite abstract, and did not really understand what this related to in their day to day. And by this I mean they found it related to many things, but just couldn't figure out what is, if any, the best way to use this...<br><br>Some cases were should Projects be the type of data it is, like confocal, light microscopy, optical projection tomography or the grant project or etc.. And then Datasets could be the type of the experiment or species or probe imaged or etc...<br><br>They found it very hard to relate these two entities to just single real world scenarios... And people came up with many many different ways this could be used...<br><br>So maybe this is something the OMERO community can help us with. What kind of things do you represent with the Project/Dataset hierarchy, is there any "best practice" I can guide them with?<br><br></div></blockquote><div><br></div><div>Yes, this can be confusing. The fact is that there is no mandated way to use "PDI", and users are free to use it in any way that suits them. For example, I use "Projects" to delineate high level classes of experiments, and Datasets to mean experiments. One postdoc in my lab makes every experiment a diiferent Project, named by date, and individual experimental conditions (ctrl, siRNA, etc.) as Datasets. Both work, and are, as far as we know, just fine.</div><div><br></div><div>However, you can imagine that people writing analysis tools against an OMERO API would define some pattern of PDI for processing: process all images in a Dataset, or a Project, but not both. My personal preference is that these applications should be mindful of the different approaches and support some flexibility (User chooses to process all images in a Dataset, or all images within defined Datasets in a Project). As you know the OMERO API supports this.</div><div><br></div><br><blockquote type="cite"><div>2) Data sharing...<br><br>In the lab we have a strong policy of data sharing, where the notion of users does not really exist. For example we use a wiki to publish/report/talk about our finding, where everyone can see everything and contribute to anything.</div></blockquote><div><br></div><div>Sounds great.</div><br><blockquote type="cite"><div><br><br>Likewise for our file store, this is a common network drive, where no data is divided on a per user basis.<br><br></div></blockquote><div><br></div><div>OK.</div><br><blockquote type="cite"><div>This is mainly done for data longevity, in that when people leave, we know where to find the ex-members data, as we all store our data in the same way. As what we found was when someone left, if they had their own personal way of storing data, then this would be very difficult for anyone else to actually find it again. What makes sense to you doesn't necessarily make sense to someone else, is the motto here really...</div></blockquote><div><br></div><div>Understood.</div><br><blockquote type="cite"><div><br><br>So when looking at the OMERO.insight people where a bit worried how each user can have their own data hierarchy, as this is something we have tried to stay away from. <br><br>What I thought we could do, was still manage the data on a per-user level but also have a special single account for the whole lab, and make sure all data is also kept in this common hierarchy, but there might be better ways to address this.</div></blockquote><div><br></div><div>OMERO supports this concept, and I suspect, you might like how this works.</div><div><br></div><blockquote type="cite"><div><br>I also see that in OMERO.insight that Projects/Datasets/Images seem to default as private. What implications does this exactly have? And I can't seem to find any way to change this status to public.</div></blockquote><div><br></div><div>You might remember OMERO-Beta3-- users within a group could see each other's data. Some people loved this, some people really did not like it-- just not what they need. So we needed to fix this. For various technical reasons, we needed to switch all exisiting databases back to all private, and ensure that was all OK. We did that in Beta4.0. That will enable us to allow users to set their own permissions in upcoming releases. </div><div><br></div><div>Once that is the case, you can set a separate account ("MyLab") and create new datasets by including images from other users within the group. This just makes links, and doesn't create any copies of the images or associated data.</div><div><br></div><div>As you know, our priorities for 4.1 have been set on the DataIn/Out issues and DataDupe by the feedback from the Paris mtg. We've been VERY focussed on all that. We very much want to get the permissions available for users to start playing with, but need to make sure this is ready to go. Once Josh and Jean-Marie are back from well-earned holidays, we'll talk about this and let you know where we stand.</div><div><br></div><blockquote type="cite"><div><br><br>3) Tags and importing...<br><br>People understood the power of Tags, and really liked it.<br><br>However there was some concern over how this happens after the import, and that this was really a recipe for people just not bothering to tag anything. People seemed to agree on at least a minimum of what we called core tags, like what species it is, probe used, etc.. This minimum is something that we found should be forced on data import. To ensure all data has a minimum description. There was also some concerns over how tags have to be added one by one, and this can quickly become tedious so the idea of templates for tags was something they liked.</div></blockquote><div><br></div><div>You're not the first to mention this-- a number of others have brought this up as well, in many contexts. Of course, there's the alternative view, that many have, summarised as "let me do what i want".</div><div><br></div><div>We very much want to look at this. Maybe one way to start is to use OMERO.editor to define a set of tags that your lab will use. It's templating functionality would be very good for that. We have various ideas about extending the integration of editor and insight, and this might help drive that. Of course, the BBSRC didn't fund our request for more funding for OMERO.editor, so we're trying to figure out what to do there. Any feedback would be most welcome. If you think we should build an annotation workflow during import (for all the reasons you mentioned), let us know.</div><br><blockquote type="cite"><div><br>That's really the main feedback I got at the meeting, the next meeting we will be having is defining what tags we use. As this is something we think we need to have a good stab at getting right from the start.</div></blockquote><div><br></div><div>Understood.</div><div> </div><blockquote type="cite"><div><br>Of course all I said here really only reflects how we would like to use OMERO and I understand this does not reflect the whole community as a whole. And the great thing is we can still implement our own clients/importers to customize OMERO to our needs...</div></blockquote><div><br></div><div>Exactly, that is what it fundamentally comes down to. We never expect to be able to do everything. Please let us know what we can do to help.</div><div><br></div><blockquote type="cite"><div><br>But nonetheless I thought this would be useful to firstly give you some feedback, and secondly check that we haven't misunderstood how it should be used, so if anything I've said is something you disagree with please do say so!</div></blockquote><div><br></div><div>Nope, it's all great!</div><div><br></div><div>Thanks so much! Gives us lots to discuss and mull over. Keep it coming. Our best to all your users!</div><div><br></div><div>Cheers,</div><div><br></div><div>Jason</div><br><blockquote type="cite"><div><br><br>J.<br><br>_________________________________________________________________<br>Celebrate a decade of Messenger with free winks, emoticons, display pics, and more.<br><a href="http://clk.atdmt.com/UKM/go/157562755/direct/01/">http://clk.atdmt.com/UKM/go/157562755/direct/01/</a><br>_______________________________________________<br>ome-users mailing list<br>ome-users@lists.openmicroscopy.org.uk<br>http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users<br></div></blockquote></div><br><div> <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-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: 0; "><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: <a href="http://www.dundee.ac.uk/lifesciences/swedlow/">http://www.dundee.ac.uk/lifesciences/swedlow/</a></span></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; "><span class="Apple-style-span" style="font-family: Helvetica; ">**************************</span></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><br></div></body></html>