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From: William P. <wil...@ya...> - 2010-02-24 03:43:44
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On Feb 21, 2010, at 2:18 PM, Hilmar Lapp wrote: > Bill - > > can you get me the total number of trees and how many (unique) taxa they represent that are currently in TreeBASE? > > I presume I can't obtain that number simply from the TB2 instance at NESCent because it would exclude the ones submitted since Jan 2009. > > -hilmar There are currently 6,528 trees that have about 117,000 distinct OTU labels, of which about 106,000 are mappable to about 60,000 distinct taxa. bp |
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From: William P. <wil...@ya...> - 2010-02-24 03:42:48
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I'm back. It's back up running. bp On Feb 23, 2010, at 8:10 AM, Rutger Vos wrote: > Hi, > > just got a tweet from Rod Page (with the snarky #fail tag) that > http://www.treebase.org/treebase/console.html is down. Does anyone > know what's up? > > Rutger > > -- > Dr. Rutger A. Vos > School of Biological Sciences > Philip Lyle Building, Level 4 > University of Reading > Reading > RG6 6BX > United Kingdom > Tel: +44 (0) 118 378 7535 > http://www.nexml.org > http://rutgervos.blogspot.com > > ------------------------------------------------------------------------------ > Download Intel® Parallel Studio Eval > Try the new software tools for yourself. Speed compiling, find bugs > proactively, and fine-tune applications for parallel performance. > See why Intel Parallel Studio got high marks during beta. > http://p.sf.net/sfu/intel-sw-dev > _______________________________________________ > Treebase-devel mailing list > Tre...@li... > https://lists.sourceforge.net/lists/listinfo/treebase-devel |
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From: Hilmar L. <hl...@ne...> - 2010-02-23 14:45:23
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The page is making queries to 130.132.27.194 which time out. I don't think anyone else other than Bill can remedy that. BTW TB1 was down for 2 weeks last year when Bill was away ... -hilmar On Feb 23, 2010, at 8:10 AM, Rutger Vos wrote: > Hi, > > just got a tweet from Rod Page (with the snarky #fail tag) that > http://www.treebase.org/treebase/console.html is down. Does anyone > know what's up? > > Rutger > > -- > Dr. Rutger A. Vos > School of Biological Sciences > Philip Lyle Building, Level 4 > University of Reading > Reading > RG6 6BX > United Kingdom > Tel: +44 (0) 118 378 7535 > http://www.nexml.org > http://rutgervos.blogspot.com > > ------------------------------------------------------------------------------ > Download Intel® Parallel Studio Eval > Try the new software tools for yourself. Speed compiling, find bugs > proactively, and fine-tune applications for parallel performance. > See why Intel Parallel Studio got high marks during beta. > http://p.sf.net/sfu/intel-sw-dev > _______________________________________________ > Treebase-devel mailing list > Tre...@li... > https://lists.sourceforge.net/lists/listinfo/treebase-devel -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : =========================================================== |
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From: Rutger V. <rut...@gm...> - 2010-02-23 13:17:57
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Hi, just got a tweet from Rod Page (with the snarky #fail tag) that http://www.treebase.org/treebase/console.html is down. Does anyone know what's up? Rutger -- Dr. Rutger A. Vos School of Biological Sciences Philip Lyle Building, Level 4 University of Reading Reading RG6 6BX United Kingdom Tel: +44 (0) 118 378 7535 http://www.nexml.org http://rutgervos.blogspot.com |
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From: Vladimir G. <vla...@du...> - 2010-02-22 16:48:26
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Bill, I am setting up an SQL script to update TI info, following your suggestions in an earlier email (below). Besides what you mentioned there, would you want to update table fields taxonvaiant.tb1legacyid and taxon.tb1legacyid? I first thought they should be updated by propagating the value of legacy_id from the taxon_labels.tab file. However, this column contains string values like "T98303", while tb1legacyid fields in the tables are declared as integers. So, should I patch the TB2 schema to use varchar for these fileds, update them with integers taken from the taxon_label_id field in the file, try to drop "T" and convert strings to integers, do nothing, or something else? Also, I'll set 1 in the 'version' field in all 3 tables, unless there is different advice. --Vladimir On Jan 28, 2010, at 11:27 PM, William Piel wrote: > > On Jan 28, 2010, at 6:19 PM, Vladimir Gapeyev wrote: > >> Here is one important piece of info I could not find: What is the >> meaning of each column in the taxon intelligence files >> (taxon_labels.tab, taxon_variants.tab, taxa.tab)? > > > taxon: > taxon_id (PK) > namebankid > namestring > ncbi_taxid > > taxon_variants: > taxon_variant_id (PK) > taxon_id (FK) > namebankid > namestring > fullnamestring > lexicalqualifier > > taxon_labels: > taxon_label_id (PK) > taxon_variant_id (FK) > legacy_id (from TreeBASE1) > taxon_label (from TreeBASE1 -- useful for mapping output from > headless Mesquite to TV table) > > I thing the process should go something like this: > > 1. In the taxonlabel table, update all values in the taxonvariant_id > column to NULL > 2. Delete all records in the taxonvariant and taxon tables. > 3. The first two files can be sucked straight into the taxa and > taxonvariant tables (the mapping among columns should be fairly > obvious -- let me know if you have questions) > 4. For mapping the taxonlabel table with the taxonvariant table, I'd > suggest that you upload the third file into a temporary table, and > then write an update statement to do the matching: use the last > column of the taxon_labels file to match against the taxonlabel > column in the taxonlabel table. Wherever there is a match, put the > value of the second column in the taxon_labels file in the > taxonvariant_id column of the taxonlabel table. Recall that in the > third file, each value in the last column (the "taxon_label") is > unique; by contrast, the taxonlabel column in the taxonlabel table > are not unique. > 5. Drop the temporary table. > > bp > > > > > > > > > ------------------------------------------------------------------------------ > The Planet: dedicated and managed hosting, cloud storage, colocation > Stay online with enterprise data centers and the best network in the > business > Choose flexible plans and management services without long-term > contracts > Personal 24x7 support from experience hosting pros just a phone call > away. > http://p.sf.net/sfu/theplanet-com > _______________________________________________ > Treebase-devel mailing list > Tre...@li... > https://lists.sourceforge.net/lists/listinfo/treebase-devel |
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From: Hilmar L. <hl...@ne...> - 2010-02-21 19:19:04
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Bill - can you get me the total number of trees and how many (unique) taxa they represent that are currently in TreeBASE? I presume I can't obtain that number simply from the TB2 instance at NESCent because it would exclude the ones submitted since Jan 2009. -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : =========================================================== |
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From: Rutger V. <rut...@gm...> - 2010-02-19 21:07:46
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Done. On Fri, Feb 19, 2010 at 8:39 PM, youjun guo <you...@gm...> wrote: > Hi,Rutger > > I just fix "Bugs item #2947925", can you re-build and deploy the TreeBase? > > Thanks > > Youjun > > ------------------------------------------------------------------------------ > Download Intel® Parallel Studio Eval > Try the new software tools for yourself. Speed compiling, find bugs > proactively, and fine-tune applications for parallel performance. > See why Intel Parallel Studio got high marks during beta. > http://p.sf.net/sfu/intel-sw-dev > _______________________________________________ > Treebase-devel mailing list > Tre...@li... > https://lists.sourceforge.net/lists/listinfo/treebase-devel > > -- Dr. Rutger A. Vos School of Biological Sciences Philip Lyle Building, Level 4 University of Reading Reading RG6 6BX United Kingdom Tel: +44 (0) 118 378 7535 http://www.nexml.org http://rutgervos.blogspot.com |
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From: youjun g. <you...@gm...> - 2010-02-19 20:39:10
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Hi,Rutger I just fix "Bugs item #2947925", can you re-build and deploy the TreeBase? Thanks Youjun |
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From: Hilmar L. <hl...@ne...> - 2010-02-18 22:24:06
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We won't go live until the first week of March. -hilmar On Feb 18, 2010, at 5:12 PM, Jon Auman wrote: > I've got on my calendar to make the switch today. Bill got me setup > to make the DNS changes to point treebase.org to the NESCent server. > Is that still the plan, or has that been changed? > > The current URL for the current production system is: > http://treebase.nescent.org/ > > I'll not do anything until I get a definite go ahead. > > -Jon > ------------------------------------------------------- > Jon Auman > Systems Administrator > National Evolutionary Synthesis Center > Duke University > http:www.nescent.org > jon...@ne... > ------------------------------------------------------ > > > > ------------------------------------------------------------------------------ > Download Intel® Parallel Studio Eval > Try the new software tools for yourself. Speed compiling, find bugs > proactively, and fine-tune applications for parallel performance. > See why Intel Parallel Studio got high marks during beta. > http://p.sf.net/sfu/intel-sw-dev_______________________________________________ > Treebase-devel mailing list > Tre...@li... > https://lists.sourceforge.net/lists/listinfo/treebase-devel -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : =========================================================== |
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From: Jon A. <jon...@ne...> - 2010-02-18 22:12:43
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I've got on my calendar to make the switch today. Bill got me setup to make the DNS changes to point treebase.org to the NESCent server. Is that still the plan, or has that been changed? The current URL for the current production system is: http://treebase.nescent.org/ I'll not do anything until I get a definite go ahead. -Jon ------------------------------------------------------- Jon Auman Systems Administrator National Evolutionary Synthesis Center Duke University http:www.nescent.org jon...@ne... ------------------------------------------------------ |
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From: youjun g. <you...@ya...> - 2010-02-17 15:05:28
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I wonder why the page was set up that way, Rutger, do you know some background of this? Youjun On Wed, Feb 17, 2010 at 9:51 AM, Vladimir Gapeyev <vla...@du... > wrote: > > I'd suggest to keep the ticket open: a buggy feature is a bug. This one > would make it too easy for 2-3 users to bring even our production server to > a crawl, not to mention their frustration. > --VG > > > On Feb 17, 2010, at 9:41 AM, youjun guo wrote: > > This is the behavior it suppose to be. I will suggest we close the ticket > for now, and discuss with Bill about modifying the way it work after > release. > > Youjun > > > > On Wed, Feb 17, 2010 at 9:22 AM, Vladimir Gapeyev < > vla...@du...> wrote: > >> >> It could be. If this indeed is what happens, the question becomes whether >> this behavior is a bug or a buggy feature? >> --VG >> >> On Feb 17, 2010, at 6:51 AM, youjun guo wrote: >> >> Vladimir, >> >> At that specific page, if user keep switching tags between taxa, tree and >> matrix without discard the previous search results, the output of first >> operation will turn to the input of next when user click on those tags. The >> result set will accumulate very fast and easily hang up. >> >> Could this be the cause of the problem in your ticket? >> >> >> Youjun >> >> On Tue, Feb 16, 2010 at 8:16 PM, Vladimir Gapeyev < >> vla...@du...> wrote: >> >>> >>> Jon and I have closed two recent tickets (increasing apache proxy timeout >>> and creating indexes to spet up tree reconstruction) related to the problem >>> that clicking on some tabs in search results would hang forever. It now >>> appears there is (are?) application issues contributing to this behavior, >>> see >>> >>> https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2953212&group_id=248804 >>> >>> Unless someone knows right away what may be going on, figuring this out >>> can be a major project. (To start, one would need to reproduce the behavior >>> on a local DB, since bugging Jon to kill server processes after each new >>> hang-up would not be feasible.) >>> >>> --Vladimir >>> >>> >>> >>> ------------------------------------------------------------------------------ >>> SOLARIS 10 is the OS for Data Centers - provides features such as DTrace, >>> Predictive Self Healing and Award Winning ZFS. Get Solaris 10 NOW >>> http://p.sf.net/sfu/solaris-dev2dev >>> _______________________________________________ >>> Treebase-devel mailing list >>> Tre...@li... >>> https://lists.sourceforge.net/lists/listinfo/treebase-devel >>> >>> >> >> >> >> ------------------------------------------------------------------------------ >> SOLARIS 10 is the OS for Data Centers - provides features such as DTrace, >> Predictive Self Healing and Award Winning ZFS. Get Solaris 10 NOW >> http://p.sf.net/sfu/solaris-dev2dev >> _______________________________________________ >> Treebase-devel mailing list >> Tre...@li... >> https://lists.sourceforge.net/lists/listinfo/treebase-devel >> >> > > > > ------------------------------------------------------------------------------ > SOLARIS 10 is the OS for Data Centers - provides features such as DTrace, > Predictive Self Healing and Award Winning ZFS. Get Solaris 10 NOW > http://p.sf.net/sfu/solaris-dev2dev > _______________________________________________ > Treebase-devel mailing list > Tre...@li... > https://lists.sourceforge.net/lists/listinfo/treebase-devel > > |
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From: Vladimir G. <vla...@du...> - 2010-02-17 14:51:49
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I'd suggest to keep the ticket open: a buggy feature is a bug. This one would make it too easy for 2-3 users to bring even our production server to a crawl, not to mention their frustration. --VG On Feb 17, 2010, at 9:41 AM, youjun guo wrote: > This is the behavior it suppose to be. I will suggest we close the > ticket for now, and discuss with Bill about modifying the way it > work after release. > > Youjun > > > > On Wed, Feb 17, 2010 at 9:22 AM, Vladimir Gapeyev <vla...@du... > > wrote: > > It could be. If this indeed is what happens, the question becomes > whether this behavior is a bug or a buggy feature? > --VG > > On Feb 17, 2010, at 6:51 AM, youjun guo wrote: > >> Vladimir, >> >> At that specific page, if user keep switching tags between taxa, >> tree and matrix without discard the previous search results, the >> output of first operation will turn to the input of next when user >> click on those tags. The result set will accumulate very fast and >> easily hang up. >> >> Could this be the cause of the problem in your ticket? >> >> >> Youjun >> >> On Tue, Feb 16, 2010 at 8:16 PM, Vladimir Gapeyev <vla...@du... >> > wrote: >> >> Jon and I have closed two recent tickets (increasing apache proxy >> timeout and creating indexes to spet up tree reconstruction) >> related to the problem that clicking on some tabs in search results >> would hang forever. It now appears there is (are?) application >> issues contributing to this behavior, see >> https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2953212&group_id=248804 >> >> Unless someone knows right away what may be going on, figuring this >> out can be a major project. (To start, one would need to reproduce >> the behavior on a local DB, since bugging Jon to kill server >> processes after each new hang-up would not be feasible.) >> >> --Vladimir >> >> >> ------------------------------------------------------------------------------ >> SOLARIS 10 is the OS for Data Centers - provides features such as >> DTrace, >> Predictive Self Healing and Award Winning ZFS. Get Solaris 10 NOW >> http://p.sf.net/sfu/solaris-dev2dev >> _______________________________________________ >> Treebase-devel mailing list >> Tre...@li... >> https://lists.sourceforge.net/lists/listinfo/treebase-devel >> >> > > > ------------------------------------------------------------------------------ > SOLARIS 10 is the OS for Data Centers - provides features such as > DTrace, > Predictive Self Healing and Award Winning ZFS. Get Solaris 10 NOW > http://p.sf.net/sfu/solaris-dev2dev > _______________________________________________ > Treebase-devel mailing list > Tre...@li... > https://lists.sourceforge.net/lists/listinfo/treebase-devel > > |
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From: youjun g. <you...@ya...> - 2010-02-17 14:41:52
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This is the behavior it suppose to be. I will suggest we close the ticket for now, and discuss with Bill about modifying the way it work after release. Youjun On Wed, Feb 17, 2010 at 9:22 AM, Vladimir Gapeyev <vla...@du... > wrote: > > It could be. If this indeed is what happens, the question becomes whether > this behavior is a bug or a buggy feature? > --VG > > On Feb 17, 2010, at 6:51 AM, youjun guo wrote: > > Vladimir, > > At that specific page, if user keep switching tags between taxa, tree and > matrix without discard the previous search results, the output of first > operation will turn to the input of next when user click on those tags. The > result set will accumulate very fast and easily hang up. > > Could this be the cause of the problem in your ticket? > > > Youjun > > On Tue, Feb 16, 2010 at 8:16 PM, Vladimir Gapeyev < > vla...@du...> wrote: > >> >> Jon and I have closed two recent tickets (increasing apache proxy timeout >> and creating indexes to spet up tree reconstruction) related to the problem >> that clicking on some tabs in search results would hang forever. It now >> appears there is (are?) application issues contributing to this behavior, >> see >> >> https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2953212&group_id=248804 >> >> Unless someone knows right away what may be going on, figuring this out >> can be a major project. (To start, one would need to reproduce the behavior >> on a local DB, since bugging Jon to kill server processes after each new >> hang-up would not be feasible.) >> >> --Vladimir >> >> >> >> ------------------------------------------------------------------------------ >> SOLARIS 10 is the OS for Data Centers - provides features such as DTrace, >> Predictive Self Healing and Award Winning ZFS. Get Solaris 10 NOW >> http://p.sf.net/sfu/solaris-dev2dev >> _______________________________________________ >> Treebase-devel mailing list >> Tre...@li... >> https://lists.sourceforge.net/lists/listinfo/treebase-devel >> >> > > > > ------------------------------------------------------------------------------ > SOLARIS 10 is the OS for Data Centers - provides features such as DTrace, > Predictive Self Healing and Award Winning ZFS. Get Solaris 10 NOW > http://p.sf.net/sfu/solaris-dev2dev > _______________________________________________ > Treebase-devel mailing list > Tre...@li... > https://lists.sourceforge.net/lists/listinfo/treebase-devel > > |
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From: Vladimir G. <vla...@du...> - 2010-02-17 14:22:44
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It could be. If this indeed is what happens, the question becomes whether this behavior is a bug or a buggy feature? --VG On Feb 17, 2010, at 6:51 AM, youjun guo wrote: > Vladimir, > > At that specific page, if user keep switching tags between taxa, > tree and matrix without discard the previous search results, the > output of first operation will turn to the input of next when user > click on those tags. The result set will accumulate very fast and > easily hang up. > > Could this be the cause of the problem in your ticket? > > > Youjun > > On Tue, Feb 16, 2010 at 8:16 PM, Vladimir Gapeyev <vla...@du... > > wrote: > > Jon and I have closed two recent tickets (increasing apache proxy > timeout and creating indexes to spet up tree reconstruction) related > to the problem that clicking on some tabs in search results would > hang forever. It now appears there is (are?) application issues > contributing to this behavior, see > https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2953212&group_id=248804 > > Unless someone knows right away what may be going on, figuring this > out can be a major project. (To start, one would need to reproduce > the behavior on a local DB, since bugging Jon to kill server > processes after each new hang-up would not be feasible.) > > --Vladimir > > > ------------------------------------------------------------------------------ > SOLARIS 10 is the OS for Data Centers - provides features such as > DTrace, > Predictive Self Healing and Award Winning ZFS. Get Solaris 10 NOW > http://p.sf.net/sfu/solaris-dev2dev > _______________________________________________ > Treebase-devel mailing list > Tre...@li... > https://lists.sourceforge.net/lists/listinfo/treebase-devel > > |
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From: youjun g. <you...@ya...> - 2010-02-17 11:51:13
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Vladimir, At that specific page, if user keep switching tags between taxa, tree and matrix without discard the previous search results, the output of first operation will turn to the input of next when user click on those tags. The result set will accumulate very fast and easily hang up. Could this be the cause of the problem in your ticket? Youjun On Tue, Feb 16, 2010 at 8:16 PM, Vladimir Gapeyev <vla...@du... > wrote: > > Jon and I have closed two recent tickets (increasing apache proxy timeout > and creating indexes to spet up tree reconstruction) related to the problem > that clicking on some tabs in search results would hang forever. It now > appears there is (are?) application issues contributing to this behavior, > see > > https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2953212&group_id=248804 > > Unless someone knows right away what may be going on, figuring this out can > be a major project. (To start, one would need to reproduce the behavior on > a local DB, since bugging Jon to kill server processes after each new > hang-up would not be feasible.) > > --Vladimir > > > > ------------------------------------------------------------------------------ > SOLARIS 10 is the OS for Data Centers - provides features such as DTrace, > Predictive Self Healing and Award Winning ZFS. Get Solaris 10 NOW > http://p.sf.net/sfu/solaris-dev2dev > _______________________________________________ > Treebase-devel mailing list > Tre...@li... > https://lists.sourceforge.net/lists/listinfo/treebase-devel > > |
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From: Vladimir G. <vla...@du...> - 2010-02-17 01:16:13
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Jon and I have closed two recent tickets (increasing apache proxy timeout and creating indexes to spet up tree reconstruction) related to the problem that clicking on some tabs in search results would hang forever. It now appears there is (are?) application issues contributing to this behavior, see https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2953212&group_id=248804 Unless someone knows right away what may be going on, figuring this out can be a major project. (To start, one would need to reproduce the behavior on a local DB, since bugging Jon to kill server processes after each new hang-up would not be feasible.) --Vladimir |
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From: Arlin S. <sto...@um...> - 2010-02-16 17:34:54
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It doesn't bother me. I'm thinking of has_External_Reference as kind of a kludge, but thats only because its not sub-classed in a reasonable way. Arlin On Feb 16, 2010, at 10:58 AM, Rutger Vos wrote: > Hi all, > > I had a Twitter discussion with Rod Page about the correct predicate > for linking treebase objects, through either NeXML or CDAO, to > external taxonomies. We're now using cdao:has_External_Reference for > these relations, but perhaps it makes more sense to use > skos:closeMatch or skos:exactMatch for this. How do you feel about > this? > > Rutger > > -- > Dr. Rutger A. Vos > School of Biological Sciences > Philip Lyle Building, Level 4 > University of Reading > Reading > RG6 6BX > United Kingdom > Tel: +44 (0) 118 378 7535 > http://www.nexml.org > http://rutgervos.blogspot.com > > ------------------------------------------------------------------------------ > SOLARIS 10 is the OS for Data Centers - provides features such as > DTrace, > Predictive Self Healing and Award Winning ZFS. Get Solaris 10 NOW > http://p.sf.net/sfu/solaris-dev2dev > _______________________________________________ > Nexml-discuss mailing list > Nex...@li... > https://lists.sourceforge.net/lists/listinfo/nexml-discuss ------- Arlin Stoltzfus (sto...@um...) Fellow, CARB; Adj. Assoc. Prof., UMBI; Research Biologist, NIST CARB, 9600 Gudelsky Drive, Rockville, MD tel: 240 314 6208; web: www.molevol.org |
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From: Rutger V. <rut...@gm...> - 2010-02-16 15:58:57
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Hi all, I had a Twitter discussion with Rod Page about the correct predicate for linking treebase objects, through either NeXML or CDAO, to external taxonomies. We're now using cdao:has_External_Reference for these relations, but perhaps it makes more sense to use skos:closeMatch or skos:exactMatch for this. How do you feel about this? Rutger -- Dr. Rutger A. Vos School of Biological Sciences Philip Lyle Building, Level 4 University of Reading Reading RG6 6BX United Kingdom Tel: +44 (0) 118 378 7535 http://www.nexml.org http://rutgervos.blogspot.com |
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From: Arlin S. <sto...@um...> - 2010-02-16 15:57:41
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If you folks could give the CDAO group a specific use-case or user scenario involving a segmented alignment, with data, we can try to represent it using current CDAO concepts, and if thats not possible, we'll explore possible revisions. I'm imagining that the use case is going to be something like this. There is a character-data-and-trees thing based on sequence data, in which the "alignment" is a hybrid in which, for a given OTU, the row that belongs to the OTU combines multiple data sources. A specific example would be that for a species called OTU1, the first part of the sequence comes from specimen (isolate, strain) A of that species, and the second part comes from specimen B which was sequenced in a different lab. For OTU2, it might be the case that the whole sequence comes from one specimen. To complete this use case, we would like to know what kinds of queries or operations need to be supported. Arlin ------- Arlin Stoltzfus (sto...@um...) Fellow, CARB; Adj. Assoc. Prof., UMBI; Research Biologist, NIST CARB, 9600 Gudelsky Drive, Rockville, MD tel: 240 314 6208; web: www.molevol.org On Feb 12, 2010, at 4:25 PM, Francisco Prosdocimi wrote: > Hi Hilmar, > > -----Mensagem original----- > De: Hilmar Lapp [mailto:hl...@ne...] >> If the alignment isn't concatenated with sequences from multiple >> specimens, couldn't (in fact, shouldn't) you attach the lat/long to >> the OTU, though? I.e., where do you attach the specimen currently, >> and >> it do you attach lat/long in a different fashion than the specimen? > > If I understood well the problem... > CDAO presents an OTU annotation concept, and users can instantiate > it with any desirable information about the specimen, such as lat/ > long. > One can also develop and inherit other ontologies into CDAO to > provide more sophisticated concepts for specific applications and > annotations. > > >> CDAOers: what are status and plans for describing the parts of an >> alignment right now, and is there support, current or planned, for >> partitions / segments of an alignment? > > Current CDAO version has already incorporated Julie's Multiple > Alignment Ontology (MAO; Thompson et al., 2005). > MAO presents concepts such as "domain" and "subalignment", I suppose > they can be used in this context. > > Ciao, > Francisco > > > > -- > Prof. Francisco Prosdocimi, PhD > ----------------------------- > Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia > Universidade Católica de Brasília - UCB > SGAN 916 Módulo B, Bloco C Sala 213 > 70.790-160 - Brasília / DF - Brasil > Fone: +55 61 34487173 > http://biotec.icb.ufmg.br/chicopros > > ------------------------------------------------------------------------------ > SOLARIS 10 is the OS for Data Centers - provides features such as > DTrace, > Predictive Self Healing and Award Winning ZFS. Get Solaris 10 NOW > http://p.sf.net/sfu/solaris-dev2dev > _______________________________________________ > CDAO-discuss mailing list > CDA...@li... > https://lists.sourceforge.net/lists/listinfo/cdao-discuss |
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From: Matt <dia...@gm...> - 2010-02-15 19:03:21
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A coordinate system would be nice. It, or something similar, would be necessary for structural alignments which predict pairing of individual sites separated by some number of nucleotides (e.g. positions 2 and 34 pair). Many visualization programs also use co-ordinates on individual nucleotides. It might be better though to abstract coordinates given context, to only calculate the "absolute" coordinates on demand. A paired structure, as above, could be tied together via ids(?), then translated/transformed to particular coordinates based on the context. In real life MSAs will be truncated, extended, extracted from, concatenated etc. etc., coordinate management could be come a big overhead. Matt On Mon, Feb 15, 2010 at 11:57 AM, Arlin Stoltzfus <sto...@um...> wrote: > On Feb 12, 2010, at 9:38 AM, Hilmar Lapp wrote: > >> CDAOers: what are status and plans for describing the parts of an >> alignment right now, and is there support, current or planned, for >> partitions / segments of an alignment? > > Right now there is not even a fully worked out concept of sequence, > only states of characters. So, in the matrix: > > OTU1 TCAAG > OTU2 TAAAG > > there is no "sequence" concept telling us that "T" and "C" in OTU1 are > sequentially ordered residues. They are treated just like classical > character states in that sense. > > One way to deal with this is via MAO, the multiple alignment > ontology. We developed a mapping between MAO and CDAO last summer > that might be useful for this. MAO has a concept of sub-alignments > that might be useful here. > > Also, in CDAO there is a "coordinate system" concept that we intended > to use to impose a mapping on characters in a sequence. The concept > has not been fleshed out yet. > > If there is a coordinate system CS1, with "T" and "C" assigned > coordinates "1" and "2", and another coordinate system CS2 with "A", > "A", and "G" assigned coordinates "1", "2" and "3", then this would be > a way to represent that the data from OTU1 come from 2 different > sequences. > > Arlin > > > ------------------------------------------------------------------------------ > SOLARIS 10 is the OS for Data Centers - provides features such as DTrace, > Predictive Self Healing and Award Winning ZFS. Get Solaris 10 NOW > http://p.sf.net/sfu/solaris-dev2dev > _______________________________________________ > CDAO-discuss mailing list > CDA...@li... > https://lists.sourceforge.net/lists/listinfo/cdao-discuss > |
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From: Rutger V. <rut...@gm...> - 2010-02-15 18:16:15
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OK, so this is up and running. The property is called "treebase.purl.domain", the method is getPurlDomain(), and the value is "http://purl.org/phylo/treebase/phylows/". This purl subdomain is administered by Hilmar, Bill and myself (since the db interop hackathon, if I recall correctly) and now points to treebase-dev.nescent.org:6666. As a side note, the URL equivalence issue that Bill notes (is a treebase.org URL the same as a purl?) is of course a hairy issue, especially if we also consider other data resources. The consensus from the BioHackathon in Tokyo this week is that one should use URLs as identifiers, that one should be using the *canonical* URLs as recommended by the data resource, that if worst comes to worst (i.e. one has become dependent on non-standard URLs) one should define owl:sameAs so that the resources are collapsed into one. This is supposed to become known as the Tokyo Manifesto, according to the more pompous attendants to the meeting. Rutger On Fri, Jan 15, 2010 at 9:25 PM, Hilmar Lapp <hl...@ne...> wrote: > > On Jan 15, 2010, at 4:17 PM, Vladimir Gapeyev wrote: > >> >> On Jan 14, 2010, at 4:38 PM, Hilmar Lapp wrote: >> >>> I don't see a problem if for the time being PURL URIs always go to >>> production regardless of origin. That is not different, for example, >>> for Dryad, where all handle URIs resolve to production, whether they >>> originate from development or production, or if we used DOIs. >> >> This would resolve my concerns. (That is, in all instances, >> treebase.domain.name / treebase.purl.domain always contains the same >> value, "purl.org" or "treebase.org"). > > Right. > > -hilmar > > > -- > =========================================================== > : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : > =========================================================== > > > > > ------------------------------------------------------------------------------ > Throughout its 18-year history, RSA Conference consistently attracts the > world's best and brightest in the field, creating opportunities for Conference > attendees to learn about information security's most important issues through > interactions with peers, luminaries and emerging and established companies. > http://p.sf.net/sfu/rsaconf-dev2dev > _______________________________________________ > Treebase-devel mailing list > Tre...@li... > https://lists.sourceforge.net/lists/listinfo/treebase-devel > -- Dr. Rutger A. Vos School of Biological Sciences Philip Lyle Building, Level 4 University of Reading Reading RG6 6BX United Kingdom Tel: +44 (0) 118 378 7535 http://www.nexml.org http://rutgervos.blogspot.com |
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From: Arlin S. <sto...@um...> - 2010-02-15 16:57:55
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On Feb 12, 2010, at 9:38 AM, Hilmar Lapp wrote: > CDAOers: what are status and plans for describing the parts of an > alignment right now, and is there support, current or planned, for > partitions / segments of an alignment? Right now there is not even a fully worked out concept of sequence, only states of characters. So, in the matrix: OTU1 TCAAG OTU2 TAAAG there is no "sequence" concept telling us that "T" and "C" in OTU1 are sequentially ordered residues. They are treated just like classical character states in that sense. One way to deal with this is via MAO, the multiple alignment ontology. We developed a mapping between MAO and CDAO last summer that might be useful for this. MAO has a concept of sub-alignments that might be useful here. Also, in CDAO there is a "coordinate system" concept that we intended to use to impose a mapping on characters in a sequence. The concept has not been fleshed out yet. If there is a coordinate system CS1, with "T" and "C" assigned coordinates "1" and "2", and another coordinate system CS2 with "A", "A", and "G" assigned coordinates "1", "2" and "3", then this would be a way to represent that the data from OTU1 come from 2 different sequences. Arlin |
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From: youjun g. <you...@ya...> - 2010-02-15 16:39:30
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Jon and Vladimir, I am working on the bug 2945410, it looks like a Apache server problem because: 1. the error massage is quite Apache style Proxy Error The proxy server received an invalid response from an upstream server. The proxy server could not handle the request GET /treebase-web/search/treeSearch.html." Reason: Error reading from remote serve 2. Bill's complain If I do a taxon search (e.g. search for "Homo sapiens" as taxon variant name under the Taxa tab), and then click on the Trees tab (i.e. to get a selection of trees based on the selection of two Homo sapiens records) I get the proxy error below after exactly 2 minutes. and based on my test this same operation will need at least six and half mins in my person tomcat (without a Apache server in front of it). can you guys check the Apache setup to make sure "keepalives" and "timeout" if any are setup properly? Youjun |
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From: Todd V. <tj...@bi...> - 2010-02-15 13:20:11
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> Lastly, TreeBASE's system of annotating row segments allows multiple annotations for the same character elements. e.g. you can attach, say, 20 lat/long pairs and specimen IDs to the same row segment. This is particularly valuable for morphological data, in which the character scorings are applied to a set of identifiable specimens that were examined. But this does not mean that all characters were scored from the same specimens (if for no other reason that some characters can only be scored from males, others only from females). I would hate to see this valuable chain of provenance lost through the effect of "homogenizing" at the point of serialization. This is consistent with the model in Phenoscape, as well, in that each phenotype annotation for a given taxon is tied to zero, one or more specimens, and the specimens need not correspond among different phenotypes for the same taxon. Todd |
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From: Rutger V. <rut...@gm...> - 2010-02-15 12:52:48
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Ok, adding that info to treebase-web.xml has fixed things on 6666 On Fri, Feb 12, 2010 at 2:32 AM, Jon Auman via RT <he...@ne...> wrote: > Bill, > > OK. I fixed it (again). There are two things that need to be set for mesquite to work: > > 1)Add this to the Tomcat startup script: > > # Headless mesquite needs a window server (a virtual one is OK) > export DISPLAY=localhost:1.0 > > 2) Add this to the CATALINA_HOME/conf/Catalina/localhost/treebase-web.xml file: > > <Environment name="tb2/MesquiteFolder" value="/home/treebasedev/mesquite- > 2.01.tb" > type="java.lang.String" override="false" > description="Absolute path to the directory where headless Mesquite is unpacked on > the host system."/> > > I had changed the path for treebasedev home directory, and forgot to change it in treebase- > web.xml. It's in my notes now and I'll make sure its gets entered in the treebase wiki at > Sourceforge. > > > BTW, the output form uploading the test file you sent me yesterday is: > > File upload summary: > One matrix uploaded > One tree uploaded > > > The Parser Log: > Reading NEXUS file testfile.nex > Reading special block: DATA > Reading block: CODONS > Reading block: TREES > Reading block: ASSUMPTIONS > Reading block: Mesquite > NOTICE null > ************************* > The current release version of Mesquite is 2.72 build 527 (the version you have installed is > 2.01). The latest version is downloadable at: > http://mesquiteproject.org/mesquite/download/download.html > ************************* > > File reading complete (file testfile.nex) > > -Jon > > On Thu Feb 11 04:55:15 2010, wil...@ya... wrote: >> >> On Feb 9, 2010, at 4:59 PM, Jon Auman wrote: >> >> > Bill, >> > >> > This has been fixed. Mesquite requires that the tomcat startup >> script export the display >> >> Hi Jon, >> >> Thanks for whatever you did... but I still can't seem to upload any >> nexus files... I get a "File upload summary: No matrices or trees >> uploaded" message. I'm using the dev instance -- tried it with >> both the port 80 and port 6666 builds. Is there a particular >> deployment that I should be testing? (attached is a test file, if >> you need something to try). >> >> Bill >> >> >> > > > -- > Jon Auman > NESCent, Systems Administrator > jon...@ne... > 919-627-2708 > > > > For more info: > Ticket <URL: https://help.nescent.org/Ticket/Display.html?id=7349 > > > > ------------------------------------------------------------------------------ > SOLARIS 10 is the OS for Data Centers - provides features such as DTrace, > Predictive Self Healing and Award Winning ZFS. Get Solaris 10 NOW > http://p.sf.net/sfu/solaris-dev2dev > _______________________________________________ > Treebase-devel mailing list > Tre...@li... > https://lists.sourceforge.net/lists/listinfo/treebase-devel > -- Dr. Rutger A. Vos School of Biological Sciences Philip Lyle Building, Level 4 University of Reading Reading RG6 6BX United Kingdom Tel: +44 (0) 118 378 7535 http://www.nexml.org http://rutgervos.blogspot.com |
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