[InterMine Dev] list in flymine

sergio contrino sergio at modencode.org
Mon Aug 17 15:41:20 BST 2015

Dear Tim,
i am happy that you are managing with the update. your message has been 
very useful, we are now thinking of making the simple id changes 
(synonyms) automatic, please let us know what you think (especially 
after your current updating experience..).
probably also our current interface could be clearer.
i think your list was in the upper part of the page because successfully 
upgraded (without intervention). i cc the list again, so if anyone has 
further comments will let you know.
any suggestion from you on how to make the process easier (but not much 
less transparent for the user) will be very welcome, and if you need any 
help with the current update please let us know.
thank you

On 17/08/15 15:12, Tim Karr wrote:
> Dear Sergio,
> Thanks so much for the prompt reply.  Actually on second thought this is
> a good time for me to cull some of these lists that are no longer
> used/needed!  So manual it is.  The one list that is a problem just
> happens to be the one I use the most!  Actually, while writing this
> email and looking more carefully at this VERY long list of Lists(!)
> noticed that the upper list (with the UP arrows) has the list I was
> looking for in the lower list!  Why is is not in the lower list with the
> others?  Very odd way to do the upgrade, am I the only one with this
> problem?  There are about 85 lists that need upgrading…, ugh!
> BTW, absolutely love FlyMine!  Best thing out there (minus these pesky
> upgrades!)
> Thanks again,
> cheers,
> Tim
>> On Aug 17, 2015, at 10:12 PM, sergio contrino <sergio at modencode.org
>> <mailto:sergio at modencode.org>> wrote:
>> Dear Tim,
>> FLyMine had a new release a few days ago. When this happens there is
>> the need to upgrade your lists to the new identifiers. For some list
>> there could be changes (e.g. an identifier becoming obsolete) and the
>> advantage of updating them manually is that you can verify the changes
>> done to the list.
>> if you prefer we could, i think, simply apply the changes without you
>> being made aware.
>> usually only a few of your lists will require your intervention.
>> could you also point to the corrupted list of proteins?
>> thank you
>> sergio
>> From: timkarr at kit.ac.jp <mailto:timkarr at kit.ac.jp>
>> Subject: Upgrade lists?  Lost lists?
>> Date: Mon, 17 Aug 2015 05:46:32 +0100
>> To: info at flymine.org <mailto:info at flymine.org>
>> Name: Tim Karr
>> Email: timkarr at kit.ac.jp <mailto:timkarr at kit.ac.jp>
>> FM has been working flawlessly until a few days ago when it suddenly
>> began what appeared to be an automatic of all of the list in MyMine.
>> After chugging along for a bit, it suddenly stopped and asked me to
>> "manually update my lists"?  All 200+?? This seems to be a non-starter
>> and it puts researchers in a difficult position to have invested so
>> much time into making the lists...
>> Also, please note that one of the lists I need is either lost or
>> corrupted somehow as the list name is present, but contains the wrong
>> list of proteins.
>> I hope you can help,
>> Thank you, TimKarr
>> ---- Current page: ----
>> /flymine/bagDetails.do?bagName=Protein+list+for+Drosophila+melanogaster+-+Sat+Jul+20+2013
>> ---- Current query: ----
>> <query name="" model="genomic" view="Protein.primaryIdentifier
>> Protein.primaryAccession Protein.organism.name"
>> longDescription=""><constraint path="Protein" op="IN" value="Protein
>> list for Drosophila melanogaster - Sat Jul 20 2013"/></query>
>> ---- Browser: ----
>> Mozilla/5.0 (Macintosh; Intel Mac OS X 10_10_5) AppleWebKit/600.8.9
>> (KHTML, like Gecko) Version/8.0.8 Safari/600.8.9
>> --
>> sergio contrino                  InterMine, University of Cambridge
>> https://sergiocontrino.github.io http://www.intermine.org
> --
> Timothy Karr
> Visiting International Research Fellow
> Drosophila Genetic Resource Center
> Kyoto Institute of Technology
> Saga Ippongi-cho, Ukyo-ku, Kyoto 616-8354, Japan
> Phone: 075-873-2660
> Facsimile: 075-861-088
> http://www.dgrc.kit.ac.jp
> blog: www.kurumakarr.me
> about.me/timkarr
> http://

sergio contrino                  InterMine, University of Cambridge
https://sergiocontrino.github.io           http://www.intermine.org

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