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From: Rutger V. <rut...@gm...> - 2010-01-24 00:46:13
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Hi all, let's say we're near the point of being able to roll out the "mission accomplished" banner and launch TreeBASE2. Doesn't that mean there ought to be a publication (or application note) to mark that occasion? 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: Hilmar L. <hl...@ne...> - 2010-01-24 20:04:38
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I suppose that would go into the Jan 2011 NAR database issue? I believe they accept submissions year-round now, though that needs to be double-checked. Unless there are enough intellectual (beyond informatics and implementation) novelties to make a more general case. What did you have in mind? Although there are a variety of publications cited for and about TreeBASE, as far as my recollection goes there doesn't seem to be one that is easily accessible and comprehensive to the degree that it would serve as the natural reference citation. So there could be an opportunity here to change that for TB2. -hilmar On Jan 23, 2010, at 7:46 PM, Rutger Vos wrote: > Hi all, > > let's say we're near the point of being able to roll out the "mission > accomplished" banner and launch TreeBASE2. Doesn't that mean there > ought to be a publication (or application note) to mark that occasion? > > 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 > > ------------------------------------------------------------------------------ > 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 -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : =========================================================== |
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From: Val T. <va...@ci...> - 2010-01-24 20:53:15
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I agree that we need something that can be used as a reference citation. Val On Jan 24, 2010, at 3:04 PM, Hilmar Lapp wrote: > I suppose that would go into the Jan 2011 NAR database issue? I > believe they accept submissions year-round now, though that needs to > be double-checked. Unless there are enough intellectual (beyond > informatics and implementation) novelties to make a more general case. > What did you have in mind? > > Although there are a variety of publications cited for and about > TreeBASE, as far as my recollection goes there doesn't seem to be one > that is easily accessible and comprehensive to the degree that it > would serve as the natural reference citation. So there could be an > opportunity here to change that for TB2. > > -hilmar > > On Jan 23, 2010, at 7:46 PM, Rutger Vos wrote: > >> Hi all, >> >> let's say we're near the point of being able to roll out the "mission >> accomplished" banner and launch TreeBASE2. Doesn't that mean there >> ought to be a publication (or application note) to mark that occasion? >> >> 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 >> >> ------------------------------------------------------------------------------ >> 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 > > -- > =========================================================== > : 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 |
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From: William P. <wil...@ya...> - 2010-01-25 02:06:06
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On Jan 24, 2010, at 3:04 PM, Hilmar Lapp wrote: > I suppose that would go into the Jan 2011 NAR database issue? I > believe they accept submissions year-round now, though that needs to > be double-checked Yeah, NAR is an option. There is a database issue in January and a webserver issue in july. About 2-4 pages per article. Another option is the application notes in Bioinformatics -- but also quite short (perhaps shorter). Maybe it makes sense to have one shorter "announcement" pub (in NAR or Bioinf, etc) and then separately something more focused and beefier elsewhere. e.g., Rutger, you could head-up an article on how to program with the API -- e.g., perhaps something similar to the well-used and oft-cited description of the NEXUS format that Swofford and the Maddison's published in Syst Bio. (for that kind of article, which is somewhat singular compared to the usual Sys Bio papers, we'd probably need a nod from the editor of Syst Bio ahead of time). bp |
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From: Rutger V. <rut...@gm...> - 2010-01-25 10:39:52
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On Mon, Jan 25, 2010 at 1:34 AM, William Piel <wil...@ya...> wrote: > > On Jan 24, 2010, at 3:04 PM, Hilmar Lapp wrote: > >> I suppose that would go into the Jan 2011 NAR database issue? I >> believe they accept submissions year-round now, though that needs to >> be double-checked > > Yeah, NAR is an option. There is a database issue in January and a webserver issue in july. About 2-4 pages per article. Another option is the application notes in Bioinformatics -- but also quite short (perhaps shorter). > > Maybe it makes sense to have one shorter "announcement" pub (in NAR or Bioinf, etc) and then separately something more focused and beefier elsewhere. e.g., Rutger, you could head-up an article on how to program with the API -- e.g., perhaps something similar to the well-used and oft-cited description of the NEXUS format that Swofford and the Maddison's published in Syst Bio. (for that kind of article, which is somewhat singular compared to the usual Sys Bio papers, we'd probably need a nod from the editor of Syst Bio ahead of time). Perhaps as a manuscript that also introduces PhyloWS by example? -- 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: William P. <wil...@ya...> - 2010-01-25 14:01:33
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On Jan 25, 2010, at 5:39 AM, Rutger Vos wrote: > On Mon, Jan 25, 2010 at 1:34 AM, William Piel <wil...@ya...> wrote: >> >> On Jan 24, 2010, at 3:04 PM, Hilmar Lapp wrote: >> >>> I suppose that would go into the Jan 2011 NAR database issue? I >>> believe they accept submissions year-round now, though that needs to >>> be double-checked >> >> Yeah, NAR is an option. There is a database issue in January and a webserver issue in july. About 2-4 pages per article. Another option is the application notes in Bioinformatics -- but also quite short (perhaps shorter). >> >> Maybe it makes sense to have one shorter "announcement" pub (in NAR or Bioinf, etc) and then separately something more focused and beefier elsewhere. e.g., Rutger, you could head-up an article on how to program with the API -- e.g., perhaps something similar to the well-used and oft-cited description of the NEXUS format that Swofford and the Maddison's published in Syst Bio. (for that kind of article, which is somewhat singular compared to the usual Sys Bio papers, we'd probably need a nod from the editor of Syst Bio ahead of time). > > Perhaps as a manuscript that also introduces PhyloWS by example? Yeah, that's what I had in mind. A "manual" to PhyloWS using TreeBASE API as the first implementation of it. bp |
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From: Hilmar L. <hl...@ne...> - 2010-01-25 23:19:30
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On Jan 25, 2010, at 9:01 AM, William Piel wrote: > > Yeah, that's what I had in mind. A "manual" to PhyloWS using > TreeBASE API as the first implementation of it. That would indeed be a good example for a manual, but I think pretty strongly that PhyloWS needs to go into an evolutionary data interoperability story combining PhyloWS with NeXML and relevant ontologies (such as CDAO). -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : =========================================================== |
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From: Rutger V. <rut...@gm...> - 2012-03-01 09:47:20
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Hi Bill, all, I've noticed that Bill has made some edits to the shared tb2_doc dropbox folder (members of this folder are Harry, Bill and I - please indicate if you want access as well). Does this mean we are moving forward on a TreeBASE manuscript? If so, I guess we need to decide some things: * where do we want to send it? Systbiol would be nice, but perhaps we should ask if they're interested. Or are we shopping this around elsewhere? * who's the corresponding author (Bill, I'm guessing)? * can we come up with a "to do" list of things to make this into a ready submision? Rutger On Tue, Jan 26, 2010 at 12:19 AM, Hilmar Lapp <hl...@ne...> wrote: > > On Jan 25, 2010, at 9:01 AM, William Piel wrote: > >> >> Yeah, that's what I had in mind. A "manual" to PhyloWS using TreeBASE API >> as the first implementation of it. > > > That would indeed be a good example for a manual, but I think pretty > strongly that PhyloWS needs to go into an evolutionary data interoperability > story combining PhyloWS with NeXML and relevant ontologies (such as CDAO). > > -hilmar > > > -- > =========================================================== > : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : > =========================================================== > > > -- Dr. Rutger A. Vos Bioinformaticist NCB Naturalis Visiting address: Office A109, Einsteinweg 2, 2333 CC, Leiden, the Netherlands Mailing address: Postbus 9517, 2300 RA, Leiden, the Netherlands http://rutgervos.blogspot.com |
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