From jeedward at yahoo.com Wed Jan 23 06:31:57 2008 From: jeedward at yahoo.com (John Edward) Date: Wed, 23 Jan 2008 03:31:57 -0800 (PST) Subject: [MOBY-l] BCBGC-08 Final call for papers Message-ID: <309082.16875.qm@web45907.mail.sp1.yahoo.com> BCBGC-08 Final call for papers The 2008 International Conference on Bioinformatics, Computational Biology, Genomics and Chemoinformatics (BCBGC-08) (website: www.PromoteResearch.org ) will be held during July 7-10 2008 in Orlando, FL, USA. We invite draft paper submissions. The conference will be held at the same time and place where several other major events are taking place. The website contains more details. Sincerely John Edward --------------------------------- Looking for last minute shopping deals? Find them fast with Yahoo! Search. From maliha.aziz at yahoo.com Wed Jan 30 18:37:52 2008 From: maliha.aziz at yahoo.com (maliha aziz) Date: Wed, 30 Jan 2008 15:37:52 -0800 (PST) Subject: [MOBY-l] biomoby services missing in dashboard?? Message-ID: <186090.73000.qm@web57403.mail.re1.yahoo.com> hi I am a bit confused and would be really glad if someone could solve this mystery... I have these 4 services of service type "Parsing" that i get when i use the biomoby API and download directly from the server parsePDBIntoChains parseSwissIntoPDBids parseBlastReportIntoHits runBlast2gene BUT when i try looking for them in the dashboard list of services they are simply not present there! :S :S ???????? maliha --------------------------------- Never miss a thing. Make Yahoo your homepage. From groscurt at mpiz-koeln.mpg.de Thu Jan 31 03:38:10 2008 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Thu, 31 Jan 2008 09:38:10 +0100 Subject: [MOBY-l] biomoby services missing in dashboard?? In-Reply-To: <186090.73000.qm@web57403.mail.re1.yahoo.com> References: <186090.73000.qm@web57403.mail.re1.yahoo.com> Message-ID: <200801310938.10938.groscurt@mpiz-koeln.mpg.de> HI Maliha, are you sure you are working on the Calgary production central in Dashboard ? Because I do have these services .... andreas On Thursday 31 January 2008 00:37, maliha aziz wrote: > hi > I am a bit confused and would be really glad if someone could solve this > mystery... I have these 4 services of service type "Parsing" that i get > when i use the biomoby API and download directly from the server > > parsePDBIntoChains > parseSwissIntoPDBids > parseBlastReportIntoHits > runBlast2gene > > BUT when i try looking for them in the dashboard list of services they are > simply not present there! :S :S ???????? > > maliha > > > --------------------------------- > Never miss a thing. Make Yahoo your homepage. > _______________________________________________ > moby-l mailing list > moby-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-l -- Andreas Groscurth Bioinformatics Developer Max Planck Institute for Plant Breeding Research Carl-von-Linn?-Weg 10 50829 Cologne Germany E-mail: ? ?groscurt at mpiz-koeln.mpg.de Phone: ? ?+49(0)221-5062-449 From gordonp at ucalgary.ca Thu Jan 31 13:00:40 2008 From: gordonp at ucalgary.ca (Paul Gordon) Date: Thu, 31 Jan 2008 11:00:40 -0700 Subject: [MOBY-l] Moby 1.0 paper now "Advanced Access" Message-ID: <47A20CC8.9050502@ucalgary.ca> http://bib.oxfordjournals.org/cgi/reprint/bbn003v1 From markw at illuminae.com Thu Jan 31 14:23:09 2008 From: markw at illuminae.com (Mark Wilkinson) Date: Thu, 31 Jan 2008 11:23:09 -0800 Subject: [MOBY-l] Fwd: Your article has been published in Briefings in Bioinformatics In-Reply-To: <20080131104248.4E82E2DEA19@marz.stanford.edu> References: <20080131104248.4E82E2DEA19@marz.stanford.edu> Message-ID: ------- Forwarded message ------- From: bib-tfl at highwire.stanford.edu To: markw at illuminae.com Cc: bib at oxfordjournals.org Subject: Your article has been published in Briefings in Bioinformatics Date: Thu, 31 Jan 2008 02:42:49 -0800 Dear Author I am pleased to inform you that Oxford Journals has published your article in Briefings in Bioinformatics. Here are the free-access links to your online article: Abstract: http://bib.oxfordjournals.org/cgi/content/abstract/bbn003? ijkey=7jMqiO6BpntmxyT&keytype=ref Full Text: http://bib.oxfordjournals.org/cgi/content/full/bbn003? ijkey=7jMqiO6BpntmxyT&keytype=ref PDF: http://bib.oxfordjournals.org/cgi/reprint/bbn003? ijkey=7jMqiO6BpntmxyT&keytype=ref The full citation for your article is: Interoperability with Moby 1.0--It's better than sharing your toothbrush! The BioMoby Consortium Briefings in Bioinformatics 2008; doi: 10.1093/bib/bbn003 This is the final published version of your article and it can be cited using the DOI given above (for more information on DOIs see http://www.doi.org). Please see below for additional information and the conditions of use for the links. You can view information about how your article has been accessed on your Article Data Webpage, a new service for Oxford Journals? authors. 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From maliha.aziz at yahoo.com Thu Jan 31 19:14:28 2008 From: maliha.aziz at yahoo.com (maliha aziz) Date: Thu, 31 Jan 2008 16:14:28 -0800 (PST) Subject: [MOBY-l] get lineage function Message-ID: <413138.91363.qm@web57409.mail.re1.yahoo.com> hi I am trying to use the getlineage function to retrieve the lineage of a few data types but its giving me the following error MobyDataType[] dt_typ=dttyp[counter].getLineage(); ERORR is as follows Cannot parse MOBY Object Ontology: java.lang.NullPointerException hmmmm.... i used the getlineage function for the service types and it worked perfectly fine... :S so what am i going wrong here maliha --------------------------------- Never miss a thing. Make Yahoo your homepage. From maliha.aziz at yahoo.com Thu Jan 31 19:32:29 2008 From: maliha.aziz at yahoo.com (maliha aziz) Date: Thu, 31 Jan 2008 16:32:29 -0800 (PST) Subject: [MOBY-l] get lineage function and my registry is poinitng to the correct address :) In-Reply-To: <413138.91363.qm@web57409.mail.re1.yahoo.com> Message-ID: <816550.4409.qm@web57409.mail.re1.yahoo.com> maliha aziz wrote: hi I am trying to use the getlineage function to retrieve the lineage of a few data types but its giving me the following error MobyDataType[] dt_typ=dttyp[counter].getLineage(); ERORR is as follows Cannot parse MOBY Object Ontology: java.lang.NullPointerException hmmmm.... i used the getlineage function for the service types and it worked perfectly fine... :S so what am i going wrong here maliha p.s. and yea ive configured the registry to point to the new address... --------------------------------- Never miss a thing. Make Yahoo your homepage. _______________________________________________ moby-l mailing list moby-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-l --------------------------------- Never miss a thing. Make Yahoo your homepage. From maliha.aziz at yahoo.com Thu Jan 31 19:46:46 2008 From: maliha.aziz at yahoo.com (maliha aziz) Date: Thu, 31 Jan 2008 16:46:46 -0800 (PST) Subject: [MOBY-l] one more question Message-ID: <152541.47291.qm@web57414.mail.re1.yahoo.com> sorry for bombarding you with questions but i really need to find out the answers the function getAllChildren()... MobyRelationship[] dt=dttyp[countz].getAllChildren(); does it return children of all relation types or just HAS HASA... i know itz written tht itz only HAS HASA types are returned but just wanted to confirm and if I want to obtain children with ISA relationships which function shud i use??? thnks maliha --------------------------------- Looking for last minute shopping deals? 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