From ak.miller at auckland.ac.nz Wed Oct 1 12:11:17 2008 From: ak.miller at auckland.ac.nz (Andrew Miller) Date: Wed, 01 Oct 2008 12:11:17 +1300 Subject: [cellml-discussion] Finalising CellML Metadata 1.0 specification Message-ID: <48E2B215.6070207@auckland.ac.nz> Dear all, I would like to draw your attention to tracker item 1405, which can be viewed at https://tracker.physiomeproject.org/show_bug.cgi?id=1405 . This tracker item proposes that a decision on finalising the CellML Metadata Specification be made on the 15th of October 2008. Please add any comments you may have on this on the tracker item (users without an account at the tracker already can create one), and add yourself to the CC list for the tracker item if you are interesting in receiving updates when others add comments. From the tracker item: " The current draft of the CellML Metadata 1.0 specification has never been finalised, but has been widely cited and adopted. The specification requires work, but due to the number of people citing and adopting the draft, it would make sense to finalise it as it is now, and then start work on the next value of the specification to address these problems. I propose that a decision on whether to finalise the specification be made on the 18th of October 2008, by the group established for making such specification decisions, based on community discussions prior to then. " Best regards, Andrew From starnight1020 at gmail.com Tue Oct 7 08:57:37 2008 From: starnight1020 at gmail.com (song zhen) Date: Mon, 6 Oct 2008 15:57:37 -0400 Subject: [cellml-discussion] installation of CellML DOM API: Core implementation for all platforms Message-ID: <1bc88cd40810061257x7eb203en38ec71fac36a5be3@mail.gmail.com> Hi, I have a trouble in installation of this source file. when I ran "./configure" command in x11, there was an error message stating that "configure: error: GSL CBLAS library required". And actually, I have updated fink and also installed the "gsl" package already. What else should I do to fix this error? Thanks in advance! Song -------------- next part -------------- An HTML attachment was scrubbed... URL: From alan.garny at dpag.ox.ac.uk Tue Oct 7 09:17:38 2008 From: alan.garny at dpag.ox.ac.uk (Alan Garny) Date: Mon, 6 Oct 2008 21:17:38 +0100 Subject: [cellml-discussion] installation of CellML DOM API: Core implementation for all platforms In-Reply-To: <1bc88cd40810061257x7eb203en38ec71fac36a5be3@mail.gmail.com> References: <1bc88cd40810061257x7eb203en38ec71fac36a5be3@mail.gmail.com> Message-ID: <003c01c927f0$94d2ff60$be78fe20$@garny@dpag.ox.ac.uk> Dear Song, Did you have a look at the installation documentation? https://svn.physiomeproject.org/svn/physiome/CellML_DOM_API/trunk/docs/ Hopefully, you use one of the Linux systems for which we have some documentation. Regards, Alan From: cellml-discussion-bounces at cellml.org [mailto:cellml-discussion-bounces at cellml.org] On Behalf Of song zhen Sent: 06 October 2008 20:58 To: cellml-discussion at cellml.org Subject: [cellml-discussion] installation of CellML DOM API: Core implementation for all platforms Hi, I have a trouble in installation of this source file. when I ran "./configure" command in x11, there was an error message stating that "configure: error: GSL CBLAS library required". And actually, I have updated fink and also installed the "gsl" package already. What else should I do to fix this error? Thanks in advance! Song -------------- next part -------------- An HTML attachment was scrubbed... URL: From song.z at neu.edu Tue Oct 7 08:47:35 2008 From: song.z at neu.edu (Zhen Song) Date: Mon, 06 Oct 2008 15:47:35 -0400 Subject: [cellml-discussion] installation of CellML DOM API: Core implementation for all platforms Message-ID: <5B50619E-1BAB-45D3-811E-883849489179@neu.edu> Hi, I have a trouble in installation of this source file. when I ran "./ configure" command in x11, there was an error message stating that "configure: error: GSL CBLAS library required". And actually, I have updated fink and also installed the "gsl" package already. What else should I do to fix this error? Thanks in advance! Song From jonovik at gmail.com Tue Oct 7 19:26:24 2008 From: jonovik at gmail.com (Jon Olav Vik) Date: Tue, 7 Oct 2008 06:26:24 +0000 (UTC) Subject: [cellml-discussion] =?utf-8?q?installation_of_CellML_DOM_API=3A_C?= =?utf-8?q?ore=09implementation_for_all_platforms?= References: <1bc88cd40810061257x7eb203en38ec71fac36a5be3@mail.gmail.com> <6603.27118025652$1223324394@news.gmane.org> Message-ID: Alan Garny writes: > > I have a trouble in installation of this source file. when I ran > > "./configure" command in x11, there was an error message stating that > > "configure: error: GSL CBLAS library required". And actually, I have > > updated fink and also installed the "gsl" package already. What else > > should I do to fix this error? > > Thanks in advance! > > Song > > Dear Song, > Did you have a look at the installation documentation? https:// svn.physiomeproject.org/svn/physiome/CellML_DOM_API/trunk/docs/ > > Hopefully, you use one of the Linux systems for which we have > some documentation. 8-) I am currently getting the same error under Windows XP with MinGW and MSYS. I have downloaded GSL for Windows ( http://gnuwin32.sourceforge.net/packages/ gsl.htm ), but apparently need to tell the configure script where to find the GSL. Unfortunately, I cannot make sense of the following explanation (from the abovementioned web page): "If you will be using one of the dynamic libraries, add GSL_DLL to the list of predefined macros; so for use with Mingw / GCC, add - DGSL_DLL". I think this applies to me, but have no idea *where* (nor *how*) to "add -DGSL_DLL". Is the "list of predefined macros" in a file somewhere? Is - DGSL_DLL a command-line flag? (Just to ensure that this is worth the hassle: Am I correct that the CellML API is the intended way to implement the surely-very-common workflow of "download model from cellml.org; modify parameters; compute trajectory"? I would hope to avoid the overhead of parsing CellML for every evaluation of the ODE. What would be a "good" way of doing that, assuming I have something that can use a compiled C function?) Best regards, Jon Olav From starnight1020 at gmail.com Wed Oct 8 06:25:01 2008 From: starnight1020 at gmail.com (song zhen) Date: Tue, 7 Oct 2008 13:25:01 -0400 Subject: [cellml-discussion] installation of CellML DOM API: Core implementation for all platforms In-Reply-To: <-4902275540324933261@unknownmsgid> References: <1bc88cd40810061257x7eb203en38ec71fac36a5be3@mail.gmail.com> <-4902275540324933261@unknownmsgid> Message-ID: <1bc88cd40810071025x38f7e33dk34c71a59c32c0d06@mail.gmail.com> Hi Alan, I have read those documentations, but I am not familiar with this kind stuff, and the problem is that I don't really know what kind of the Linux systems I am using. Here is the information for my iMac: Mac OS X Version 10.4.11 (Tiger), Fink installed. Could you tell me which documentation in the website you attached is useful for me? And another question is that is CellML DOM API enough to open and use the model file that I downloaded from CellML? Thanks!! Best, Song On Mon, Oct 6, 2008 at 4:17 PM, Alan Garny wrote: > Dear Song, > > > > Did you have a look at the installation documentation? > https://svn.physiomeproject.org/svn/physiome/CellML_DOM_API/trunk/docs/ > > > > Hopefully, you use one of the Linux systems for which we have some > documentation. > > > > Regards, Alan > > > > *From:* cellml-discussion-bounces at cellml.org [mailto: > cellml-discussion-bounces at cellml.org] *On Behalf Of *song zhen > *Sent:* 06 October 2008 20:58 > *To:* cellml-discussion at cellml.org > *Subject:* [cellml-discussion] installation of CellML DOM API: Core > implementation for all platforms > > > > Hi, > I have a trouble in installation of this source file. when I ran > "./configure" command in x11, there was an error message stating that > "configure: error: GSL CBLAS library required". And actually, I have updated > fink and also installed the "gsl" package already. What else should I do to > fix this error? > > Thanks in advance! > > Song > > _______________________________________________ > cellml-discussion mailing list > cellml-discussion at cellml.org > http://www.cellml.org/mailman/listinfo/cellml-discussion > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From ak.miller at auckland.ac.nz Wed Oct 8 09:58:08 2008 From: ak.miller at auckland.ac.nz (Andrew Miller) Date: Wed, 08 Oct 2008 09:58:08 +1300 Subject: [cellml-discussion] installation of CellML DOM API: Core implementation for all platforms In-Reply-To: <1bc88cd40810071025x38f7e33dk34c71a59c32c0d06@mail.gmail.com> References: <1bc88cd40810061257x7eb203en38ec71fac36a5be3@mail.gmail.com> <-4902275540324933261@unknownmsgid> <1bc88cd40810071025x38f7e33dk34c71a59c32c0d06@mail.gmail.com> Message-ID: <48EBCD60.2080207@auckland.ac.nz> song zhen wrote: > Hi Alan, > I have read those documentations, but I am not familiar with this kind > stuff, and the problem is that I don't really know what kind of the > Linux systems I am using. Here is the information for my iMac: Mac OS > X Version 10.4.11 (Tiger), Fink installed. Could you tell me which > documentation in the website you attached is useful for me? > > And another question is that is CellML DOM API enough to open and use > the model file that I downloaded from CellML? Thanks!! Hi Song, The CellML DOM API is a programmatic interface, and is the thing to use if you want to write a program for processing CellML models. If you are looking for a program with a graphical user interface which can be used to edit CellML models and run simulations etc..., try PCEnv, which makes use of the CellML API but exposes it through a user interface. Although PCEnv builds on Mac OS X, there are a number of usability issues at present, so I would recommend downloading a Linux snapshot and running the Linux version in a virtual machine. We are looking to improve OS X support in future. Best wishes, Andrew > > Best, > > Song > > On Mon, Oct 6, 2008 at 4:17 PM, Alan Garny > wrote: > > Dear Song, > > > > Did you have a look at the installation documentation? > https://svn.physiomeproject.org/svn/physiome/CellML_DOM_API/trunk/docs/ > > > > Hopefully, you use one of the Linux systems for which we have some > documentation. > > > > Regards, Alan > > > > *From:* cellml-discussion-bounces at cellml.org > > [mailto:cellml-discussion-bounces at cellml.org > ] *On Behalf Of *song > zhen > *Sent:* 06 October 2008 20:58 > *To:* cellml-discussion at cellml.org > > *Subject:* [cellml-discussion] installation of CellML DOM API: > Core implementation for all platforms > > > > Hi, > I have a trouble in installation of this source file. when I ran > "./configure" command in x11, there was an error message stating > that "configure: error: GSL CBLAS library required". And actually, > I have updated fink and also installed the "gsl" package already. > What else should I do to fix this error? > > Thanks in advance! > > Song > > > _______________________________________________ > cellml-discussion mailing list > cellml-discussion at cellml.org > http://www.cellml.org/mailman/listinfo/cellml-discussion > > > ------------------------------------------------------------------------ > > _______________________________________________ > cellml-discussion mailing list > cellml-discussion at cellml.org > http://www.cellml.org/mailman/listinfo/cellml-discussion > From starnight1020 at gmail.com Wed Oct 8 10:07:03 2008 From: starnight1020 at gmail.com (song zhen) Date: Tue, 7 Oct 2008 17:07:03 -0400 Subject: [cellml-discussion] installation of CellML DOM API: Core implementation for all platforms In-Reply-To: <48EBCD60.2080207@auckland.ac.nz> References: <1bc88cd40810061257x7eb203en38ec71fac36a5be3@mail.gmail.com> <-4902275540324933261@unknownmsgid> <1bc88cd40810071025x38f7e33dk34c71a59c32c0d06@mail.gmail.com> <48EBCD60.2080207@auckland.ac.nz> Message-ID: <1bc88cd40810071407m6082fa4ck2f7e49dd04b74e4d@mail.gmail.com> thanks a lot!! On Tue, Oct 7, 2008 at 4:58 PM, Andrew Miller wrote: > song zhen wrote: > >> Hi Alan, >> I have read those documentations, but I am not familiar with this kind >> stuff, and the problem is that I don't really know what kind of the Linux >> systems I am using. Here is the information for my iMac: Mac OS X Version >> 10.4.11 (Tiger), Fink installed. Could you tell me which documentation in >> the website you attached is useful for me? >> >> And another question is that is CellML DOM API enough to open and use the >> model file that I downloaded from CellML? Thanks!! >> > Hi Song, > > The CellML DOM API is a programmatic interface, and is the thing to use if > you want to write a program for processing CellML models. If you are looking > for a program with a graphical user interface which can be used to edit > CellML models and run simulations etc..., try PCEnv, which makes use of the > CellML API but exposes it through a user interface. > > Although PCEnv builds on Mac OS X, there are a number of usability issues > at present, so I would recommend downloading a Linux snapshot and running > the Linux version in a virtual machine. We are looking to improve OS X > support in future. > > Best wishes, > Andrew > > >> Best, >> >> Song >> >> On Mon, Oct 6, 2008 at 4:17 PM, Alan Garny > alan.garny at dpag.ox.ac.uk>> wrote: >> >> Dear Song, >> >> >> Did you have a look at the installation documentation? >> >> https://svn.physiomeproject.org/svn/physiome/CellML_DOM_API/trunk/docs/ >> >> >> Hopefully, you use one of the Linux systems for which we have some >> documentation. >> >> >> Regards, Alan >> >> >> *From:* cellml-discussion-bounces at cellml.org >> >> [mailto:cellml-discussion-bounces at cellml.org >> ] *On Behalf Of *song >> zhen >> *Sent:* 06 October 2008 20:58 >> *To:* cellml-discussion at cellml.org >> >> *Subject:* [cellml-discussion] installation of CellML DOM API: >> Core implementation for all platforms >> >> >> Hi, >> I have a trouble in installation of this source file. when I ran >> "./configure" command in x11, there was an error message stating >> that "configure: error: GSL CBLAS library required". And actually, >> I have updated fink and also installed the "gsl" package already. >> What else should I do to fix this error? >> >> Thanks in advance! >> >> Song >> >> >> _______________________________________________ >> cellml-discussion mailing list >> cellml-discussion at cellml.org >> http://www.cellml.org/mailman/listinfo/cellml-discussion >> >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> cellml-discussion mailing list >> cellml-discussion at cellml.org >> http://www.cellml.org/mailman/listinfo/cellml-discussion >> >> > > _______________________________________________ > cellml-discussion mailing list > cellml-discussion at cellml.org > http://www.cellml.org/mailman/listinfo/cellml-discussion > -------------- next part -------------- An HTML attachment was scrubbed... URL: From starnight1020 at gmail.com Wed Oct 8 10:26:27 2008 From: starnight1020 at gmail.com (song zhen) Date: Tue, 7 Oct 2008 17:26:27 -0400 Subject: [cellml-discussion] installation of CellML DOM API: Core implementation for all platforms In-Reply-To: <48EBCD60.2080207@auckland.ac.nz> References: <1bc88cd40810061257x7eb203en38ec71fac36a5be3@mail.gmail.com> <-4902275540324933261@unknownmsgid> <1bc88cd40810071025x38f7e33dk34c71a59c32c0d06@mail.gmail.com> <48EBCD60.2080207@auckland.ac.nz> Message-ID: <1bc88cd40810071426t40b949f5sa408719c24665922@mail.gmail.com> Hi everyone, I just downloaded PCEnv 0.4 source code tarball for Mac OS X. Could anyone tell me how to install it? I am new at CellML... On Tue, Oct 7, 2008 at 4:58 PM, Andrew Miller wrote: > song zhen wrote: > >> Hi Alan, >> I have read those documentations, but I am not familiar with this kind >> stuff, and the problem is that I don't really know what kind of the Linux >> systems I am using. Here is the information for my iMac: Mac OS X Version >> 10.4.11 (Tiger), Fink installed. Could you tell me which documentation in >> the website you attached is useful for me? >> >> And another question is that is CellML DOM API enough to open and use the >> model file that I downloaded from CellML? Thanks!! >> > Hi Song, > > The CellML DOM API is a programmatic interface, and is the thing to use if > you want to write a program for processing CellML models. If you are looking > for a program with a graphical user interface which can be used to edit > CellML models and run simulations etc..., try PCEnv, which makes use of the > CellML API but exposes it through a user interface. > > Although PCEnv builds on Mac OS X, there are a number of usability issues > at present, so I would recommend downloading a Linux snapshot and running > the Linux version in a virtual machine. We are looking to improve OS X > support in future. > > Best wishes, > Andrew > > >> Best, >> >> Song >> >> On Mon, Oct 6, 2008 at 4:17 PM, Alan Garny > alan.garny at dpag.ox.ac.uk>> wrote: >> >> Dear Song, >> >> >> Did you have a look at the installation documentation? >> >> https://svn.physiomeproject.org/svn/physiome/CellML_DOM_API/trunk/docs/ >> >> >> Hopefully, you use one of the Linux systems for which we have some >> documentation. >> >> >> Regards, Alan >> >> >> *From:* cellml-discussion-bounces at cellml.org >> >> [mailto:cellml-discussion-bounces at cellml.org >> ] *On Behalf Of *song >> zhen >> *Sent:* 06 October 2008 20:58 >> *To:* cellml-discussion at cellml.org >> >> *Subject:* [cellml-discussion] installation of CellML DOM API: >> Core implementation for all platforms >> >> >> Hi, >> I have a trouble in installation of this source file. when I ran >> "./configure" command in x11, there was an error message stating >> that "configure: error: GSL CBLAS library required". And actually, >> I have updated fink and also installed the "gsl" package already. >> What else should I do to fix this error? >> >> Thanks in advance! >> >> Song >> >> >> _______________________________________________ >> cellml-discussion mailing list >> cellml-discussion at cellml.org >> http://www.cellml.org/mailman/listinfo/cellml-discussion >> >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> cellml-discussion mailing list >> cellml-discussion at cellml.org >> http://www.cellml.org/mailman/listinfo/cellml-discussion >> >> > > _______________________________________________ > cellml-discussion mailing list > cellml-discussion at cellml.org > http://www.cellml.org/mailman/listinfo/cellml-discussion > -------------- next part -------------- An HTML attachment was scrubbed... URL: From j.marsh at auckland.ac.nz Wed Oct 8 17:21:43 2008 From: j.marsh at auckland.ac.nz (Justin Marsh) Date: Wed, 08 Oct 2008 17:21:43 +1300 Subject: [cellml-discussion] CellML DOM API 1.5rc1 (release candidate for CellML DOM API 1.5) out Message-ID: <48EC3557.8040808@auckland.ac.nz> Hi all, The first release candidate for the CellML DOM API, version 1.5, has been released. Information about the released files is available at: http://www.cellml.org/downloads/cellml_api/releases/1.5rc1/ Once a reasonable amount of time has elapsed, and no problems with the release candidate are identified, the CellML DOM API version 1.5 will be released. Please report any bugs you find at https://tracker.physiomeproject.org/, or to this list, or directly to j.marsh at auckland.ac.nz Best regards, Justin Marsh. From j.marsh at auckland.ac.nz Wed Oct 8 17:23:55 2008 From: j.marsh at auckland.ac.nz (Justin Marsh) Date: Wed, 08 Oct 2008 17:23:55 +1300 Subject: [cellml-discussion] Announcement of PCEnv 0.5rc1 (release candidate for PCEnv 0.5) Message-ID: <48EC35DB.4090308@auckland.ac.nz> Hi all, The first release candidate for PCEnv version 0.5 has been released. Information about the released files is available at: http://www.cellml.org/downloads/pcenv/releases/0.5rc1 A release candidate will become a release one week from announcement on this list if there are no problems identified with it. Please report any bugs you find at https://tracker.physiomeproject.org/, or to this list, or directly to j.marsh at auckland.ac.nz Best regards, Justin Marsh. From j.lawson at auckland.ac.nz Thu Oct 9 13:55:50 2008 From: j.lawson at auckland.ac.nz (James Lawson) Date: Thu, 09 Oct 2008 13:55:50 +1300 Subject: [cellml-discussion] Finalising CellML Metadata 1.0 specification In-Reply-To: <48E2B215.6070207@auckland.ac.nz> References: <48E2B215.6070207@auckland.ac.nz> Message-ID: <48ED5696.7010903@auckland.ac.nz> It appears nobody has commented on this directly within cellml-discussion. I understand you hold some opposition to finalising what you believe to be a draft specification, Andre. Could you please elaborate? The current consensus (for reasons Andrew mentions below) is that we should proceed with this with a view to creating the next version of the metadata specification as soon as possible so we can fix the problems with the current spec. Peter Hunter's proposed for this work timeframe is by April 2009, in time for the planned CellML / SBO / MIASE, BioPAX combined workshop. Currently, the process for making final decisions on the specification is discussed in this past email: http://www.mail-archive.com/cellml-discussion at cellml.org/msg00966.html If anyone else has an opinion, please let us know. Additionally, if there is something you would like to see addressed in CellML metadata, please let us know. A collection of known issues can currently be found at: https://tracker.physiomeproject.org/show_bug.cgi?id=1406 Thanks, James Andrew Miller wrote: > Dear all, > > I would like to draw your attention to tracker item 1405, which can be > viewed at https://tracker.physiomeproject.org/show_bug.cgi?id=1405 . > This tracker item proposes that a decision on finalising the CellML > Metadata Specification be made on the 15th of October 2008. Please add > any comments you may have on this on the tracker item (users without > an account at the tracker already can create one), and add yourself to > the CC list for the tracker item if you are interesting in receiving > updates when others add comments. > > From the tracker item: > " > The current draft of the CellML Metadata 1.0 specification has never been > > finalised, but has been widely cited and adopted. The specification > requires > work, but due to the number of people citing and adopting the draft, > it would > make sense to finalise it as it is now, and then start work on the > next value > of the specification to address these problems. > > I propose that a decision on whether to finalise the specification be > made on > the 18th of October 2008, by the group established for making such > specification decisions, based on community discussions prior to then. > > " > > Best regards, > Andrew > _______________________________________________ > cellml-discussion mailing list > cellml-discussion at cellml.org > http://www.cellml.org/mailman/listinfo/cellml-discussion -------------- next part -------------- A non-text attachment was scrubbed... Name: j_lawson.vcf Type: text/x-vcard Size: 278 bytes Desc: not available URL: From david.nickerson at gmail.com Thu Oct 9 15:20:18 2008 From: david.nickerson at gmail.com (David Nickerson) Date: Thu, 9 Oct 2008 10:20:18 +0800 Subject: [cellml-discussion] Finalising CellML Metadata 1.0 specification In-Reply-To: <48ED5696.7010903@auckland.ac.nz> References: <48E2B215.6070207@auckland.ac.nz> <48ED5696.7010903@auckland.ac.nz> Message-ID: On Thu, Oct 9, 2008 at 8:55 AM, James Lawson wrote: > It appears nobody has commented on this directly within cellml-discussion. I > understand you hold some opposition to finalising what you believe to be a > draft specification, Andre. Could you please elaborate? I just think that because the current draft has been clearly marked as a draft that it is not unreasonable to correct known deficiencies prior to releasing the a final 1.0 specification. I'm also a bit wary of setting a precedent of "finalising" a specification with known problems... I guess I would prefer to see the current 1.0 draft not be finalised, at least until a draft of the next version of the specification is available. Then the status of the 1.0 draft would become more of a historical reference which clearly directs users to a specification which is much more useful. > The current consensus (for reasons Andrew mentions below) is that we should > proceed with this with a view to creating the next version of the metadata > specification as soon as possible so we can fix the problems with the > current spec. Peter Hunter's proposed for this work timeframe is by April > 2009, in time for the planned CellML / SBO / MIASE, BioPAX combined > workshop. As I say above, I think work should begin on the next version without waiting to release the 1.0 specification. People citing or adopting a draft specification do so knowing that it is likely to change, and in fact I have had reviewers ask for more detail to be specified when referencing draft specifications in order to allow readers to be clear what is "standard" and what is draft, and what version drafts were used in the work to ensure readers are able to find the appropriate specifications. I think the proposed timeframe is reasonable to get the next version of the specification, at least in draft form, and then at that point the 1.0 specification could be finalised with the link to the new (1.1?) specification draft. Having said that, if releasing the current draft as-is is the only way to make progress on the next version, then I have no strenuous objections to doing so as the actual defects in the specification are quite minor. If this approach is taken, then I would like to see the status section of the specification note this and link to appropriate tracker item(s) detailing the work being done to define a more useful metadata specification. Andre. From j.lawson at auckland.ac.nz Fri Oct 10 10:09:00 2008 From: j.lawson at auckland.ac.nz (James Lawson) Date: Fri, 10 Oct 2008 10:09:00 +1300 Subject: [cellml-discussion] Finalising CellML Metadata 1.0 specification In-Reply-To: References: <48E2B215.6070207@auckland.ac.nz> <48ED5696.7010903@auckland.ac.nz> Message-ID: <48EE72EC.6020601@auckland.ac.nz> > I just think that because the current draft has been clearly marked as > a draft that it is not unreasonable to correct known deficiencies > prior to releasing the a final 1.0 specification. I'm also a bit wary > of setting a precedent of "finalising" a specification with known > problems... > Just to clarify to people here, the main issue is that the link to the BQS spec is now out of date and broken. I doubt this will break anyone's dependencies. -------------- next part -------------- A non-text attachment was scrubbed... Name: j_lawson.vcf Type: text/x-vcard Size: 278 bytes Desc: not available URL: From j.marsh at auckland.ac.nz Wed Oct 15 16:19:55 2008 From: j.marsh at auckland.ac.nz (Justin Marsh) Date: Wed, 15 Oct 2008 16:19:55 +1300 Subject: [cellml-discussion] Announcing CellML DOM API 1.5 Message-ID: <48F5615B.3010202@auckland.ac.nz> Hi all, The CellML DOM API version 1.5 has been released, and is available at http://www.cellml.org/downloads/cellml_api/releases/1.5/ Please report any bugs you find at https://tracker.physiomeproject.org/, or to this list, or directly to j.marsh at auckland.ac.nz Best regards, Justin Marsh. From j.marsh at auckland.ac.nz Wed Oct 15 16:20:30 2008 From: j.marsh at auckland.ac.nz (Justin Marsh) Date: Wed, 15 Oct 2008 16:20:30 +1300 Subject: [cellml-discussion] Announcing PCEnv 0.5 Message-ID: <48F5617E.5060202@auckland.ac.nz> Hi all, PCEnv version 0.5 has been released, and is available at http://www.cellml.org/downloads/pcenv/releases/0.5 Please report any bugs you find at https://tracker.physiomeproject.org/, or to this list, or directly to j.marsh at auckland.ac.nz Best regards, Justin Marsh. From j.marsh at auckland.ac.nz Thu Oct 16 14:16:21 2008 From: j.marsh at auckland.ac.nz (Justin Marsh) Date: Thu, 16 Oct 2008 14:16:21 +1300 Subject: [cellml-discussion] Planning the CellML DOM API 1.6 and PCEnv 0.6 Message-ID: <20081016141621.skbssrixwkgww4ss@webmail.bioeng.auckland.ac.nz> Hi all, We have started a thread of discussion on features for the next set of releases for the CellML DOM API and PCEnv. The discussion can be found at https://tracker.physiomeproject.org/show_bug.cgi?id=1435 Anyone with a tracker account can participate in the discussion thread; tracker accounts can be easily created at https://tracker.physiomeproject.org/createaccount.cgi Best Regards, Justin. ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. From heiland at indiana.edu Thu Oct 16 23:18:44 2008 From: heiland at indiana.edu (Randy Heiland) Date: Thu, 16 Oct 2008 06:18:44 -0400 Subject: [cellml-discussion] Announcing PCEnv 0.5 In-Reply-To: References: Message-ID: Hi Justin, What about us Mac users? :) Any plans for a binary Mac (Intel) build? I tried downloading the source and 'configure' gave me: ... checking for your Mozilla dist directory... not found configure: error: Mozilla distribution directory /usr/local/lib/ mozilla not found. Try --with-mozilla=/path/to/mozilla/dist I do have/use Firefox, so I will try to resolve that error and push ahead unless I hear otherwise from you. I'd welcome a brief/simple explanation of your dependence on Mozilla for PCEnv, or just a link to an explanation. thanks, Randy On Oct 15, 2008, at 7:00 PM, cellml-discussion-request at cellml.org wrote: > > Message: 2 > Date: Wed, 15 Oct 2008 16:20:30 +1300 > From: Justin Marsh > Subject: [cellml-discussion] Announcing PCEnv 0.5 > To: CellML Discussion List > Message-ID: <48F5617E.5060202 at auckland.ac.nz> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Hi all, > > PCEnv version 0.5 has been released, and is available at > http://www.cellml.org/downloads/pcenv/releases/0.5 > > > > Please report any bugs you find at https:// > tracker.physiomeproject.org/, > or to this list, or directly to j.marsh at auckland.ac.nz > > Best regards, > Justin Marsh. > From alan.garny at dpag.ox.ac.uk Thu Oct 16 23:48:47 2008 From: alan.garny at dpag.ox.ac.uk (Alan Garny) Date: Thu, 16 Oct 2008 11:48:47 +0100 Subject: [cellml-discussion] Announcing PCEnv 0.5 In-Reply-To: References: Message-ID: <002901c92f7c$c4a30d00$4de92700$@garny@dpag.ox.ac.uk> Hi Randy, I hope Justin won't mind me stepping in, though I am sure he will in case I have got something wrong! > What about us Mac users? :) Any plans for a binary Mac (Intel) > build? I tried downloading the source and 'configure' gave me: A Mac version is in the work, but it is not quite ready for general use yet. > ... > checking for your Mozilla dist directory... not found > configure: error: Mozilla distribution directory /usr/local/lib/ > mozilla not found. Try --with-mozilla=/path/to/mozilla/dist > > I do have/use Firefox, so I will try to resolve that error and push > ahead unless I hear otherwise from you. I'd welcome a brief/simple > explanation of your dependence on Mozilla for PCEnv, or just a link > to an explanation. To have Firefox is not sufficient. You need the source code as well. As far as I am aware, there is no documentation for building PCEnv under Mac OSX, only for various flavours of Linux. In case you are interested by those, please check the following: - To build the Mozilla framework and PCEnv: https://svn.physiomeproject.org/svn/physiome/pce/trunk/docs/; and - To build the CellML DOM API: https://svn.physiomeproject.org/svn/physiome/CellML_DOM_API/trunk/docs/. The order in which the build should be done is: - Mozilla framework; - CellML DOM API; and - PCEnv. HTH, Alan. From dj.cowan at auckland.ac.nz Tue Oct 21 14:56:54 2008 From: dj.cowan at auckland.ac.nz (Dougal Cowan) Date: Tue, 21 Oct 2008 14:56:54 +1300 Subject: [cellml-discussion] Meeting minutes 2008-10-15 Message-ID: <48FD36E6.8020501@auckland.ac.nz> To the correct list at last, we all hope; The minutes from last week's ABI CellML Team meeting are up at: http://www.cellml.org/meeting_minutes/abi-meeting-minutes-2008-10-15 Dougal From dj.cowan at auckland.ac.nz Wed Oct 29 07:48:11 2008 From: dj.cowan at auckland.ac.nz (Dougal Cowan) Date: Wed, 29 Oct 2008 07:48:11 +1300 Subject: [cellml-discussion] Meeting minutes 2008-10-22 Message-ID: <49075E6B.10505@auckland.ac.nz> The minutes from last week's ABI CellML Team meeting are up at: http://www.cellml.org/meeting_minutes/abi-meeting-minutes-2008-10-22 Dougal From j.lawson at auckland.ac.nz Wed Oct 29 15:54:50 2008 From: j.lawson at auckland.ac.nz (James Lawson) Date: Wed, 29 Oct 2008 15:54:50 +1300 Subject: [cellml-discussion] CellML Metadata Specification development Message-ID: <4907D07A.9000400@auckland.ac.nz> Dear CellML community, We are currently working on a roadmap for future developments in the CellML Metadata Specification. We'd like to direct you to an initial draft of this roadmap at: http://www.cellml.org/Members/jlaw060/cellml-metadata-roadmap/ This is a work-in-progress and still being updated daily, so we would very much appreciate any feedback or questions you might have. Specifically, we would like to compile a draft CellML Metadata 1.1 Specification in time for the 3rd CellML Workshop in April 2009, so this is the main area which we are seeking feedback for. Kind regards, James Lawson -------------- next part -------------- A non-text attachment was scrubbed... Name: j_lawson.vcf Type: text/x-vcard Size: 278 bytes Desc: not available URL: From c.lloyd at auckland.ac.nz Thu Oct 30 12:06:03 2008 From: c.lloyd at auckland.ac.nz (Catherine Lloyd) Date: Thu, 30 Oct 2008 12:06:03 +1300 Subject: [cellml-discussion] CellML, SBGN, SBO, BioPAX, and MIASE 2009 Workshop Message-ID: Dear All We would like to provide you with some more information about the upcoming CellML SBGN SBO BioPAX and MIASE 2009 Workshop, and point out that the registration form has been updated. "Housekeeping" The meeting will be held at Waiheke Island Resort from Sunday 5th - Thursday 9th April. I understand that many of you will be travelling from overseas and will be arriving in New Zealand a day early to allow for jet lag recovery. I have also reserved a number of rooms at the conference centre for the Saturday night. When you fill in the registration form please indicate if you will be arriving on the 4th or the 5th. Also, if you are travelling with your partner or with your family please let me know so I can allocate the rooms appropriately. At past conferences we have asked people if they would mind sharing a room (single sex allocation and, rest assured, everyone gets their own bed!). Please let me know if this is a problem and I will endeavour to get you your own room. Transport from Auckland Airport to the conference centre is reasonably straight forward. There are taxis (~$60), shuttle buses (~$30), and the airport bus (which runs every 15 min $15 single or $22 return http://www.airbus.co.nz/home/) . Ask for the downtown ferry building. Ferries to Waiheke run roughly every hour on the hour (http://www.fullers.co.nz/index.php/pi_pageid/210 ). Ferry tickets will be provided. Please give your name and the "Auckland Bioengineering Institute" as a password at the ticket office on pier 2 and a return ticket will be given to you. To get from the Waiheke Wharf to the Conference Centre there are buses that meet the ferry (destination Palm Beach, ask the driver exactly where to get off for the Waiheke Island Resort), and also taxis (~$30) and shuttle buses (shared fare). Breakfast, morning tea, lunch and afternoon tea will be provided, and there will also be a couple of conference dinners. On the other evenings, meals can be purchased from the conference centre, or you may choose to dine out at one of the cafes, restaurants, or vineyards on the island (http://www.waihekenz.com/waiheke_island_activities_dining.html ). Programme There will be five days of talks, posters and informal discussion. Mornings will be dedicated to a series of short (5 min) talks and chaired discussion, with the early afternoon reserved for less formal, break away discussion. Late afternoons and evenings will be free for further conversation (which you may choose to relocate to the beach!) or for general recreation. Posters will be displayed around the room for the majority of the meeting. For those of you who are interested in presenting, the registration form has been updated to include an abstract box (up to 350 words), and please indicate if you would prefer to give an oral presentation or a poster. For those of you who have already registered, I apologise. Either you can submit your details again or, alternatively, you can email me with your arrival date (Sat 4th or Sun 5th), whether you will be travelling alone or with your partner (or family), and if you would like to present please send me a short abstract and an indication of whether you prefer an oral presentation or a poster. If you have any further questions or requests, please don't hesitate to contact me. Best wishes Catherine -------------- next part -------------- An HTML attachment was scrubbed... URL: From ak.miller at auckland.ac.nz Thu Oct 30 14:37:07 2008 From: ak.miller at auckland.ac.nz (Andrew Miller) Date: Thu, 30 Oct 2008 14:37:07 +1300 Subject: [cellml-discussion] [Fwd: Visual model design and editing capabilities for CellML] Message-ID: <49090FC3.6000303@auckland.ac.nz> Forwarding to cellml-discussion as this is the most appropriate mailing list. -------- Original Message -------- Subject: Visual model design and editing capabilities for CellML Date: Thu, 30 Oct 2008 14:03:14 +1300 From: Abhishek Tiwari To: team at cellml.org, Andrew Miller , David Nickerson Hi all, Here I am attaching a proposal document "Visual model design and editing capabilities for CellML", which I created long back and only few of you have accessed the document. The document is more like a conceptual sketch of how we can make CellML tools more user friendly and versatile. I don't claim that this will be very useful for CellML team especially when document is incomplete, but it can convey the concepts and requirements. In recent there have been a lot of discussion about metadata specification roadmap and I thought this would be appropriate time to get feedback from CellML team and other users, as concept describe in document may need some extended versions of these specifications. To develop a visual model design and editing capabilities for CellML, we need 1) Defined set of symbols for network diagrams, like SBGN or Edinburgh Pathway Notation but more optimized for CellML. (Do we need CellML sepcific visual notations or we should fallow existing standards ? ) 2) Model visual representation metadata specification (updated http://www.cellml.org/Members/jlaw060/cellml-metadata-roadmap/), it will be closely related with visual notation system we select for CellML tools The terms, definition and other requirements mentioned in proposal are not standard at all, and open for comments and feedbacks. thanks for valuable time and comments/suggestions. Abhishek -------------- next part -------------- A non-text attachment was scrubbed... Name: VisualDesigne2nd.pdf Type: application/pdf Size: 192512 bytes Desc: not available URL: From m.cooling at auckland.ac.nz Thu Oct 30 14:50:18 2008 From: m.cooling at auckland.ac.nz (Michael Cooling) Date: Thu, 30 Oct 2008 14:50:18 +1300 Subject: [cellml-discussion] [Fwd: Visual model design and editing capabilities for CellML] In-Reply-To: <49090FC3.6000303@auckland.ac.nz> References: <49090FC3.6000303@auckland.ac.nz> Message-ID: <20081030145018.uso4h1diqsgk0k8o@webmail.bioeng.auckland.ac.nz> ooo something close to my heart but unfortunately Abhishek I can't seem to open your document...hope it's not my machine...? Regards, Mike Cooling, PhD Research Fellow Auckland Bioengineering Institute New Zealand http://www.bioeng.auckland.ac.nz/people/mcoo001 Quoting Andrew Miller : > Forwarding to cellml-discussion as this is the most appropriate mailing list. > > -------- Original Message -------- > Subject: Visual model design and editing capabilities for CellML > Date: Thu, 30 Oct 2008 14:03:14 +1300 > From: Abhishek Tiwari > To: team at cellml.org, Andrew Miller , David > Nickerson > > > > Hi all, > Here I am attaching a proposal document "Visual model design and > editing capabilities for CellML", which I created long back and only > few of you have accessed the document. The document is more like a > conceptual sketch of how we can make CellML tools more user friendly > and versatile. I don't claim that this will be very useful for CellML > team especially when document is incomplete, but it can convey the > concepts and requirements. In recent there have been a lot of > discussion about metadata specification roadmap and I thought this > would be appropriate time to get feedback from CellML team and other > users, as concept describe in document may need some extended versions > of these specifications. To develop a visual model design and editing > capabilities for CellML, we need > 1) Defined set of symbols for network diagrams, like SBGN or Edinburgh > Pathway Notation but more optimized for CellML. (Do we need CellML > sepcific visual notations or we should fallow existing standards ? ) > 2) Model visual representation metadata specification (updated > http://www.cellml.org/Members/jlaw060/cellml-metadata-roadmap/), it > will be closely related with visual notation system we select for > CellML tools > The terms, definition and other requirements mentioned in proposal are > not standard at all, and open for comments and feedbacks. > > thanks for valuable time and comments/suggestions. > Abhishek ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. From j.lawson at auckland.ac.nz Thu Oct 30 14:58:30 2008 From: j.lawson at auckland.ac.nz (James Lawson) Date: Thu, 30 Oct 2008 14:58:30 +1300 Subject: [cellml-discussion] [Fwd: Visual model design and editing capabilities for CellML] In-Reply-To: <20081030145018.uso4h1diqsgk0k8o@webmail.bioeng.auckland.ac.nz> References: <49090FC3.6000303@auckland.ac.nz> <20081030145018.uso4h1diqsgk0k8o@webmail.bioeng.auckland.ac.nz> Message-ID: <490914C6.4080801@auckland.ac.nz> Likewise. Would be very interested to read this though. Thanks, James Michael Cooling wrote: > ooo > > something close to my heart > > but unfortunately Abhishek I can't seem to open your document...hope > it's not my machine...? > > Regards, > > Mike Cooling, PhD > Research Fellow > Auckland Bioengineering Institute > New Zealand > http://www.bioeng.auckland.ac.nz/people/mcoo001 > > > > Quoting Andrew Miller : > >> Forwarding to cellml-discussion as this is the most appropriate >> mailing list. >> >> -------- Original Message -------- >> Subject: Visual model design and editing capabilities for CellML >> Date: Thu, 30 Oct 2008 14:03:14 +1300 >> From: Abhishek Tiwari >> To: team at cellml.org, Andrew Miller , David >> Nickerson >> >> >> >> Hi all, >> Here I am attaching a proposal document "Visual model design and >> editing capabilities for CellML", which I created long back and only >> few of you have accessed the document. The document is more like a >> conceptual sketch of how we can make CellML tools more user friendly >> and versatile. I don't claim that this will be very useful for CellML >> team especially when document is incomplete, but it can convey the >> concepts and requirements. In recent there have been a lot of >> discussion about metadata specification roadmap and I thought this >> would be appropriate time to get feedback from CellML team and other >> users, as concept describe in document may need some extended versions >> of these specifications. To develop a visual model design and editing >> capabilities for CellML, we need >> 1) Defined set of symbols for network diagrams, like SBGN or Edinburgh >> Pathway Notation but more optimized for CellML. (Do we need CellML >> sepcific visual notations or we should fallow existing standards ? ) >> 2) Model visual representation metadata specification (updated >> http://www.cellml.org/Members/jlaw060/cellml-metadata-roadmap/), it >> will be closely related with visual notation system we select for >> CellML tools >> The terms, definition and other requirements mentioned in proposal are >> not standard at all, and open for comments and feedbacks. >> >> thanks for valuable time and comments/suggestions. >> Abhishek > > > > ---------------------------------------------------------------- > This message was sent using IMP, the Internet Messaging Program. > > _______________________________________________ > cellml-discussion mailing list > cellml-discussion at cellml.org > http://www.cellml.org/mailman/listinfo/cellml-discussion -------------- next part -------------- A non-text attachment was scrubbed... Name: j_lawson.vcf Type: text/x-vcard Size: 278 bytes Desc: not available URL: From sarala.dissanayake at auckland.ac.nz Thu Oct 30 15:03:49 2008 From: sarala.dissanayake at auckland.ac.nz (Sarala Dissanayake) Date: Thu, 30 Oct 2008 15:03:49 +1300 Subject: [cellml-discussion] [Fwd: Visual model design and editing capabilities for CellML] In-Reply-To: <49090FC3.6000303@auckland.ac.nz> References: <49090FC3.6000303@auckland.ac.nz> Message-ID: <20081030150349.osqfiq5bacw4c8s8@webmail.bioeng.auckland.ac.nz> Hi Abhishek, I can't seem to open the file either. However, I'm working on visualization of CellML models. I've already looked at using existing notations to visualize CellML models. Currently I have my own notation and I'm also looking at using SBGN. I've developed a work flow to annotate and visualise CellML models. So I'm not quite sure how this work is going to be different (ref last paragraph on the CellML metadata road map page). Please let me know if you want to know more about what I'm working on. Cheers, Sarala Quoting Andrew Miller : > Forwarding to cellml-discussion as this is the most appropriate mailing list. > > -------- Original Message -------- > Subject: Visual model design and editing capabilities for CellML > Date: Thu, 30 Oct 2008 14:03:14 +1300 > From: Abhishek Tiwari > To: team at cellml.org, Andrew Miller , David > Nickerson > > > > Hi all, > Here I am attaching a proposal document "Visual model design and > editing capabilities for CellML", which I created long back and only > few of you have accessed the document. The document is more like a > conceptual sketch of how we can make CellML tools more user friendly > and versatile. I don't claim that this will be very useful for CellML > team especially when document is incomplete, but it can convey the > concepts and requirements. In recent there have been a lot of > discussion about metadata specification roadmap and I thought this > would be appropriate time to get feedback from CellML team and other > users, as concept describe in document may need some extended versions > of these specifications. To develop a visual model design and editing > capabilities for CellML, we need > 1) Defined set of symbols for network diagrams, like SBGN or Edinburgh > Pathway Notation but more optimized for CellML. (Do we need CellML > sepcific visual notations or we should fallow existing standards ? ) > 2) Model visual representation metadata specification (updated > http://www.cellml.org/Members/jlaw060/cellml-metadata-roadmap/), it > will be closely related with visual notation system we select for > CellML tools > The terms, definition and other requirements mentioned in proposal are > not standard at all, and open for comments and feedbacks. > > thanks for valuable time and comments/suggestions. > Abhishek ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. From j.lawson at auckland.ac.nz Thu Oct 30 16:05:24 2008 From: j.lawson at auckland.ac.nz (James Lawson) Date: Thu, 30 Oct 2008 16:05:24 +1300 Subject: [cellml-discussion] [Fwd: Visual model design and editing capabilities for CellML] In-Reply-To: <49090FC3.6000303@auckland.ac.nz> References: <49090FC3.6000303@auckland.ac.nz> Message-ID: <49092474.7080407@auckland.ac.nz> Attached is a version of the document that is readable Andrew Miller wrote: > Forwarding to cellml-discussion as this is the most appropriate > mailing list. > > -------- Original Message -------- > Subject: Visual model design and editing capabilities for CellML > Date: Thu, 30 Oct 2008 14:03:14 +1300 > From: Abhishek Tiwari > To: team at cellml.org, Andrew Miller , > David Nickerson > > > > Hi all, > Here I am attaching a proposal document "Visual model design and > editing capabilities for CellML", which I created long back and only > few of you have accessed the document. The document is more like a > conceptual sketch of how we can make CellML tools more user friendly > and versatile. I don't claim that this will be very useful for CellML > team especially when document is incomplete, but it can convey the > concepts and requirements. In recent there have been a lot of > discussion about metadata specification roadmap and I thought this > would be appropriate time to get feedback from CellML team and other > users, as concept describe in document may need some extended versions > of these specifications. To develop a visual model design and editing > capabilities for CellML, we need > 1) Defined set of symbols for network diagrams, like SBGN or Edinburgh > Pathway Notation but more optimized for CellML. (Do we need CellML > sepcific visual notations or we should fallow existing standards ? ) > 2) Model visual representation metadata specification (updated > http://www.cellml.org/Members/jlaw060/cellml-metadata-roadmap/), it > will be closely related with visual notation system we select for > CellML tools > The terms, definition and other requirements mentioned in proposal are > not standard at all, and open for comments and feedbacks. > > thanks for valuable time and comments/suggestions. > Abhishek > > > ------------------------------------------------------------------------ > > _______________________________________________ > cellml-discussion mailing list > cellml-discussion at cellml.org > http://www.cellml.org/mailman/listinfo/cellml-discussion > -------------- next part -------------- A non-text attachment was scrubbed... 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Name: j_lawson.vcf Type: text/x-vcard Size: 278 bytes Desc: not available URL: From a.tiwari at auckland.ac.nz Thu Oct 30 16:15:44 2008 From: a.tiwari at auckland.ac.nz (Abhishek Tiwari) Date: Thu, 30 Oct 2008 16:15:44 +1300 Subject: [cellml-discussion] cellml-discussion Digest, Vol 51, Issue 14 In-Reply-To: References: Message-ID: <490926E0.7050600@auckland.ac.nz> Hi all, Please find the PDF attachment on tracker for the same topic https://tracker.physiomeproject.org/show_bug.cgi?id=1464 else, I am attaching the PDF document again regards Abhishek cellml-discussion-request at cellml.org wrote: > Send cellml-discussion mailing list submissions to > cellml-discussion at cellml.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.cellml.org/mailman/listinfo/cellml-discussion > or, via email, send a message with subject or body 'help' to > cellml-discussion-request at cellml.org > > You can reach the person managing the list at > cellml-discussion-owner at cellml.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of cellml-discussion digest..." > > > Today's Topics: > > 1. Re: [Fwd: Visual model design and editing capabilities for > CellML] (Michael Cooling) > 2. Re: [Fwd: Visual model design and editing capabilities for > CellML] (James Lawson) > 3. Re: [Fwd: Visual model design and editing capabilities for > CellML] (Sarala Dissanayake) > 4. Re: [Fwd: Visual model design and editing capabilities for > CellML] (James Lawson) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 30 Oct 2008 14:50:18 +1300 > From: Michael Cooling > Subject: Re: [cellml-discussion] [Fwd: Visual model design and editing > capabilities for CellML] > To: cellml-discussion at cellml.org > Message-ID: > <20081030145018.uso4h1diqsgk0k8o at webmail.bioeng.auckland.ac.nz> > Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; > format="flowed" > > ooo > > something close to my heart > > but unfortunately Abhishek I can't seem to open your document...hope > it's not my machine...? > > Regards, > > Mike Cooling, PhD > Research Fellow > Auckland Bioengineering Institute > New Zealand > http://www.bioeng.auckland.ac.nz/people/mcoo001 > > > > Quoting Andrew Miller : > > >> Forwarding to cellml-discussion as this is the most appropriate mailing list. >> >> -------- Original Message -------- >> Subject: Visual model design and editing capabilities for CellML >> Date: Thu, 30 Oct 2008 14:03:14 +1300 >> From: Abhishek Tiwari >> To: team at cellml.org, Andrew Miller , David >> Nickerson >> >> >> >> Hi all, >> Here I am attaching a proposal document "Visual model design and >> editing capabilities for CellML", which I created long back and only >> few of you have accessed the document. The document is more like a >> conceptual sketch of how we can make CellML tools more user friendly >> and versatile. I don't claim that this will be very useful for CellML >> team especially when document is incomplete, but it can convey the >> concepts and requirements. In recent there have been a lot of >> discussion about metadata specification roadmap and I thought this >> would be appropriate time to get feedback from CellML team and other >> users, as concept describe in document may need some extended versions >> of these specifications. To develop a visual model design and editing >> capabilities for CellML, we need >> 1) Defined set of symbols for network diagrams, like SBGN or Edinburgh >> Pathway Notation but more optimized for CellML. (Do we need CellML >> sepcific visual notations or we should fallow existing standards ? ) >> 2) Model visual representation metadata specification (updated >> http://www.cellml.org/Members/jlaw060/cellml-metadata-roadmap/), it >> will be closely related with visual notation system we select for >> CellML tools >> The terms, definition and other requirements mentioned in proposal are >> not standard at all, and open for comments and feedbacks. >> >> thanks for valuable time and comments/suggestions. >> Abhishek >> > > > > ---------------------------------------------------------------- > This message was sent using IMP, the Internet Messaging Program. > > > > ------------------------------ > > Message: 2 > Date: Thu, 30 Oct 2008 14:58:30 +1300 > From: James Lawson > Subject: Re: [cellml-discussion] [Fwd: Visual model design and editing > capabilities for CellML] > To: CellML Discussion List > Message-ID: <490914C6.4080801 at auckland.ac.nz> > Content-Type: text/plain; charset="iso-8859-1"; Format="flowed" > > Likewise. Would be very interested to read this though. > > Thanks, > James > > Michael Cooling wrote: > >> ooo >> >> something close to my heart >> >> but unfortunately Abhishek I can't seem to open your document...hope >> it's not my machine...? >> >> Regards, >> >> Mike Cooling, PhD >> Research Fellow >> Auckland Bioengineering Institute >> New Zealand >> http://www.bioeng.auckland.ac.nz/people/mcoo001 >> >> >> >> Quoting Andrew Miller : >> >> >>> Forwarding to cellml-discussion as this is the most appropriate >>> mailing list. >>> >>> -------- Original Message -------- >>> Subject: Visual model design and editing capabilities for CellML >>> Date: Thu, 30 Oct 2008 14:03:14 +1300 >>> From: Abhishek Tiwari >>> To: team at cellml.org, Andrew Miller , David >>> Nickerson >>> >>> >>> >>> Hi all, >>> Here I am attaching a proposal document "Visual model design and >>> editing capabilities for CellML", which I created long back and only >>> few of you have accessed the document. The document is more like a >>> conceptual sketch of how we can make CellML tools more user friendly >>> and versatile. I don't claim that this will be very useful for CellML >>> team especially when document is incomplete, but it can convey the >>> concepts and requirements. In recent there have been a lot of >>> discussion about metadata specification roadmap and I thought this >>> would be appropriate time to get feedback from CellML team and other >>> users, as concept describe in document may need some extended versions >>> of these specifications. To develop a visual model design and editing >>> capabilities for CellML, we need >>> 1) Defined set of symbols for network diagrams, like SBGN or Edinburgh >>> Pathway Notation but more optimized for CellML. (Do we need CellML >>> sepcific visual notations or we should fallow existing standards ? ) >>> 2) Model visual representation metadata specification (updated >>> http://www.cellml.org/Members/jlaw060/cellml-metadata-roadmap/), it >>> will be closely related with visual notation system we select for >>> CellML tools >>> The terms, definition and other requirements mentioned in proposal are >>> not standard at all, and open for comments and feedbacks. >>> >>> thanks for valuable time and comments/suggestions. >>> Abhishek >>> >> >> ---------------------------------------------------------------- >> This message was sent using IMP, the Internet Messaging Program. >> >> _______________________________________________ >> cellml-discussion mailing list >> cellml-discussion at cellml.org >> http://www.cellml.org/mailman/listinfo/cellml-discussion >> > > -------------- next part -------------- > A non-text attachment was scrubbed... > Name: j_lawson.vcf > Type: text/x-vcard > Size: 278 bytes > Desc: not available > URL: > > ------------------------------ > > Message: 3 > Date: Thu, 30 Oct 2008 15:03:49 +1300 > From: Sarala Dissanayake > Subject: Re: [cellml-discussion] [Fwd: Visual model design and editing > capabilities for CellML] > To: cellml-discussion at cellml.org > Message-ID: > <20081030150349.osqfiq5bacw4c8s8 at webmail.bioeng.auckland.ac.nz> > Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; > format="flowed" > > Hi Abhishek, > > I can't seem to open the file either. > > However, I'm working on visualization of CellML models. I've already > looked at using existing notations to visualize CellML models. > Currently I have my own notation and I'm also looking at using SBGN. > I've developed a work flow to annotate and visualise CellML models. So > I'm not quite sure how this work is going to be different (ref last > paragraph on the CellML metadata road map page). > > Please let me know if you want to know more about what I'm working on. > > Cheers, > Sarala > > Quoting Andrew Miller : > > >> Forwarding to cellml-discussion as this is the most appropriate mailing list. >> >> -------- Original Message -------- >> Subject: Visual model design and editing capabilities for CellML >> Date: Thu, 30 Oct 2008 14:03:14 +1300 >> From: Abhishek Tiwari >> To: team at cellml.org, Andrew Miller , David >> Nickerson >> >> >> >> Hi all, >> Here I am attaching a proposal document "Visual model design and >> editing capabilities for CellML", which I created long back and only >> few of you have accessed the document. The document is more like a >> conceptual sketch of how we can make CellML tools more user friendly >> and versatile. I don't claim that this will be very useful for CellML >> team especially when document is incomplete, but it can convey the >> concepts and requirements. In recent there have been a lot of >> discussion about metadata specification roadmap and I thought this >> would be appropriate time to get feedback from CellML team and other >> users, as concept describe in document may need some extended versions >> of these specifications. To develop a visual model design and editing >> capabilities for CellML, we need >> 1) Defined set of symbols for network diagrams, like SBGN or Edinburgh >> Pathway Notation but more optimized for CellML. (Do we need CellML >> sepcific visual notations or we should fallow existing standards ? ) >> 2) Model visual representation metadata specification (updated >> http://www.cellml.org/Members/jlaw060/cellml-metadata-roadmap/), it >> will be closely related with visual notation system we select for >> CellML tools >> The terms, definition and other requirements mentioned in proposal are >> not standard at all, and open for comments and feedbacks. >> >> thanks for valuable time and comments/suggestions. >> Abhishek >> > > > > ---------------------------------------------------------------- > This message was sent using IMP, the Internet Messaging Program. > > > > ------------------------------ > > Message: 4 > Date: Thu, 30 Oct 2008 16:05:24 +1300 > From: James Lawson > Subject: Re: [cellml-discussion] [Fwd: Visual model design and editing > capabilities for CellML] > To: CellML Discussion List > Message-ID: <49092474.7080407 at auckland.ac.nz> > Content-Type: text/plain; charset="iso-8859-1"; Format="flowed" > > Attached is a version of the document that is readable > > Andrew Miller wrote: > >> Forwarding to cellml-discussion as this is the most appropriate >> mailing list. >> >> -------- Original Message -------- >> Subject: Visual model design and editing capabilities for CellML >> Date: Thu, 30 Oct 2008 14:03:14 +1300 >> From: Abhishek Tiwari >> To: team at cellml.org, Andrew Miller , >> David Nickerson >> >> >> >> Hi all, >> Here I am attaching a proposal document "Visual model design and >> editing capabilities for CellML", which I created long back and only >> few of you have accessed the document. The document is more like a >> conceptual sketch of how we can make CellML tools more user friendly >> and versatile. I don't claim that this will be very useful for CellML >> team especially when document is incomplete, but it can convey the >> concepts and requirements. In recent there have been a lot of >> discussion about metadata specification roadmap and I thought this >> would be appropriate time to get feedback from CellML team and other >> users, as concept describe in document may need some extended versions >> of these specifications. To develop a visual model design and editing >> capabilities for CellML, we need >> 1) Defined set of symbols for network diagrams, like SBGN or Edinburgh >> Pathway Notation but more optimized for CellML. (Do we need CellML >> sepcific visual notations or we should fallow existing standards ? ) >> 2) Model visual representation metadata specification (updated >> http://www.cellml.org/Members/jlaw060/cellml-metadata-roadmap/), it >> will be closely related with visual notation system we select for >> CellML tools >> The terms, definition and other requirements mentioned in proposal are >> not standard at all, and open for comments and feedbacks. >> >> thanks for valuable time and comments/suggestions. >> Abhishek >> >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> cellml-discussion mailing list >> cellml-discussion at cellml.org >> http://www.cellml.org/mailman/listinfo/cellml-discussion >> >> > > -------------- next part -------------- > A non-text attachment was scrubbed... > Name: visual_cellml_editor.pdf > Type: application/pdf > Size: 908000 bytes > Desc: not available > URL: > -------------- next part -------------- > A non-text attachment was scrubbed... > Name: j_lawson.vcf > Type: text/x-vcard > Size: 278 bytes > Desc: not available > URL: > > ------------------------------ > > _______________________________________________ > cellml-discussion mailing list > cellml-discussion at cellml.org > http://www.cellml.org/mailman/listinfo/cellml-discussion > > > End of cellml-discussion Digest, Vol 51, Issue 14 > ************************************************* > -------------- next part -------------- A non-text attachment was scrubbed... Name: VisualDesigne2nd.pdf Type: application/pdf Size: 908000 bytes Desc: not available URL: From mhucka at caltech.edu Thu Oct 30 16:24:06 2008 From: mhucka at caltech.edu (Michael Hucka) Date: Wed, 29 Oct 2008 20:24:06 -0700 Subject: [cellml-discussion] [Fwd: Visual model design and editing capabilities for CellML] In-Reply-To: <49092474.7080407@auckland.ac.nz> References: <49090FC3.6000303@auckland.ac.nz> <49092474.7080407@auckland.ac.nz> Message-ID: <18697.10454.173385.204137@frantic.local> Whoaaah. The notation shown in Figure 5 of this document as the "SBGN" draft is not SBGN. It was CellDesigner notation, and is significantly different from what SBGN is now. The current specification on sbgn.org includes a one-page summary of the process diagram notation. Please make sure to use that, and not figure 5, when making any evaluation of SBGN :-). (This is not a criticism and I'm not trying to be picky; I only want to clarify this one point because it can be potentially important in a decision about choice of notations. I know it's hard to track what's going on in different efforts, and that this document is several months old.) MH P.S. As far as I'm aware, EPE (Edinburgh Pathway Editor) is in the process of switching to SBGN, so the EPN notation may be becoming a bit irrelevant. From lenov at ebi.ac.uk Thu Oct 30 21:00:45 2008 From: lenov at ebi.ac.uk (Nicolas Le Novere) Date: Thu, 30 Oct 2008 08:00:45 +0000 Subject: [cellml-discussion] [Fwd: Visual model design and editing capabilities for CellML] In-Reply-To: <18697.10454.173385.204137@frantic.local> References: <49090FC3.6000303@auckland.ac.nz> <49092474.7080407@auckland.ac.nz> <18697.10454.173385.204137@frantic.local> Message-ID: <490969AD.2010105@ebi.ac.uk> Michael Hucka wrote: > Whoaaah. The notation shown in Figure 5 of this document as > the "SBGN" draft is not SBGN. It was CellDesigner notation, > and is significantly different from what SBGN is now. Indeed :-) > P.S. As far as I'm aware, EPE (Edinburgh Pathway Editor) is > in the process of switching to SBGN, so the EPN notation may > be becoming a bit irrelevant. You may also be interested in the following software that have started to implement SBGN: VANTED http://vanted.ipk-gatersleben.de/ ARCADIA http://personalpages.manchester.ac.uk/staff/Alice.Villeger/arcadia.html -- Nicolas LE NOVERE, Computational Neurobiology, EMBL-EBI, Wellcome-Trust Genome Campus, Hinxton CB101SD UK, Mob:+447833147074, Tel:+441223494521 Fax:468, Skype:n.lenovere, AIM:nlenovere, MSN:nlenovere at hotmail.com http://www.ebi.ac.uk/~lenov/, http://www.ebi.ac.uk/compneur/ From lenov at ebi.ac.uk Thu Oct 30 21:03:28 2008 From: lenov at ebi.ac.uk (Nicolas Le Novere) Date: Thu, 30 Oct 2008 08:03:28 +0000 Subject: [cellml-discussion] [Fwd: Visual model design and editing capabilities for CellML] In-Reply-To: <18697.10454.173385.204137@frantic.local> References: <49090FC3.6000303@auckland.ac.nz> <49092474.7080407@auckland.ac.nz> <18697.10454.173385.204137@frantic.local> Message-ID: <49096A50.9050109@ebi.ac.uk> Michael Hucka wrote: > The current specification on sbgn.org includes a one-page > summary of the process diagram notation. Please make sure > to use that, and not figure 5, when making any evaluation of > SBGN :-). Attached is the reference card for SBGN Process Diagram Level 1 You can find examples at: http://www.sbgn.org/Documents/Examples Best. -- Nicolas LE NOVERE, Computational Neurobiology, EMBL-EBI, Wellcome-Trust Genome Campus, Hinxton CB101SD UK, Mob:+447833147074, Tel:+441223494521 Fax:468, Skype:n.lenovere, AIM:nlenovere, MSN:nlenovere at hotmail.com http://www.ebi.ac.uk/~lenov/, http://www.ebi.ac.uk/compneur/ -------------- next part -------------- A non-text attachment was scrubbed... Name: Refcard_small.png Type: image/png Size: 119751 bytes Desc: not available URL: From a.tiwari at auckland.ac.nz Fri Oct 31 00:00:02 2008 From: a.tiwari at auckland.ac.nz (Abhishek Tiwari) Date: Fri, 31 Oct 2008 00:00:02 +1300 Subject: [cellml-discussion] cellml-discussion Digest, Vol 51, Issue 16 In-Reply-To: References: Message-ID: <20081031000002.kat5zkmvc4gkgc4s@webmail.bioeng.auckland.ac.nz> Dear Michael and Nicolas, Thanks for your comments. Definitely the Figure 5 is not SBGN Process Diagrams Level 1 (released around Aug '08, parallel with new SBGN website). When I wrote this proposal (around April '08), there was no official release for SBGN Process Diagrams, but that time CellDesigner website mentioned that CellDesigner's Graphical Notation conforms to SBGN proposal (as of April '08 draft), and thats why I used the image from CellDesigner's Graphical Notation to give a representative idea about SBGN, and there was nothing wrong especially when many of CellDesigner team members are respected authors of the SBGN Progress Diagrams specification. Meanwhile I will make sure that final version have updated SBGN notations. thanks Abhishek P.S. regarding different standards or notation systems, it will be never irrelevant to have multiple standards (domination may be mantra of Microsoft), it gives freedom to choose and that's beauty of open community based projects. Quoting cellml-discussion-request at cellml.org: > Send cellml-discussion mailing list submissions to > cellml-discussion at cellml.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.cellml.org/mailman/listinfo/cellml-discussion > or, via email, send a message with subject or body 'help' to > cellml-discussion-request at cellml.org > > You can reach the person managing the list at > cellml-discussion-owner at cellml.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of cellml-discussion digest..." > > > Today's Topics: > > 1. Re: [Fwd: Visual model design and editing capabilities for > CellML] (Michael Hucka) > 2. Re: [Fwd: Visual model design and editing capabilities for > CellML] (Nicolas Le Novere) > 3. Re: [Fwd: Visual model design and editing capabilities for > CellML] (Nicolas Le Novere) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 29 Oct 2008 20:24:06 -0700 > From: "Michael Hucka" > Subject: Re: [cellml-discussion] [Fwd: Visual model design and editing > capabilities for CellML] > To: CellML Discussion List > Message-ID: <18697.10454.173385.204137 at frantic.local> > Content-Type: text/plain; charset=us-ascii > > Whoaaah. The notation shown in Figure 5 of this document as > the "SBGN" draft is not SBGN. It was CellDesigner notation, > and is significantly different from what SBGN is now. > > The current specification on sbgn.org includes a one-page > summary of the process diagram notation. Please make sure > to use that, and not figure 5, when making any evaluation of > SBGN :-). > > (This is not a criticism and I'm not trying to be picky; I > only want to clarify this one point because it can be > potentially important in a decision about choice of > notations. I know it's hard to track what's going on in > different efforts, and that this document is several months > old.) > > MH > > P.S. As far as I'm aware, EPE (Edinburgh Pathway Editor) is > in the process of switching to SBGN, so the EPN notation may > be becoming a bit irrelevant. > > > > ------------------------------ > > Message: 2 > Date: Thu, 30 Oct 2008 08:00:45 +0000 > From: Nicolas Le Novere > Subject: Re: [cellml-discussion] [Fwd: Visual model design and editing > capabilities for CellML] > To: CellML Discussion List > Message-ID: <490969AD.2010105 at ebi.ac.uk> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Michael Hucka wrote: >> Whoaaah. The notation shown in Figure 5 of this document as >> the "SBGN" draft is not SBGN. It was CellDesigner notation, >> and is significantly different from what SBGN is now. > > Indeed :-) > >> P.S. As far as I'm aware, EPE (Edinburgh Pathway Editor) is >> in the process of switching to SBGN, so the EPN notation may >> be becoming a bit irrelevant. > > You may also be interested in the following software that have > started to implement SBGN: > > VANTED > http://vanted.ipk-gatersleben.de/ > > ARCADIA > http://personalpages.manchester.ac.uk/staff/Alice.Villeger/arcadia.html > > -- > Nicolas LE NOVERE, Computational Neurobiology, EMBL-EBI, Wellcome-Trust > Genome Campus, Hinxton CB101SD UK, Mob:+447833147074, Tel:+441223494521 > Fax:468, Skype:n.lenovere, AIM:nlenovere, MSN:nlenovere at hotmail.com > http://www.ebi.ac.uk/~lenov/, http://www.ebi.ac.uk/compneur/ > > > ------------------------------ > > Message: 3 > Date: Thu, 30 Oct 2008 08:03:28 +0000 > From: Nicolas Le Novere > Subject: Re: [cellml-discussion] [Fwd: Visual model design and editing > capabilities for CellML] > To: CellML Discussion List > Message-ID: <49096A50.9050109 at ebi.ac.uk> > Content-Type: text/plain; charset="iso-8859-1"; Format="flowed" > > Michael Hucka wrote: > >> The current specification on sbgn.org includes a one-page >> summary of the process diagram notation. Please make sure >> to use that, and not figure 5, when making any evaluation of >> SBGN :-). > > Attached is the reference card for SBGN Process Diagram Level 1 > > You can find examples at: > > http://www.sbgn.org/Documents/Examples > > Best. > > -- > Nicolas LE NOVERE, Computational Neurobiology, EMBL-EBI, Wellcome-Trust > Genome Campus, Hinxton CB101SD UK, Mob:+447833147074, Tel:+441223494521 > Fax:468, Skype:n.lenovere, AIM:nlenovere, MSN:nlenovere at hotmail.com > http://www.ebi.ac.uk/~lenov/, http://www.ebi.ac.uk/compneur/ > -------------- next part -------------- > A non-text attachment was scrubbed... > Name: Refcard_small.png > Type: image/png > Size: 119751 bytes > Desc: not available > URL: > > > ------------------------------ > > _______________________________________________ > cellml-discussion mailing list > cellml-discussion at cellml.org > http://www.cellml.org/mailman/listinfo/cellml-discussion > > > End of cellml-discussion Digest, Vol 51, Issue 16 > ************************************************* > ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. From lenov at ebi.ac.uk Fri Oct 31 00:23:43 2008 From: lenov at ebi.ac.uk (=?ISO-8859-1?Q?Nicolas_Le_nov=E8re?=) Date: Thu, 30 Oct 2008 11:23:43 +0000 Subject: [cellml-discussion] Visual model design and editing capabilities for CellML In-Reply-To: <20081031000002.kat5zkmvc4gkgc4s@webmail.bioeng.auckland.ac.nz> References: <20081031000002.kat5zkmvc4gkgc4s@webmail.bioeng.auckland.ac.nz> Message-ID: <4909993F.8040909@ebi.ac.uk> Abhishek Tiwari wrote: > P.S. regarding different standards or notation systems, it will be never > irrelevant to have multiple standards (domination may be mantra of > Microsoft), it gives freedom to choose and that's beauty of open > community based projects. You are absolutely right when it comes to "notation systems". EPE or Vanted are a good examples, where you can choose different way of representing things. Like for style-sheets in HTML, on can use different rendering to enrich the concept presented. When it comes to "standards" I beg to differ. The purpose of SBGN is to have a language that can be unambiguously interpreted, by all, without any legend. It is for exchange of maps. Not just for display. Imagine a world where Boing, Airbus and Lockeed used different graphical notations for electrical circuits. Now imagine you are one of the dozens of subcontractors working for the three of them. Imagine you are an engineer in charge of the safety in a major airport. SBGN is not like SBML or CellML, where there are API, libraries etc. to help with reading, writing and converting. SBGN is standalone, and has to be understood by a student, an experimental biologist, a modeler, from an article, a powerpoint slide, a pathway software, all that without any additional information ... -- Nicolas LE NOVERE, Computational Neurobiology, EMBL-EBI, Wellcome-Trust Genome Campus, Hinxton CB101SD UK, Mob:+447833147074, Tel:+441223494521 Fax:468, Skype:n.lenovere, AIM:nlenovere, MSN:nlenovere at hotmail.com http://www.ebi.ac.uk/~lenov/, http://www.ebi.ac.uk/compneur/ From mhucka at caltech.edu Fri Oct 31 03:08:13 2008 From: mhucka at caltech.edu (Michael Hucka) Date: Thu, 30 Oct 2008 07:08:13 -0700 Subject: [cellml-discussion] cellml-discussion Digest, Vol 51, Issue 16 In-Reply-To: <20081031000002.kat5zkmvc4gkgc4s@webmail.bioeng.auckland.ac.nz> References: <20081031000002.kat5zkmvc4gkgc4s@webmail.bioeng.auckland.ac.nz> Message-ID: <18697.49101.266698.665367@frantic.local> AT> website mentioned that CellDesigner's Graphical AT> Notation conforms to SBGN proposal (as of April '08 AT> draft), and thats why I used the image from AT> CellDesigner's Graphical Notation to give a AT> representative idea about SBGN, and there was nothing AT> wrong especially when many of CellDesigner team AT> members are respected authors of the SBGN Progress AT> Diagrams specification. I see. There is an unfortunate, um, discrepancy, between what is claimed on the Celldesigner website about SBGN and what is actual SBGN. Right on the front page, even. We will have to contact them about it. MH From mhucka at caltech.edu Fri Oct 31 14:10:06 2008 From: mhucka at caltech.edu (Michael Hucka) Date: Thu, 30 Oct 2008 18:10:06 -0700 Subject: [cellml-discussion] Opinion on multiple standards Message-ID: <18698.23278.226265.896647@frantic.local> AT> P.S. regarding different standards or notation AT> systems, it will be never irrelevant to have multiple AT> standards (domination may be mantra of Microsoft), it AT> gives freedom to choose and that's beauty of open AT> community based projects. What follows is personal opinion, not an official position on behalf of any group I'm involved with. Agreement on single open standards for single domains or application areas *is* beneficial and a goal to strive for. An example of this is today's web. Would the web be what it is today if people had not settled on one set of standards (HTML for describing pages, HTTP for the protocol)? Agreement on single standards in single application areas is what enables practical interoperability in those areas. (Sure, you can have interoperability even in the face of multiple standards, but it's a lot more expensive to implement, and thus not practical in the long run.) Note that my claim is specifically about *single* domains. Multiple standards are definitely needed for non-overlapping (or mostly non-overlapping) domains or application areas. Multiple proposed standards for the same single domain arise (1) in the early stages when people are still grappling with understanding their needs on the one hand, and implications of specific format/notation/whatever choices on the other; (2) when an established standard is found to be deficient as a result of experience, evolution, and/or innovation. For #2, if things have been going well, people will want to update an existing standard (e.g., version 1->2) rather than replace it entirely, but in other cases, wholesale replacement may be called for. I hypothesize that when people say "multiple standards are good in open community projects", it's because people actually are thinking about multiple application areas, or an area has not settle on common standards, or people are dissatisfied with the existing standards. People sometimes bring up Microsoft as a counter-example to single standards. The actual problem is not the adoption of single standards, it's Microsoft's specific approach, which involves (i) a single entity making top-down decisions for its own needs without consultation with other groups, (ii) not documenting the formats, (iii) changing the formats roughly every time they update their applications without prior announcement, and (iv) a belligerent business style. In other words, people's problem with Microsoft is actually rooted in Microsoft's lack of an open process. I wager Microsoft would be viewed much more favorably if they developed their document formats using a bottom-up community process. In summary, I claim that there are reasons why an area might end up with multiple proposed standards, but it is false that having multiple standards is better than using one standard when a single one can be agreed upon. Agreement on a single standard certainly takes a lot of effort, exploration, and time, on both the technical aspects of defining the standard and the social aspects of arranging community buy-in. Sometimes it takes decades before quiescence is reached on a given topic. But once a sufficiently good single standard for a given area can be found, it is far better to stick with it, and spend your efforts on something else. MH