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From: Hilmar L. <hl...@ne...> - 2011-06-03 12:59:56
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How long do you expect the downtime to be? Since this is production, is there a chance that this can be scheduled during or closer to what would be off-hours at least in the Americas? E.g., 8am Eastern or earlier? -hilmar Sent with a tap. On Jun 3, 2011, at 6:27 AM, David Palmer <dav...@ne...> wrote: > NESCent would like to schedule a build on the production TreeBASE site to the latest version. We are tentatively scheduling this change for 2:00 pm EST. Please let me know if you have questions or concerns. > > David Palmer > NESCent > IT Analyst > "dav...@ne..." > 919 668 6520 > ------------------------------------------------------------------------------ > Simplify data backup and recovery for your virtual environment with vRanger. > Installation's a snap, and flexible recovery options mean your data is safe, > secure and there when you need it. Discover what all the cheering's about. > Get your free trial download today. > http://p.sf.net/sfu/quest-dev2dev2 > _______________________________________________ > Treebase-devel mailing list > Tre...@li... > https://lists.sourceforge.net/lists/listinfo/treebase-devel |
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From: David P. <dav...@ne...> - 2011-06-03 12:50:07
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NESCent would like to schedule a build on the production TreeBASE site to the latest version. We are tentatively scheduling this change for 2:00 pm EST. Please let me know if you have questions or concerns. David Palmer NESCent IT Analyst "dav...@ne..." 919 668 6520 |
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From: David P. <dav...@ne...> - 2011-06-03 12:41:03
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NESCent would like to schedule a password change for the TreeBASE service account on the development server. This change is tentatively being set for 3:00 pm EST. Please let me know if you have questions or concerns. Thanks, David David Palmer NESCent IT Analyst "dav...@ne..." |
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From: Rutger V. <rut...@gm...> - 2011-06-02 20:28:18
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I think posting to the mailing list is a pretty good approach, certainly better than having individual people sign off on it in a way that is not discussed and logged in a public forum. It would be good to allow enough time for responses to come in though, at least from Harry, Bill and I in addition to whoever else is actively contributing at any time. On Thu, Jun 2, 2011 at 9:17 PM, David Palmer <dav...@ne...> wrote: > I have been asked to deploy the development version of TreeBASE to > production. With Jon Auman leaving NESCent, I want to establish a > procedure that is acceptable to everyone. Who should I be getting an Ok > from before deploying to production and is sending a notice to the > TreeBASE developers list adequate for announcing the change > (https://lists.sourceforge.net/lists/listinfo/treebase-devel)? Thank you > in advance for you input. > > David Palmer > IT Analyst > NESCent > 919 668 6520 > > On 6/2/11 4:07 PM, "Shyket, Harry via RT" <hel...@ne...> wrote: > >> >><URL: https://help.nescent.org/Ticket/Display.html?id=11218 > >> >>Rutger should be notified (although he should be on treebase-devel). >>Also someone named loloyohe has made some commits as well. >> >>Harry Shyket >>Digital Media Specialist >>Yale University Peabody Museum >>ph. 203-436-9428 >>har...@ya... >> >> >>-----Original Message----- >>From: David Palmer via RT [mailto:hel...@ne...] >>Sent: Thursday, June 02, 2011 4:01 PM >>To: Shyket, Harry >>Subject: Re: [help.nescent.org #11218] Updating robots.txt on TreeBASE >> >>I can assist with this also. Do I need to warn anyone prior to the >>deployment (https://lists.sourceforge.net/lists/listinfo/treebase-devel). >> >>Thanks, David >> >>On 6/2/11 3:57 PM, "Shyket, Harry via RT" <hel...@ne...> wrote: >> >>> >>><URL: https://help.nescent.org/Ticket/Display.html?id=11218 > >>> >>>Thanks! >>> >>>I also made a request to Hilmar (he...@ne...) for deployment from >>>dev to production. >>> >>>Harry Shyket >>>Digital Media Specialist >>>Yale University Peabody Museum >>>ph. 203-436-9428 >>>har...@ya... >>> >>> >>>-----Original Message----- >>>From: David Palmer via RT [mailto:hel...@ne...] >>>Sent: Thursday, June 02, 2011 3:54 PM >>>To: Shyket, Harry >>>Subject: [help.nescent.org #11218] Updating robots.txt on TreeBASE >>> >>>I have made the changes to the "robots.txt" file on the production >>>version of >>>Treebase. >>> >>>Thanks, David >>> >>>On Thu Jun 02 15:36:22 2011, hlapp wrote: >>>> Yes, this looks OK and feel free to deploy it. >>>> >>>> -hilmar >>>> >>>> On Jun 2, 2011, at 11:44 AM, David Palmer via RT wrote: >>>> >>>> > >>>> > https://help.nescent.org/Ticket/Display.html?id=11218 >>>> > This is a comment. It is not sent to the Requestor(s): >>>> > >>>> > Hilmar, >>>> > >>>> > If you are ok with Harry's changes, I will update the robot.txt file >>>> > on the >>>> > Treebase production server. >>>> > >>>> > Thanks, David >>>> > >>>> > On Thu Jun 02 12:40:52 2011, har...@ya... wrote: >>>> >> Hi Hilmar, >>>> >> >>>> >> I have updated the contents. I believe that this should >>>> >> work. The only way to really test it is to see what happens once it >>>> >> is on production. >>>> >> >>>> >> User-agent: Googlebot >>>> >> User-agent: Yahoo! Slurp >>>> >> User-agent: msnbot >>>> >> Disallow: /treebase-web/search/studySearch.html >>>> >> Disallow: /treebase-web/search/matrixSearch.html >>>> >> Disallow: /treebase- >>>> >> web/search/treeSearch.html >>>> >> Disallow: /treebase- >>>> >> web/search/taxonSearch.html >>>> >> Disallow: /treebase- >>>> >> web/search/treeTopSearch.html >>>> >> Disallow: /treebase-web/user >>>> >> Disallow: >>>> >> /treebase-web/search/study/anyObjectAsRDF.rdf >>>> >> Disallow: /treebase- >>>> >> web/search/downloadAStudy.html >>>> >> Disallow: /treebase- >>>> >> web/search/downloadAMatrix.html >>>> >> Disallow: /treebase- >>>> >> web/search/downloadANexusFile.htm >>>> >> Disallow: /treebase- >>>> >> web/search/downloadATree.html >>>> >> Disallow: /treebase- >>>> >> web/search/downloadAnAnalysisStep.html >>>> >> >>>> >> User-agent: * >>>> >> Disallow: / >>>> >> Disallow: /treebase-web >>>> >> >>>> >> Harry Shyket >>>> >> Digital Media Specialist >>>> >> Yale University Peabody Museum >>>> >> ph. 203-436-9428 >>>> >> har...@ya... >>>> >> >>>> >> >>>> >> -----Original Message----- >>>> >> From: Hilmar >>>> >> Lapp via RT [mailto:he...@ne...] >>>> >> Sent: Thursday, June 02, 2011 >>>> >> 12:09 PM >>>> >> To: Shyket, Harry >>>> >> Subject: Re: [help.nescent.org #11218] >>>> >> Updating robots.txt on TreeBASE >>>> >> >>>> >> Harry - if you want to allow >>>> >> specific robots, can we please allow only >>>> >> those. Allowing any robot >>>> >> stands to wreak havoc - most robots hitting >>>> >> the site are actually >>>> >> advertisers and other obscure or shady operations. >>>> >> >>>> >> -hilmar >>>> >> >>>> >> On >>>> >> Jun 2, 2011, at 10:01 AM, Shyket, Harry via RT wrote: >>>> >> >>>> >>> >>>> >>> Hi >>>> >> Nescent, >>>> >>> >>>> >>> I would like to update the robots.txt file for >>>> >> TreeBASE. This is so >>>> >>> that Google, Yahoo! and Bing can crawl the >>>> >> submissions. >>>> >>> >>>> >>> Please remove the current text in the file and >>>> >> replace it with the >>>> >>> following: >>>> >>> >>>> >>> User-agent: * >>>> >>> Disallow: >>>> >> /treebase-web/search/studySearch.html >>>> >>> Disallow: /treebase- >>>> >> web/search/matrixSearch.html >>>> >>> Disallow: /treebase- >>>> >> web/search/treeSearch.html >>>> >>> Disallow: /treebase- >>>> >> web/search/taxonSearch.html >>>> >>> Disallow: /treebase- >>>> >> web/search/treeTopSearch.html >>>> >>> Disallow: /treebase-web/user >>>> >>> >>>> >> Disallow: /treebase-web/search/study/anyObjectAsRDF.rdf >>>> >>> Disallow: >>>> >> /treebase-web/search/downloadAStudy.html >>>> >>> Disallow: /treebase- >>>> >> web/search/downloadAMatrix.html >>>> >>> Disallow: /treebase- >>>> >> web/search/downloadANexusFile.htm >>>> >>> Disallow: /treebase- >>>> >> web/search/downloadATree.html >>>> >>> Disallow: /treebase- >>>> >> web/search/downloadAnAnalysisStep.html >>>> >>> >>>> >>> Thanks, >>>> >>> >>>> >>> Harry >>>> >> Shyket >>>> >>> Digital Media Specialist >>>> >>> Yale University Peabody Museum >>>> >>> ph. 203-436-9428 >>>> >>> har...@ya... >>>> >>> >>>> >>> >>>> >> >>>> >> -- >>>> >> =========================================================== >>>> >> : Hilmar >>>> >> Lapp -:- Durham, NC -:- informatics.nescent.org : >>>> >> =========================================================== >>>> >> For more info: >>>> >> Ticket <URL: >>>> >> https://help.nescent.org/Ticket/Display.html?id=11218 > >>>> > >>>> >>> >>> >>>For more info: >>>Ticket <URL: https://help.nescent.org/Ticket/Display.html?id=11218 > >>> >>> >> >> >> >>For more info: >>Ticket <URL: https://help.nescent.org/Ticket/Display.html?id=11218 > >> >> > > -- 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: Carl B. <cbo...@gm...> - 2011-06-02 20:09:51
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Dear list, I see the wiki mentions that logicals are supported on the phylo-ws queries, i.e. http://purl.org/phylo/treebase/dev/phylows/study/find?query=dcterms.contributor=Ronquist%20and%20dcterms.contributor=Hulesenbeck&format=rss1&recordSchema=tree http://purl.org/phylo/treebase/dev/phylows/study/find?query=dcterms.contributor=Ronquist%20or%20dcterms.contributor=Hulesenbeck&format=rss1&recordSchema=tree http://purl.org/phylo/treebase/dev/phylows/taxon/find?query=tb.title.taxon==%22Homo%20sapiens%22%20AND%20%22Pan%20troglodytes%22&format=rss1&recordSchema=tree This works, except that it seems that "and" is always treated as "or". Am I constructing the query incorrectly somehow? -Carl -- Carl Boettiger UC Davis http://www.carlboettiger.info/ |
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From: Karen C. <kar...@ne...> - 2011-06-01 12:35:46
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The connection information for the call this morning is in the Google Doc. Let me know if you do not have access. On Tue, May 31, 2011 at 12:19 PM, Karen Cranston <kar...@ne...> wrote: > Tomorrow morning (Wed, June 1) looks to be good for everyone, and > sooner seems better than later. I propose we talk at 9:00 am EST. I > will send connection information later today. > > Cheers, > Karen > > On Thu, May 26, 2011 at 3:00 PM, Karen Cranston > <kar...@ne...> wrote: >> There has been some interest among various groups in an ABI proposal >> for development of phyloinformatics resources. This email is an >> attempt to connect those threads and move the process forward. The >> conversations that have been happening up to this point are: >> >> 1. The Phyloinformatics Research Foundation (phylofoundation.org, >> stewards of TreeBASE and ToLWeb) started a Google doc aimed at >> TreeBASE >> 2. MIAPA developers started a wiki page >> (https://www.nescent.org/sites/evoio/NSF_ABI_2011), recognizing the >> need for coordination with TreeBASE and other resources >> 3. NESCent (Todd, Hilmar and myself), as the current TreeBASE host and >> as a third party interested in coordinated development across >> resources started a third document (now added to the already mentioned >> Google doc) >> >> If you are interested in this discussion and do not already have >> access to the Google doc entitled TreeBASE_ABI.doc, let me know and I >> can grant you access. Hilmar and I made some substantial edits earlier >> this morning. I point you specifically to the section at the end >> entitled "An attempt to re-think all of this". Briefly, we wanted to >> encourage some radical thinking and explore the idea of developing a >> PhyloCommons that incorporates both TreeBASE and ToLWeb into the >> proposal (as the data repository and the data sharing / dissemination >> / synthesis platform, respectively). >> >> The ABI deadline is July 7, so we have a short period of time to pull >> this together. Here is a link to a Doodle poll for an initial >> teleconference. >> >> http://doodle.com/zf2tz7sftyk3naxy >> >> During this meeting, we hope to come to agreement on the broad >> direction of the grant, identify possible leaders of the various >> components and create a plan for getting this pulled together in time >> for the deadline. Please feel free to continue the conversation on the >> Google doc between now and the teleconference. If there are others who >> you think should be invited, feel free to do so. Not everyone who >> participates in this first phase will end up being named on the grant, >> but these resources require input from a much larger group. >> >> Cheers, >> Karen >> >> >> -- >> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >> Karen Cranston >> Training Coordinator and Informatics Project Manager >> nescent.org >> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >> > > > > -- > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > Karen Cranston > Training Coordinator and Informatics Project Manager > nescent.org > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Karen Cranston Training Coordinator and Informatics Project Manager nescent.org ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ |
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From: Westneat, M. <mwe...@fi...> - 2011-05-31 19:14:45
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Hi all, I am definitely interested in this, but can't join in tomorrow (synthesis meeting on Cybertaxonomy this week). Will catch up and join the next meeting- Mark On Tue, May 31, 2011 at 11:19 AM, Karen Cranston <kar...@ne... > wrote: > Tomorrow morning (Wed, June 1) looks to be good for everyone, and > sooner seems better than later. I propose we talk at 9:00 am EST. I > will send connection information later today. > > Cheers, > Karen > > On Thu, May 26, 2011 at 3:00 PM, Karen Cranston > <kar...@ne...> wrote: > > There has been some interest among various groups in an ABI proposal > > for development of phyloinformatics resources. This email is an > > attempt to connect those threads and move the process forward. The > > conversations that have been happening up to this point are: > > > > 1. The Phyloinformatics Research Foundation (phylofoundation.org, > > stewards of TreeBASE and ToLWeb) started a Google doc aimed at > > TreeBASE > > 2. MIAPA developers started a wiki page > > (https://www.nescent.org/sites/evoio/NSF_ABI_2011), recognizing the > > need for coordination with TreeBASE and other resources > > 3. NESCent (Todd, Hilmar and myself), as the current TreeBASE host and > > as a third party interested in coordinated development across > > resources started a third document (now added to the already mentioned > > Google doc) > > > > If you are interested in this discussion and do not already have > > access to the Google doc entitled TreeBASE_ABI.doc, let me know and I > > can grant you access. Hilmar and I made some substantial edits earlier > > this morning. I point you specifically to the section at the end > > entitled "An attempt to re-think all of this". Briefly, we wanted to > > encourage some radical thinking and explore the idea of developing a > > PhyloCommons that incorporates both TreeBASE and ToLWeb into the > > proposal (as the data repository and the data sharing / dissemination > > / synthesis platform, respectively). > > > > The ABI deadline is July 7, so we have a short period of time to pull > > this together. Here is a link to a Doodle poll for an initial > > teleconference. > > > > http://doodle.com/zf2tz7sftyk3naxy > > > > During this meeting, we hope to come to agreement on the broad > > direction of the grant, identify possible leaders of the various > > components and create a plan for getting this pulled together in time > > for the deadline. Please feel free to continue the conversation on the > > Google doc between now and the teleconference. If there are others who > > you think should be invited, feel free to do so. Not everyone who > > participates in this first phase will end up being named on the grant, > > but these resources require input from a much larger group. > > > > Cheers, > > Karen > > > > > > -- > > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > > Karen Cranston > > Training Coordinator and Informatics Project Manager > > nescent.org > > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > > > > > > -- > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > Karen Cranston > Training Coordinator and Informatics Project Manager > nescent.org > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > -- Mark W. Westneat Curator of Zoology Robert A. Pritzker Director, Biodiversity Synthesis Center of the Encyclopedia of Life Field Museum of Natural History 1400 S Lake Shore Dr., Chicago, IL 60605-2496 (312) 665-7734 My website: http://synthesis.eol.org/users/mwestneat<http://biosync.fieldmuseum.org/users/mwestneat> BioSynC website: http://synthesis.eol.org |
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From: Karen C. <kar...@ne...> - 2011-05-31 16:20:10
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Tomorrow morning (Wed, June 1) looks to be good for everyone, and sooner seems better than later. I propose we talk at 9:00 am EST. I will send connection information later today. Cheers, Karen On Thu, May 26, 2011 at 3:00 PM, Karen Cranston <kar...@ne...> wrote: > There has been some interest among various groups in an ABI proposal > for development of phyloinformatics resources. This email is an > attempt to connect those threads and move the process forward. The > conversations that have been happening up to this point are: > > 1. The Phyloinformatics Research Foundation (phylofoundation.org, > stewards of TreeBASE and ToLWeb) started a Google doc aimed at > TreeBASE > 2. MIAPA developers started a wiki page > (https://www.nescent.org/sites/evoio/NSF_ABI_2011), recognizing the > need for coordination with TreeBASE and other resources > 3. NESCent (Todd, Hilmar and myself), as the current TreeBASE host and > as a third party interested in coordinated development across > resources started a third document (now added to the already mentioned > Google doc) > > If you are interested in this discussion and do not already have > access to the Google doc entitled TreeBASE_ABI.doc, let me know and I > can grant you access. Hilmar and I made some substantial edits earlier > this morning. I point you specifically to the section at the end > entitled "An attempt to re-think all of this". Briefly, we wanted to > encourage some radical thinking and explore the idea of developing a > PhyloCommons that incorporates both TreeBASE and ToLWeb into the > proposal (as the data repository and the data sharing / dissemination > / synthesis platform, respectively). > > The ABI deadline is July 7, so we have a short period of time to pull > this together. Here is a link to a Doodle poll for an initial > teleconference. > > http://doodle.com/zf2tz7sftyk3naxy > > During this meeting, we hope to come to agreement on the broad > direction of the grant, identify possible leaders of the various > components and create a plan for getting this pulled together in time > for the deadline. Please feel free to continue the conversation on the > Google doc between now and the teleconference. If there are others who > you think should be invited, feel free to do so. Not everyone who > participates in this first phase will end up being named on the grant, > but these resources require input from a much larger group. > > Cheers, > Karen > > > -- > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > Karen Cranston > Training Coordinator and Informatics Project Manager > nescent.org > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Karen Cranston Training Coordinator and Informatics Project Manager nescent.org ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ |
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From: Hilmar L. <hl...@ne...> - 2011-05-29 16:52:28
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Hi all, I thought this may be relevant to some of the on-going efforts at building a MIAPA-compliant metadata collection form or tool for annotating phylogenetic trees or data, such as for deposition into TreeBASE. This is an input form built apparently using Orbeon [1], for creating a MIIDI-compliant [2] metadata record: Screenshots: http://www.miidi.org/wiki/index.php/Metadata_Editor Live metadata editor: http://www.miidi.org:8080/orbeon/miidi-review/dataset This is work by Tanya Gray and David Shotton, both of whom are involved in the DryadUK project. One of the ideas here that the resulting xml file could then be submitted to Dryad along with the data object(s) itself. But that concept may well apply to TreeBASE too. (Is Laurel subscribed to this ist?) -hilmar [1] http://www.orbeon.com/ [2] Minimal Information standard for reporting an Infectious Disease Investigation (see http://www.miidi.org) -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : =========================================================== |
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From: William P. <wil...@ya...> - 2011-05-28 23:19:33
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Hi all, Myself, I don't know what code depends on this properties file. I was concerned that the dev password might be leaking out, so I searched for the password in eclipse and erased it wherever I saw it. (But of course, you're right that this would be retained in older versions...). At any rate, the OAI-PMH service works fine on dev (e.g.) even with the password now erased. Given that this code is in a "../test/.." path, I'm guessing that this properties file was being used by test/development code which Youjun wrote that is presently not needed given the way that the OAI service is currently deployed. bp On May 28, 2011, at 6:34 PM, Hilmar Lapp wrote: > That's a great suggestion. The application in question appears to be in Java, and doesn't it also run on the same server? > > Bill or Harry - could you comment on whether this is easy enough to accomplish? > > -hilmar > > On May 28, 2011, at 1:00 PM, Vladimir Gapeyev wrote: > >> In the treebase-web application, this problem of accidentally committing a password is avoided through using JNDI. This way the password is never under the source tree and never inside a WAR. Couldn't the same be done for oai-pmh_data_provider/data_provider_web, whatever it is? >> -Vladimir >> > > -- > =========================================================== > : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : > =========================================================== > |
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From: Hilmar L. <hl...@ne...> - 2011-05-28 22:34:41
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That's a great suggestion. The application in question appears to be in Java, and doesn't it also run on the same server? Bill or Harry - could you comment on whether this is easy enough to accomplish? -hilmar On May 28, 2011, at 1:00 PM, Vladimir Gapeyev wrote: > In the treebase-web application, this problem of accidentally > committing a password is avoided through using JNDI. This way the > password is never under the source tree and never inside a WAR. > Couldn't the same be done for oai-pmh_data_provider/ > data_provider_web, whatever it is? > -Vladimir > -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : =========================================================== |
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From: Hilmar L. <hl...@ne...> - 2011-05-28 16:24:15
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Yes, sorry for the noise. I realized that I was looking at an old revision only after I had sent the email. iPad isn't perfect for this ... -hilmar Sent with a tap. On May 28, 2011, at 12:17 PM, Rutger Vos <R....@re...> wrote: > Hi Hilmar, > > you note that you are looking at a javascript snippet for determining > the root in a nexml tree in preparation for displaying it in > jsPhyloSVG, right? > > Anyway, the following *doesn't* work, targetCount for the root should > be 0 or possibly 1 in the case where a rootedge is an element in the > nexEdges array. The head revision shows this done correctly. > > I was trying to get jsPhyloSVG to play nice and this was just one of > many things that weren't working properly so this ended up being > committed in that revision without actually working > > Rutger > > On Sat, May 28, 2011 at 4:43 PM, Hilmar Lapp <hl...@dr...> wrote: >> Rutger - >> >> I'm curious and am probably missing something and therefore don't fully follow why the below works. Would you mind explaining? By edges pointing into a node, do you mean incoming (from ancestor) or outgoing (to descendant) edges? It sounds like outgoing (or otherwise there wouldn't be two, right), but why does NeXML then require a node with one outgoing edge at the root of the tree, artificial or not? Or do you mean outgoing plus incoming? >> >> So I'm obviously missing something, but can you point me to what it is? >> >> -hilmar >> >> Sent with a tap. >> >> On May 19, 2011, at 9:00 AM, rv...@us... wrote: >> >>> Revision: 873 >>> http://treebase.svn.sourceforge.net/treebase/?rev=873&view=rev >>> Author: rvos >>> Date: 2011-05-19 13:00:28 +0000 (Thu, 19 May 2011) >>> >>> Log Message: >>> ----------- >>> Added additional loop to identify the root node based on the implicit topology (instead of by looking for the @root attribute). >>> >>> Modified Paths: >>> -------------- >>> trunk/treebase-web/src/main/webapp/scripts/jsphylosvg-min.js >>> >>> Modified: trunk/treebase-web/src/main/webapp/scripts/jsphylosvg-min.js >>> =================================================================== >>> --- trunk/treebase-web/src/main/webapp/scripts/jsphylosvg-min.js 2011-05-19 12:57:49 UTC (rev 872) >>> +++ trunk/treebase-web/src/main/webapp/scripts/jsphylosvg-min.js 2011-05-19 13:00:28 UTC (rev 873) >>> @@ -761,6 +761,27 @@ >>> } >>> } >>> >>> + // RAV: the root attribute is used to indicate whether an implicitly rooted >>> + // topology should, from a biological p.o.v., be considered as such. However, >>> + // valid NeXML tree structures are always rooted, even if they don't have >>> + // the root attribute, in the sense that there's always going to be one node >>> + // that doesn't have two edges pointing into it. It seems to me that we can >>> + // still render these trees, we just have to find which node is the one that >>> + // doesn't have two edges pointing in. This loop does that. >>> + if (!root){ >>> + for(i = 0; i < nexNodes.length; i++) { >>> + var targetCount = 0; >>> + for(j = 0; j < nexEdges.length; j++) { >>> + if(nexEdges[j].target == nexNodes[i].id) { >>> + targetCount++; >>> + } >>> + } >>> + if ( targetCount < 2 ) { >>> + root = nexNodes[i]; >>> + } >>> + } >>> + } >>> + >>> if(root){ >>> root = recursiveParse(root); >>> >>> >>> >>> This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. >>> >>> ------------------------------------------------------------------------------ >>> What Every C/C++ and Fortran developer Should Know! >>> Read this article and learn how Intel has extended the reach of its >>> next-generation tools to help Windows* and Linux* C/C++ and Fortran >>> developers boost performance applications - including clusters. >>> http://p.sf.net/sfu/intel-dev2devmay >>> _______________________________________________ >>> Treebase-guts mailing list >>> Tre...@li... >>> https://lists.sourceforge.net/lists/listinfo/treebase-guts >> >> ------------------------------------------------------------------------------ >> vRanger cuts backup time in half-while increasing security. >> With the market-leading solution for virtual backup and recovery, >> you get blazing-fast, flexible, and affordable data protection. >> Download your free trial now. >> http://p.sf.net/sfu/quest-d2dcopy1 >> _______________________________________________ >> 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://rutgervos.blogspot.com > > ------------------------------------------------------------------------------ > vRanger cuts backup time in half-while increasing security. > With the market-leading solution for virtual backup and recovery, > you get blazing-fast, flexible, and affordable data protection. > Download your free trial now. > http://p.sf.net/sfu/quest-d2dcopy1 > _______________________________________________ > Treebase-devel mailing list > Tre...@li... > https://lists.sourceforge.net/lists/listinfo/treebase-devel |
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From: Rutger V. <R....@re...> - 2011-05-28 16:17:29
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Hi Hilmar, you note that you are looking at a javascript snippet for determining the root in a nexml tree in preparation for displaying it in jsPhyloSVG, right? Anyway, the following *doesn't* work, targetCount for the root should be 0 or possibly 1 in the case where a rootedge is an element in the nexEdges array. The head revision shows this done correctly. I was trying to get jsPhyloSVG to play nice and this was just one of many things that weren't working properly so this ended up being committed in that revision without actually working. Rutger On Sat, May 28, 2011 at 4:43 PM, Hilmar Lapp <hl...@dr...> wrote: > Rutger - > > I'm curious and am probably missing something and therefore don't fully follow why the below works. Would you mind explaining? By edges pointing into a node, do you mean incoming (from ancestor) or outgoing (to descendant) edges? It sounds like outgoing (or otherwise there wouldn't be two, right), but why does NeXML then require a node with one outgoing edge at the root of the tree, artificial or not? Or do you mean outgoing plus incoming? > > So I'm obviously missing something, but can you point me to what it is? > > -hilmar > > Sent with a tap. > > On May 19, 2011, at 9:00 AM, rv...@us... wrote: > >> Revision: 873 >> http://treebase.svn.sourceforge.net/treebase/?rev=873&view=rev >> Author: rvos >> Date: 2011-05-19 13:00:28 +0000 (Thu, 19 May 2011) >> >> Log Message: >> ----------- >> Added additional loop to identify the root node based on the implicit topology (instead of by looking for the @root attribute). >> >> Modified Paths: >> -------------- >> trunk/treebase-web/src/main/webapp/scripts/jsphylosvg-min.js >> >> Modified: trunk/treebase-web/src/main/webapp/scripts/jsphylosvg-min.js >> =================================================================== >> --- trunk/treebase-web/src/main/webapp/scripts/jsphylosvg-min.js 2011-05-19 12:57:49 UTC (rev 872) >> +++ trunk/treebase-web/src/main/webapp/scripts/jsphylosvg-min.js 2011-05-19 13:00:28 UTC (rev 873) >> @@ -761,6 +761,27 @@ >> } >> } >> >> + // RAV: the root attribute is used to indicate whether an implicitly rooted >> + // topology should, from a biological p.o.v., be considered as such. However, >> + // valid NeXML tree structures are always rooted, even if they don't have >> + // the root attribute, in the sense that there's always going to be one node >> + // that doesn't have two edges pointing into it. It seems to me that we can >> + // still render these trees, we just have to find which node is the one that >> + // doesn't have two edges pointing in. This loop does that. >> + if (!root){ >> + for(i = 0; i < nexNodes.length; i++) { >> + var targetCount = 0; >> + for(j = 0; j < nexEdges.length; j++) { >> + if(nexEdges[j].target == nexNodes[i].id) { >> + targetCount++; >> + } >> + } >> + if ( targetCount < 2 ) { >> + root = nexNodes[i]; >> + } >> + } >> + } >> + >> if(root){ >> root = recursiveParse(root); >> >> >> >> This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. >> >> ------------------------------------------------------------------------------ >> What Every C/C++ and Fortran developer Should Know! >> Read this article and learn how Intel has extended the reach of its >> next-generation tools to help Windows* and Linux* C/C++ and Fortran >> developers boost performance applications - including clusters. >> http://p.sf.net/sfu/intel-dev2devmay >> _______________________________________________ >> Treebase-guts mailing list >> Tre...@li... >> https://lists.sourceforge.net/lists/listinfo/treebase-guts > > ------------------------------------------------------------------------------ > vRanger cuts backup time in half-while increasing security. > With the market-leading solution for virtual backup and recovery, > you get blazing-fast, flexible, and affordable data protection. > Download your free trial now. > http://p.sf.net/sfu/quest-d2dcopy1 > _______________________________________________ > 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://rutgervos.blogspot.com |
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From: Hilmar L. <hl...@dr...> - 2011-05-28 15:43:20
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Rutger - I'm curious and am probably missing something and therefore don't fully follow why the below works. Would you mind explaining? By edges pointing into a node, do you mean incoming (from ancestor) or outgoing (to descendant) edges? It sounds like outgoing (or otherwise there wouldn't be two, right), but why does NeXML then require a node with one outgoing edge at the root of the tree, artificial or not? Or do you mean outgoing plus incoming? So I'm obviously missing something, but can you point me to what it is? -hilmar Sent with a tap. On May 19, 2011, at 9:00 AM, rv...@us... wrote: > Revision: 873 > http://treebase.svn.sourceforge.net/treebase/?rev=873&view=rev > Author: rvos > Date: 2011-05-19 13:00:28 +0000 (Thu, 19 May 2011) > > Log Message: > ----------- > Added additional loop to identify the root node based on the implicit topology (instead of by looking for the @root attribute). > > Modified Paths: > -------------- > trunk/treebase-web/src/main/webapp/scripts/jsphylosvg-min.js > > Modified: trunk/treebase-web/src/main/webapp/scripts/jsphylosvg-min.js > =================================================================== > --- trunk/treebase-web/src/main/webapp/scripts/jsphylosvg-min.js 2011-05-19 12:57:49 UTC (rev 872) > +++ trunk/treebase-web/src/main/webapp/scripts/jsphylosvg-min.js 2011-05-19 13:00:28 UTC (rev 873) > @@ -761,6 +761,27 @@ > } > } > > + // RAV: the root attribute is used to indicate whether an implicitly rooted > + // topology should, from a biological p.o.v., be considered as such. However, > + // valid NeXML tree structures are always rooted, even if they don't have > + // the root attribute, in the sense that there's always going to be one node > + // that doesn't have two edges pointing into it. It seems to me that we can > + // still render these trees, we just have to find which node is the one that > + // doesn't have two edges pointing in. This loop does that. > + if (!root){ > + for(i = 0; i < nexNodes.length; i++) { > + var targetCount = 0; > + for(j = 0; j < nexEdges.length; j++) { > + if(nexEdges[j].target == nexNodes[i].id) { > + targetCount++; > + } > + } > + if ( targetCount < 2 ) { > + root = nexNodes[i]; > + } > + } > + } > + > if(root){ > root = recursiveParse(root); > > > > This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. > > ------------------------------------------------------------------------------ > What Every C/C++ and Fortran developer Should Know! > Read this article and learn how Intel has extended the reach of its > next-generation tools to help Windows* and Linux* C/C++ and Fortran > developers boost performance applications - including clusters. > http://p.sf.net/sfu/intel-dev2devmay > _______________________________________________ > Treebase-guts mailing list > Tre...@li... > https://lists.sourceforge.net/lists/listinfo/treebase-guts |
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From: Vision, T. J <tj...@bi...> - 2011-05-27 16:05:35
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It is great to see these threads coming together! Sadly, I can't be directly involved because I will be submitting a proposal to ABI in the same round (for Dryad). But that does not disqualify other NESCentians from participating. One word of caution. The document as it stands now harps a bit too much on the problems with the current system. As it gets transformed into a proposal, I would hope that the solutions take center stage, and that it emphasizes the potential for what lies ahead, rather than the limitations of what lied behind. OK, a second word of caution. I would not take entirely at face value NSF's protestations that scientific goals are not important to the success of ABI Development proposals. It may not be as important, but it stll matter. In particular, I think there's an opportunity here to really see what can be achieved by looking synthetically at a large body of phylogenetic trees. How much incongruence is there? Does incongruence descrease over time? How is it affected by the type of study (morphological vs molecular, amount of data, extent of taxonmic sampling, parsimony vs probabilistic, etc)? Where are the holes in phylogenetic knowledge? In which groups is there enough overlap to build supertrees or grafted trees? These kinds of questions can only be answered with a resource like TB, and emphasizing such synthetic outcomes would help motivate the whole endeavour. cheers, Todd On May 27, 2011, at 8:46 AM, Rutger Vos wrote: > I'd like to second this initiative, I think the blurb at the end of > the google doc nicely puts the finger on the sore spots, e.g.: > > "TreeBASE arguably falls into the latter category, with ingest and > retrieval of data constituting the predominant uses, yet the design of > its current version chiefly aims at a fully transactional database for > frequent and concurrent updates. This legacy design choice places > serious limitations on extensibility and robustness of the software, > and has resulted in a degree of complexity of the code and deployment > procedure that threatens its long-term sustainability." > > The first half, i.e. "Ideas for New Development" has a lot of good > ideas in it, hopefully we can make it so that some of those ideas are > the meat on the bones of the sentiment expressed in the second half. > > Let's fill out the doodle poll, its window is for next week. > > Rutger > > On Thu, May 26, 2011 at 8:00 PM, Karen Cranston > <kar...@ne...> wrote: >> There has been some interest among various groups in an ABI proposal >> for development of phyloinformatics resources. This email is an >> attempt to connect those threads and move the process forward. The >> conversations that have been happening up to this point are: >> >> 1. The Phyloinformatics Research Foundation (phylofoundation.org, >> stewards of TreeBASE and ToLWeb) started a Google doc aimed at >> TreeBASE >> 2. MIAPA developers started a wiki page >> (https://www.nescent.org/sites/evoio/NSF_ABI_2011), recognizing the >> need for coordination with TreeBASE and other resources >> 3. NESCent (Todd, Hilmar and myself), as the current TreeBASE host and >> as a third party interested in coordinated development across >> resources started a third document (now added to the already mentioned >> Google doc) >> >> If you are interested in this discussion and do not already have >> access to the Google doc entitled TreeBASE_ABI.doc, let me know and I >> can grant you access. Hilmar and I made some substantial edits earlier >> this morning. I point you specifically to the section at the end >> entitled "An attempt to re-think all of this". Briefly, we wanted to >> encourage some radical thinking and explore the idea of developing a >> PhyloCommons that incorporates both TreeBASE and ToLWeb into the >> proposal (as the data repository and the data sharing / dissemination >> / synthesis platform, respectively). >> >> The ABI deadline is July 7, so we have a short period of time to pull >> this together. Here is a link to a Doodle poll for an initial >> teleconference. >> >> http://doodle.com/zf2tz7sftyk3naxy >> >> During this meeting, we hope to come to agreement on the broad >> direction of the grant, identify possible leaders of the various >> components and create a plan for getting this pulled together in time >> for the deadline. Please feel free to continue the conversation on the >> Google doc between now and the teleconference. If there are others who >> you think should be invited, feel free to do so. Not everyone who >> participates in this first phase will end up being named on the grant, >> but these resources require input from a much larger group. >> >> Cheers, >> Karen >> >> >> -- >> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >> Karen Cranston >> Training Coordinator and Informatics Project Manager >> nescent.org >> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >> >> -- >> You received this message because you are subscribed to the Google >> Groups "MIAPA" group. >> For more options, visit this group at >> http://groups.google.com/group/miapa-discuss?hl=en >> > > > > -- > 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://rutgervos.blogspot.com > > -- > You received this message because you are subscribed to the Google > Groups "MIAPA" group. > For more options, visit this group at > http://groups.google.com/group/miapa-discuss?hl=en |
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From: Rutger V. <R....@re...> - 2011-05-27 12:47:06
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I'd like to second this initiative, I think the blurb at the end of the google doc nicely puts the finger on the sore spots, e.g.: "TreeBASE arguably falls into the latter category, with ingest and retrieval of data constituting the predominant uses, yet the design of its current version chiefly aims at a fully transactional database for frequent and concurrent updates. This legacy design choice places serious limitations on extensibility and robustness of the software, and has resulted in a degree of complexity of the code and deployment procedure that threatens its long-term sustainability." The first half, i.e. "Ideas for New Development" has a lot of good ideas in it, hopefully we can make it so that some of those ideas are the meat on the bones of the sentiment expressed in the second half. Let's fill out the doodle poll, its window is for next week. Rutger On Thu, May 26, 2011 at 8:00 PM, Karen Cranston <kar...@ne...> wrote: > There has been some interest among various groups in an ABI proposal > for development of phyloinformatics resources. This email is an > attempt to connect those threads and move the process forward. The > conversations that have been happening up to this point are: > > 1. The Phyloinformatics Research Foundation (phylofoundation.org, > stewards of TreeBASE and ToLWeb) started a Google doc aimed at > TreeBASE > 2. MIAPA developers started a wiki page > (https://www.nescent.org/sites/evoio/NSF_ABI_2011), recognizing the > need for coordination with TreeBASE and other resources > 3. NESCent (Todd, Hilmar and myself), as the current TreeBASE host and > as a third party interested in coordinated development across > resources started a third document (now added to the already mentioned > Google doc) > > If you are interested in this discussion and do not already have > access to the Google doc entitled TreeBASE_ABI.doc, let me know and I > can grant you access. Hilmar and I made some substantial edits earlier > this morning. I point you specifically to the section at the end > entitled "An attempt to re-think all of this". Briefly, we wanted to > encourage some radical thinking and explore the idea of developing a > PhyloCommons that incorporates both TreeBASE and ToLWeb into the > proposal (as the data repository and the data sharing / dissemination > / synthesis platform, respectively). > > The ABI deadline is July 7, so we have a short period of time to pull > this together. Here is a link to a Doodle poll for an initial > teleconference. > > http://doodle.com/zf2tz7sftyk3naxy > > During this meeting, we hope to come to agreement on the broad > direction of the grant, identify possible leaders of the various > components and create a plan for getting this pulled together in time > for the deadline. Please feel free to continue the conversation on the > Google doc between now and the teleconference. If there are others who > you think should be invited, feel free to do so. Not everyone who > participates in this first phase will end up being named on the grant, > but these resources require input from a much larger group. > > Cheers, > Karen > > > -- > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > Karen Cranston > Training Coordinator and Informatics Project Manager > nescent.org > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > > -- > You received this message because you are subscribed to the Google > Groups "MIAPA" group. > For more options, visit this group at > http://groups.google.com/group/miapa-discuss?hl=en > -- 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://rutgervos.blogspot.com |
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From: Karen C. <kar...@ne...> - 2011-05-26 19:00:20
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There has been some interest among various groups in an ABI proposal for development of phyloinformatics resources. This email is an attempt to connect those threads and move the process forward. The conversations that have been happening up to this point are: 1. The Phyloinformatics Research Foundation (phylofoundation.org, stewards of TreeBASE and ToLWeb) started a Google doc aimed at TreeBASE 2. MIAPA developers started a wiki page (https://www.nescent.org/sites/evoio/NSF_ABI_2011), recognizing the need for coordination with TreeBASE and other resources 3. NESCent (Todd, Hilmar and myself), as the current TreeBASE host and as a third party interested in coordinated development across resources started a third document (now added to the already mentioned Google doc) If you are interested in this discussion and do not already have access to the Google doc entitled TreeBASE_ABI.doc, let me know and I can grant you access. Hilmar and I made some substantial edits earlier this morning. I point you specifically to the section at the end entitled "An attempt to re-think all of this". Briefly, we wanted to encourage some radical thinking and explore the idea of developing a PhyloCommons that incorporates both TreeBASE and ToLWeb into the proposal (as the data repository and the data sharing / dissemination / synthesis platform, respectively). The ABI deadline is July 7, so we have a short period of time to pull this together. Here is a link to a Doodle poll for an initial teleconference. http://doodle.com/zf2tz7sftyk3naxy During this meeting, we hope to come to agreement on the broad direction of the grant, identify possible leaders of the various components and create a plan for getting this pulled together in time for the deadline. Please feel free to continue the conversation on the Google doc between now and the teleconference. If there are others who you think should be invited, feel free to do so. Not everyone who participates in this first phase will end up being named on the grant, but these resources require input from a much larger group. Cheers, Karen -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Karen Cranston Training Coordinator and Informatics Project Manager nescent.org ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ |
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From: Carl B. <cbo...@gm...> - 2011-05-24 19:42:54
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Hi, I'm wondering what is the recommended way to query for TreeBASE entries matching certain metadata (i.e. author) is, using the the OAI-PMH interface the way one can already do with the phylo-ws interface. I'm looking at the specification for the OAI-PMH<http://www.openarchives.org/OAI/openarchivesprotocol.html#ListIdentifiers>verb ListIdentifers, and it seems I can only specify dates using from or until, but not query by other metadata. It seems I can change the type of metadata format (oai_dc vs mets, though the wiki recommends oai_dc) and this date range. I can simply download all the metadata and search it locally, (as I do in my current implementation for the TreeBASE R package<http://www.carlboettiger.info/archives/1702>), but I was wondering if there's a better way to handle this? (Of course this would be more of a concern if the metadata were millions of files rather than a few thousand, but I'd also like my OAI-PMH methods to be consistent & intelligent enough to be applied to other databases such as Dryad, etc) Any update on getting Dryad identifiers into TreeBASE entries? Thanks much for your advice! Carl -- Carl Boettiger UC Davis http://www.carlboettiger.info/ |
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From: Laurel Y. <lol...@gm...> - 2011-05-23 13:49:11
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On Mon, May 23, 2011 at 7:35 AM, Rutger Vos <R....@re...> wrote: > > For those that do, it seems only visible in the nexus format, not > > nexml. Can we get charset tags in nexml? > > > > Yes, that should be easily doable. Maybe Laurel Yohe (a new Google Summer > of > > Code author) can implement this as an exercise to get to know TreeBASE's > > code. We need a NeXML solution both for expressing CHARSET free text and > > for expressing the row-segment metadata like the Genbank accession > number. > > That should be doable, yes. > > First task...excellent! I'll hop to it and see what I can do. > > Also, for a given matrix, is the order of characters the same, if I > > download it in nexus and nexml? If so, I suppose it would be easy to > > just pull out the charset info from the nexus file. > > > > Yes, if I understand what you're saying. Of course, the order of the > > characters are not shuffled (!!) but I don't know why you might think > that > > could happen. > > The characters are indeed in the same order. > > -- > 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://rutgervos.blogspot.com > > > ------------------------------------------------------------------------------ > What Every C/C++ and Fortran developer Should Know! > Read this article and learn how Intel has extended the reach of its > next-generation tools to help Windows* and Linux* C/C++ and Fortran > developers boost performance applications - including clusters. > http://p.sf.net/sfu/intel-dev2devmay > _______________________________________________ > Treebase-devel mailing list > Tre...@li... > https://lists.sourceforge.net/lists/listinfo/treebase-devel > |
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From: Rutger V. <R....@re...> - 2011-05-23 12:35:20
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> For those that do, it seems only visible in the nexus format, not > nexml. Can we get charset tags in nexml? > > Yes, that should be easily doable. Maybe Laurel Yohe (a new Google Summer of > Code author) can implement this as an exercise to get to know TreeBASE's > code. We need a NeXML solution both for expressing CHARSET free text and > for expressing the row-segment metadata like the Genbank accession number. That should be doable, yes. > Also, for a given matrix, is the order of characters the same, if I > download it in nexus and nexml? If so, I suppose it would be easy to > just pull out the charset info from the nexus file. > > Yes, if I understand what you're saying. Of course, the order of the > characters are not shuffled (!!) but I don't know why you might think that > could happen. The characters are indeed in the same order. -- 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://rutgervos.blogspot.com |
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From: William P. <wil...@ya...> - 2011-05-22 00:07:14
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Okay. I'll reply to the MIAPA discussion group, seeing as they are keen on formulating minimum requirements. bp On May 21, 2011, at 6:09 PM, Richard Ree wrote: > Hi Bill, > > Thanks for the info. Because the partition information is critical for data re-use, I hope this may eventually be required for DNA alignments. The gene names and genbank numbers are less important, since they are more easily inferred/discovered. But, even a non-standardized gene name provided by the author is way more informative than none at all. And, I think it would be difficult to try and deduce gene partitions from BLAST. More difficult than burdening submitters a bit more, anyway. > > -Rick > > On Sat, May 21, 2011 at 5:01 PM, William Piel <wil...@ya...> wrote: > Hi Rick, > > On May 21, 2011, at 10:53 AM, Richard Ree wrote: > >> I'm trying to decompose sequence alignments from TB into component >> gene regions. Does TB have a policy regarding uploaded matrices >> providing this information? E.g. S11152 does not - 8 cpDNA regions >> are concatenated without any charset or partition info. > > To avoid over-burdening the submitter, we don't require this. Also, I don't know that gene names in charset free text are standardized enough to make this kind of metadata as valuable as it should be. Ideally everyone would supply Genbank accession numbers, and then extract gene names from there. Currently these are downloadable only as tab-separated text (e.g. use this link to download the metadata for this dataset) -- I've asked the Mesquite people how this could be expressed in Mesquite-readable NEXUS, but so-far no answer from them. Current implementations of annotations for the NOTES block only allow for taxon-linked metadata: > > SUTM T = 4 N = genBankNumber S = AF284000; > > and single-character-linked metadata, e.g.: > > AN T = 4 C = 1 AU = TreeBASE TF = ( CM AF284000 ) TF = ( R genBankNumber ); > > ... but not for ranges or spans of characters, which is the logic used in TreeBASE. > >> For those that do, it seems only visible in the nexus format, not >> nexml. Can we get charset tags in nexml? > > Yes, that should be easily doable. Maybe Laurel Yohe (a new Google Summer of Code author) can implement this as an exercise to get to know TreeBASE's code. We need a NeXML solution both for expressing CHARSET free text and for expressing the row-segment metadata like the Genbank accession number. > >> Also, for a given matrix, is the order of characters the same, if I >> download it in nexus and nexml? If so, I suppose it would be easy to >> just pull out the charset info from the nexus file. > > > Yes, if I understand what you're saying. Of course, the order of the characters are not shuffled (!!) but I don't know why you might think that could happen. > > At any rate, I'd like to come up with a script, involving BLAST, that is smart enough to take all matrix rows and figure out (1) where gene-sequences begin and end, and (2) auto-generate Genbank accession numbers for row-segment metadata. It will be challenging to avoid introducing false-positives, and to get BLAST to match different sequences to different sections of the matrix-row. > > bp > > > |
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From: Richard R. <rr...@fi...> - 2011-05-21 22:09:17
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Hi Bill, Thanks for the info. Because the partition information is critical for data re-use, I hope this may eventually be required for DNA alignments. The gene names and genbank numbers are less important, since they are more easily inferred/discovered. But, even a non-standardized gene name provided by the author is way more informative than none at all. And, I think it would be difficult to try and deduce gene partitions from BLAST. More difficult than burdening submitters a bit more, anyway. -Rick On Sat, May 21, 2011 at 5:01 PM, William Piel <wil...@ya...> wrote: > Hi Rick, > > On May 21, 2011, at 10:53 AM, Richard Ree wrote: > > I'm trying to decompose sequence alignments from TB into component > gene regions. Does TB have a policy regarding uploaded matrices > providing this information? E.g. S11152 does not - 8 cpDNA regions > are concatenated without any charset or partition info. > > > To avoid over-burdening the submitter, we don't require this. Also, I don't > know that gene names in charset free text are standardized enough to make > this kind of metadata as valuable as it should be. Ideally everyone would > supply Genbank accession numbers, and then extract gene names from there. > Currently these are downloadable only as tab-separated text (e.g. use this<http://treebase.org/treebase-web/search/study/rowSegmentsTSV.html?matrixid=8983> link > to download the metadata for this<http://purl.org/phylo/treebase/phylows/study/TB2:S11551?format=nexus> dataset) > -- I've asked the Mesquite people how this could be expressed in > Mesquite-readable NEXUS, but so-far no answer from them. Current > implementations of annotations for the NOTES block only allow for > taxon-linked metadata: > > SUTM T = 4 N = genBankNumber S = AF284000; > > and single-character-linked metadata, e.g.: > > AN T = 4 C = 1 AU = TreeBASE TF = ( CM AF284000 ) TF = ( > R genBankNumber ); > > ... but not for ranges or spans of characters, which is the logic used in > TreeBASE. > > For those that do, it seems only visible in the nexus format, not > nexml. Can we get charset tags in nexml? > > > Yes, that should be easily doable. Maybe Laurel Yohe (a new Google Summer > of Code<http://informatics.nescent.org/wiki/PhyloSoC:_Automated_submission_of_rich_data_to_TreeBASE> author) > can implement this as an exercise to get to know TreeBASE's code. We need a > NeXML solution both for expressing CHARSET free text and for expressing the > row-segment metadata like the Genbank accession number. > > Also, for a given matrix, is the order of characters the same, if I > download it in nexus and nexml? If so, I suppose it would be easy to > just pull out the charset info from the nexus file. > > > Yes, if I understand what you're saying. Of course, the order of the > characters are not shuffled (!!) but I don't know why you might think that > could happen. > > At any rate, I'd like to come up with a script, involving BLAST, that is > smart enough to take all matrix rows and figure out (1) where gene-sequences > begin and end, and (2) auto-generate Genbank accession numbers for > row-segment metadata. It will be challenging to avoid introducing > false-positives, and to get BLAST to match different sequences to different > sections of the matrix-row. > > bp > > > > > > ------------------------------------------------------------------------------ > What Every C/C++ and Fortran developer Should Know! > Read this article and learn how Intel has extended the reach of its > next-generation tools to help Windows* and Linux* C/C++ and Fortran > developers boost performance applications - including clusters. > http://p.sf.net/sfu/intel-dev2devmay > _______________________________________________ > Treebase-devel mailing list > Tre...@li... > https://lists.sourceforge.net/lists/listinfo/treebase-devel > > |
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From: William P. <wil...@ya...> - 2011-05-21 22:01:15
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Hi Rick, On May 21, 2011, at 10:53 AM, Richard Ree wrote: > I'm trying to decompose sequence alignments from TB into component > gene regions. Does TB have a policy regarding uploaded matrices > providing this information? E.g. S11152 does not - 8 cpDNA regions > are concatenated without any charset or partition info. To avoid over-burdening the submitter, we don't require this. Also, I don't know that gene names in charset free text are standardized enough to make this kind of metadata as valuable as it should be. Ideally everyone would supply Genbank accession numbers, and then extract gene names from there. Currently these are downloadable only as tab-separated text (e.g. use this link to download the metadata for this dataset) -- I've asked the Mesquite people how this could be expressed in Mesquite-readable NEXUS, but so-far no answer from them. Current implementations of annotations for the NOTES block only allow for taxon-linked metadata: SUTM T = 4 N = genBankNumber S = AF284000; and single-character-linked metadata, e.g.: AN T = 4 C = 1 AU = TreeBASE TF = ( CM AF284000 ) TF = ( R genBankNumber ); ... but not for ranges or spans of characters, which is the logic used in TreeBASE. > For those that do, it seems only visible in the nexus format, not > nexml. Can we get charset tags in nexml? Yes, that should be easily doable. Maybe Laurel Yohe (a new Google Summer of Code author) can implement this as an exercise to get to know TreeBASE's code. We need a NeXML solution both for expressing CHARSET free text and for expressing the row-segment metadata like the Genbank accession number. > Also, for a given matrix, is the order of characters the same, if I > download it in nexus and nexml? If so, I suppose it would be easy to > just pull out the charset info from the nexus file. Yes, if I understand what you're saying. Of course, the order of the characters are not shuffled (!!) but I don't know why you might think that could happen. At any rate, I'd like to come up with a script, involving BLAST, that is smart enough to take all matrix rows and figure out (1) where gene-sequences begin and end, and (2) auto-generate Genbank accession numbers for row-segment metadata. It will be challenging to avoid introducing false-positives, and to get BLAST to match different sequences to different sections of the matrix-row. bp |
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From: Richard R. <rr...@fi...> - 2011-05-21 15:20:10
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I'm trying to decompose sequence alignments from TB into component gene regions. Does TB have a policy regarding uploaded matrices providing this information? E.g. S11152 does not - 8 cpDNA regions are concatenated without any charset or partition info. For those that do, it seems only visible in the nexus format, not nexml. Can we get charset tags in nexml? Also, for a given matrix, is the order of characters the same, if I download it in nexus and nexml? If so, I suppose it would be easy to just pull out the charset info from the nexus file. Thanks -Rick |
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From: William P. <wil...@ya...> - 2011-05-16 19:02:12
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Hi Rutger: I notice that all the examples given for date searches in CQL use ISO 8601 date styles: http://www.loc.gov/standards/sru/resources/cql-context-set-v1-2.html But both of these queries throw exceptions: http://treebase-dev.nescent.org/treebase-web/phylows/study/find?query=prism.creationDate>"2011-05-05" http://treebase-dev.nescent.org/treebase-web/phylows/study/find?query=prism.creationDate>2011-05-05 => java.text.ParseException: Unparseable date: "2011-05-05" at com.ibm.icu.text.DateFormat.parse(DateFormat.java:390) at... ... but conforming to ISO 8601 has various advantages, including the ability to include the time zone. Our OAI-PMH service seems to understand ISO 8601, e.g.: ?verb=ListRecords&metadataPrefix=oai_dc&from=2011-05-05T00:00:00Z Can the date parser for phylows be made more intelligent? bp On May 12, 2011, at 9:40 AM, Rutger Vos wrote: > http://treebase-dev.nescent.org/treebase-web/phylows/study/find?query=prism.creationDate>"May 5, 2011"&format=rss1 > > http://treebase-dev.nescent.org/treebase-web/phylows/study/find?query=prism.modificationDate>"May 5, 2011"&format=rss1 > > http://treebase-dev.nescent.org/treebase-web/phylows/study/find?query=prism.publicationDate>"May 5, 2011"&format=rss1 > > still ironing out the bugs with prism.publicationDate, but > prism.modificationDate seems to work. |
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