Re: [cellml-discussion] ABI CellML meeting minutes 2009-12-16
We (Catherine, Poul and I) were thinking that there are basically three places where you'd want to display / store this information within PMR2: in the metadata itself (thereby allowing it to be rendered by software, indexed and searched etc.), on the exposure somewhere (perhaps a rendering of the metadata,) and in the proposed blanket, site-wide 'terms of use' page. As Catherine has mentioned in the relevant tracker item (don't have the number on hand,) one of the issues which we must now decide on is whether to require that all models in the repository abide by CC attrib 3 or whether users can specify special cases. Cheers, James On 18/12/2009, at 1:25 AM, Alan Garny wrote: From: cellml-discussion-boun...@cellml.org [mailto:cellml-discussion- boun...@cellml.org] On Behalf Of Dougal Cowan Sent: 17 December 2009 01:55 To: cellml-discussion@cellml.org Subject: [cellml-discussion] ABI CellML meeting minutes 2009-12-16 I have put the minutes from this week's meeting up at: http://www.cellml.org/community/meeting/minutes/2009/12.16 Just a quick comment about the minutes: - Randall said we will need a good way to indicate which license applies to each model - possibly in metadata. -- Metadata seems like an obvious place indeed. One thing to keep in mind (and I am sure you guys did, but I didn't see any mention of it) is that the license under which a particular model comes should be very obvious to anyone using PMR2. In other words, someone shouldn't have to, say, download a model and then check its metadata so that he knows about its license. Alan ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
[cellml-discussion] I am leaving the ABI
Hi all, This is just a note to say that I will be leaving the Auckland Bioengineering Institute on January 14th 2010, after which point I will no longer be a regular contributor to the CellML project. I do plan to stay up to date with developments in the project and to keep in touch with the community after my departure. I'd like to say what a fantastic few years I've had on the project, and that I have very much enjoyed working with everyone who works tirelessly to make CellML the revolutionary technology that it is. Kind regards, James Lawson attachment: j_lawson.vcf___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
[cellml-discussion] ABI CellML meeting minutes 20091118
Dear all, The minutes for this week's ABI CellML team meeting are now available at: http://www.cellml.org/community/meeting/minutes/2009/11.18 Kind regards, James attachment: j_lawson.vcf___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
Re: [cellml-discussion] CellML and OWL
Thanks Ely, glad to see you got it published. We'll give it a read. Kind regards, James Lawson Ely Edison Matos wrote: Hello, Approximately one year ago (september, 2008) we comment on the use of OWL ontologies associated to CellML models. For whom that have some interest in the topic, part of the work developed by our group at UFJF as my Msc Thesis can be known here: http://dx.doi.org/10.1016/j.jbi.2009.08.008 We thank comments and suggestions, and we would like knowing other related works. Thanks for the attention, Ely Matos ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion attachment: j_lawson.vcf___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
[cellml-discussion] ABI CellML team meeting minutes 2009-09-26
Dear CellML community, The minutes for last week's Auckland CellML team meeting are now up at: http://www.cellml.org/community/meeting/minutes/08.26 Kind regards, James attachment: j_lawson.vcf___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
[cellml-discussion] CellML Metadata 1.0 Specification finalised
Dear CellML community, The CellML Metadata 1.0 specification has been in draft format for a number of years. Although we recognise that there are many changes and updates required in CellML metadata, we have decided to finalise the specification as it is, since it has not changed since 2005, and has been referenced in many articles. The finalised specification is now available at: http://www.cellml.org/specifications/metadata Kind regards, James Lawson begin:vcard fn:James Lawson n:Lawson;James org:Auckland Bioengineering Institute;CellML Model Repository Curator, CellML Team adr:;;University of AucklandNew Zealand email;internet:j.law...@auckland.ac.nz title:James Lawson url:http://www.cellml.org version:2.1 end:vcard ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
[cellml-discussion] IUPS2009 CellML Workshop Announcement
Dear CellML community, The IUPS2009 meeting http://www.iups2009.com/index.html will take place in Kyoto from 28th July until August 1st, 2009. Attendees from the CellML project have organised a workshop-style tutorial http://www.iups2009.com/0220/Tutorial.pdf at this event to provide an introduction to CellML, its usage, and tools for working with CellML models. This workshop will take place on the second day of the conference, *29th July 2009, from 14:15-16:45hrs, in Room K* of the conference complex. The workshop will consist of a short introductory presentation, followed by a period of hands-on tuition supervised by senior members of the CellML community. Computers and internet connections will be available, although attendees would be advised to bring a notebook computer if possible. If you are planning on attending this conference, please come join us and participate in the workshop. Further information on this workshop will be released as the details are finalised. Kind regards, James Lawson begin:vcard fn:James Lawson n:Lawson;James org:Auckland Bioengineering Institute;CellML Model Repository Curator, CellML Team adr:;;University of AucklandNew Zealand email;internet:j.law...@auckland.ac.nz title:James Lawson url:http://www.cellml.org version:2.1 end:vcard ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
Re: [cellml-discussion] [cellmlteam] Contributing CellML models to Wolfram Alpha
To be honest I'm not really so impressed with WA yet, but that's probably because I haven't learned to use it properly. Can anyone explain/speculate to me how submitting to WA would help our goals of a.) increasing uptake of CellML, b.) model distribution [this one is obvious,] c.) model reuse, d.) model mix/match/cut/paste/remix/mashup, e.) model reparameterisation, f.) merging of data sets? Simulation and graphing is nice - I guess this fits partly under distribution? Actually Abhishek, this suggest echoes that request by the BestGRID project for CellML input... (see http://www.cellml.org/meeting_minutes/abi-cellml-meeting-minutes-2009-05-20/) but potentially more accessible. Kind regards, James Alan Garny wrote: From: team-boun...@cellml.org [mailto:team-boun...@cellml.org] On Behalf Of Abhishek Tiwari By now you must have heard about computational engine Wolfram|Alpha, if not you can try here http://www.wolframalpha.com/. I am curious if anyone have thoughts about contributing cellml models to Wolfram|Alpha engine, currently they are accepting contributed structured data, models and algorithms (http://www18.wolframalpha.com/participate/algorithms.html). Alpha does lot of fantastic things, simulation and graphing is one of them. That seems like an interesting idea, but hopefully this wouldn't mean giving them CellML files as such, but rather them making use of the CellML Repository?... Alan ___ team mailing list t...@cellml.org http://www.cellml.org/mailman/listinfo/team begin:vcard fn:James Lawson n:Lawson;James org:Auckland Bioengineering Institute;CellML Model Repository Curator, CellML Team adr:;;University of AucklandNew Zealand email;internet:j.law...@auckland.ac.nz title:James Lawson url:http://www.cellml.org version:2.1 end:vcard ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
[cellml-discussion] cellml.org publications listing
Hi all, I'd like to update our CellML publications listing at http://www.cellml.org/publications/ If you have any recent publications (or in fact any old publications) which you'd like to add to this list, please send me the citation and I'll put it up. Kind regards, James begin:vcard fn:James Lawson n:Lawson;James org:Auckland Bioengineering Institute;CellML Model Repository Curator, CellML Team adr:;;University of AucklandNew Zealand email;internet:j.law...@auckland.ac.nz title:James Lawson url:http://www.cellml.org version:2.1 end:vcard ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
Re: [cellml-discussion] tools that use and / or work with CellML
Hi everyone, I've updated the CellML tools page at http://www.cellml.org/tools with some of the new tools and descriptions that people sent me. If you can think of anything further that should be up there but is not, please let me know. I'm aware that we don't have any tools from any of the Japanese groups. Thanks, James James Lawson wrote: Hi all, We'd like to put some content on the tools page that discusses the tools we list. What I'm wondering is if anyone has a presentation / poster / etc. that they wouldn't mind us putting up as a piece of featured content on the tools page. For example, I know some of you did presentations at the recent workshop about tools that work with CellML. If we could link to these, or preferably host them, that would be really fantastic. I'm trying to build up a repository of information about the software we have. If you have something you think might be useful but there are copyright issues or similar with it, please let me know and we'll see if we can work something out. Please feel free to pass this email request around. Thanks! James ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion begin:vcard fn:James Lawson n:Lawson;James org:Auckland Bioengineering Institute;CellML Model Repository Curator, CellML Team adr:;;University of AucklandNew Zealand email;internet:j.law...@auckland.ac.nz title:James Lawson url:http://www.cellml.org version:2.1 end:vcard ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
Re: [cellml-discussion] tools that use and / or work with CellML
Thanks Nico, I'll put that info up. Kind regards, James Nicolas Rodriguez wrote: James Lawson wrote: James Lawson wrote: Hi all, We're currently doing some work on the Tools page of the website at http://www.cellml.org/tools and I'd just like people to have a look through the listing there and check that your tools are all there. The listing is fairly old so I know we're missing a few. Apologies in advance if your tool is missing, but please let us know and we'll rectify that ASAP. Kind regards, James Lawson ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion In particular, we don't have the CellML - SBML translators up there. So if anyone could link me to them and maybe give me a short paragraph description about them, that would be great. The page general page about SBML converters developed at EBI is : http://www.ebi.ac.uk/compneur-srv/sbml/converters/SBMLConverters.html Specific CellML pages: http://www.ebi.ac.uk/compneur-srv/sbml/converters/SBMLtoCellML.html http://www.ebi.ac.uk/compneur-srv/sbml/converters/CellMLtoSBML.html Note : The stylesheets on these pages are not entirely up-to-date with the ones used to create the export formats of Biomodels DB, I still have to work on some issues before updating the web site. As for a really short description, they are translation tools, written using XSLT. The SBML to CellML converter is creating a CellML file using reactions and we need to update it. Andrew is currently working on writing a new version of it, the prototype is done but we need to correct some issues before to use replace the XSLT version. This new version is written in Ruby and is focusing mainly on getting the units as right as possible and using the latest CellML specs without using reactions, not doing anything about metadata yet. We are also planning to update the CellML to SBML converter, probably written in Java when the new specifications are out. Cheers, Nico ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion begin:vcard fn:James Lawson n:Lawson;James org:Auckland Bioengineering Institute;CellML Model Repository Curator, CellML Team adr:;;University of AucklandNew Zealand email;internet:j.law...@auckland.ac.nz title:James Lawson url:http://www.cellml.org version:2.1 end:vcard ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
[cellml-discussion] tools that use and / or work with CellML
Hi all, We're currently doing some work on the Tools page of the website at http://www.cellml.org/tools and I'd just like people to have a look through the listing there and check that your tools are all there. The listing is fairly old so I know we're missing a few. Apologies in advance if your tool is missing, but please let us know and we'll rectify that ASAP. Kind regards, James Lawson begin:vcard fn:James Lawson n:Lawson;James org:Auckland Bioengineering Institute;CellML Model Repository Curator, CellML Team adr:;;University of AucklandNew Zealand email;internet:j.law...@auckland.ac.nz title:James Lawson url:http://www.cellml.org version:2.1 end:vcard ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
Re: [cellml-discussion] tools that use and / or work with CellML
Hi David, That's awesome, thanks very much. Do you want to just write a paragraph on each of them, about what they do, what they're for etc.? Thanks, James David Cumin wrote: James, Attached are two matlab scripts (runMatlabCellML.m to run an exported CellML model and fitMatlabCellML.m one to do parameter fitting) and my graphical cellml editor. Regards, David Cumin PhD Student Department of Anaesthesiology / Bioengineering University of Auckland Ph: +64 9 373 7599 ext 85948 --Original Message- -From: cellml-discussion-boun...@cellml.org [mailto:cellml-discussion- -boun...@cellml.org] On Behalf Of James Lawson -Sent: Monday, 4 May 2009 1:18 p.m. -To: CellML Discussion List -Subject: [cellml-discussion] tools that use and / or work with CellML - -Hi all, - -We're currently doing some work on the Tools page of the website at -http://www.cellml.org/tools and I'd just like people to have a look -through the listing there and check that your tools are all there. The -listing is fairly old so I know we're missing a few. Apologies in -advance if your tool is missing, but please let us know and we'll -rectify that ASAP. - -Kind regards, -James Lawson ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion begin:vcard fn:James Lawson n:Lawson;James org:Auckland Bioengineering Institute;CellML Model Repository Curator, CellML Team adr:;;University of AucklandNew Zealand email;internet:j.law...@auckland.ac.nz title:James Lawson url:http://www.cellml.org version:2.1 end:vcard ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
Re: [cellml-discussion] Meeting minutes 2008-11-19
Hi Alan, The way we currently do it is the minuter writes up the minutes and releases them to the people who were present at the meeting for corrections. The full, revised minutes are then made public, usually several days later. Unfortunately we had a powercut yesterday and Dougal lost all his minutes, since plone doesn't make regular saves :( I definitely understand where you're coming from. We've talked quite a bit about how the minutes from the Auckland meeting should be done, and we've come to the conclusion that we're a bit limited by technology at the moment, since our plone site doesn't record change logs for documents properly. Would everyone prefer a more rapid, but subject to change, release of the minutes? Thanks, James Alan Garny wrote: Hi, I was wondering whether the minutes could be announced sooner? I understand that they need to be approved, but still I would expect them to be announced within 24 hours. If we look at last week's meeting, I received notice of the minutes on Monday evening (i.e. Tuesday morning NZ time), i.e. one day before you guys have your weekly CellML meeting (!!). Most importantly (maybe) is that, while reading the minutes, I could relate to issues (reported in the minutes) that had been acted upon since last week's meeting. This is obviously good, but those issues kind of came out of the blue at the time. It would have been nice if I didn't have to put 2 and 2 together, try to read people's mind behind their actions, etc. Also, to know about the outcome of the meeting within 24 hours would potentially allow people to react more efficiently (i.e. in 'real-time'). Cheers, Alan. PS: it's not a recent occurrence, since it has been going on for months. In a couple of cases, it even happened that the minutes were not announced. So, no, nothing to do with the person who currently produces the minutes... :) -Original Message- From: [EMAIL PROTECTED] [mailto:cellml-discussion- [EMAIL PROTECTED] On Behalf Of Dougal Cowan Sent: 24 November 2008 20:57 To: cellml-discussion@cellml.org Subject: [cellml-discussion] Meeting minutes 2008-11-19 The minutes from last week's ABI CellML Team meeting are up at: http://www.cellml.org/meeting_minutes/abi-meeting-minutes-2008-11-19 Dougal ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion begin:vcard fn:James Lawson n:Lawson;James org:Auckland Bioengineering Institute;CellML Model Repository Curator, CellML Team adr:;;University of AucklandNew Zealand email;internet:[EMAIL PROTECTED] title:James Lawson url:http://www.cellml.org version:2.1 end:vcard ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
Re: [cellml-discussion] Auto-generate HDF5 from CellML?
Hi Jon Olav, Sounds really interesting - the one reservation I'd have, however, is that HDF5 doesn't appear to be open-source. Cheers, James Jon Olav Vik wrote: Dear all, I'm considering HDF5 for my storage needs in simulating a CellML model under multiple parameter scenarios. HDF5 is designed for efficient storage, retrieval, navigation and subsetting of huge data sets [1], with annotation [2]. I plan on storing both raw and post-processed data, so that if I detect problems at a higher level, I can go back and look at details and possibly re- run those simulations. David Nickerson described a similar approach in an earlier post [3]. However, setting up the data structure with annotations for physical units and such is quite time-consuming. On the other hand, the CellML representation holds all the required information. It would be very helpful to auto-generate an HDF5 data structure to hold output from simulations of CellML models. Such a tool should be fairly easy to write for someone familiar with both HDF5 and CellML, and would apply to all possible CellML models. I guess it would be overly restrictive to make an output format part of the CellML metadata specification. However, offering a standard output format would save duplication of effort and make it easier to share simulation results for further visualization and analysis. I'd like the opinions of the CellML regulars, in particular whether anything similar has been discussed previously. Best regards, Jon Olav Vik [1] http://www.hdfgroup.org/about/hdf_technologies.html [2] http://www.hdfgroup.org/training/HDFtraining/UsersGuide/MF_Annot.fm1.html [3] http://article.gmane.org/gmane.text.xml.cellml.general/234/match=hdf5 ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion begin:vcard fn:James Lawson n:Lawson;James org:Auckland Bioengineering Institute;CellML Model Repository Curator, CellML Team adr:;;University of AucklandNew Zealand email;internet:[EMAIL PROTECTED] title:James Lawson url:http://www.cellml.org version:2.1 end:vcard ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
Re: [cellml-discussion] HDF5 licensing
My apologies - I should have looked a bit harder! Randy Heiland wrote: The claim below surprised me (since I used to know and work with many of the HDF group), so I had a look at the license for HDF5: All rights reserved. Contributors: National Center for Supercomputing Applications (NCSA) at the University of Illinois, Fortner Software, Unidata Program Center (netCDF), The Independent JPEG Group (JPEG), Jean-loup Gailly and Mark Adler (gzip), and Digital Equipment Corporation (DEC). Redistribution and use in source and binary forms, with or without modification, are permitted for any purpose (including commercial purposes) provided that the following conditions are met: 1. Redistributions of source code must retain the above copyright notice, this list of conditions, and the following disclaimer. 2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions, and the following disclaimer in the documentation and/or materials provided with the distribution. 3. In addition, redistributions of modified forms of the source or binary code must carry prominent notices stating that the original code was changed and the date of the change. 4. All publications or advertising materials mentioning features or use of this software are asked, but not required, to acknowledge that it was developed by The HDF Group and by the National Center for Supercomputing Applications at the University of Illinois at Urbana-Champaign and credit the contributors. 5. Neither the name of The HDF Group, the name of the University, nor the name of any Contributor may be used to endorse or promote products derived from this software without specific prior written permission from THG, the University, or the Contributor, respectively. --- I consider this about as close to open source as it gets and isn't much different that the CellML terms of use: http://www.cellml.org/terms -Randy On Nov 10, 2008, at 6:00 PM, [EMAIL PROTECTED] wrote: -- Message: 2 Date: Tue, 11 Nov 2008 11:42:28 +1300 From: James Lawson [EMAIL PROTECTED] Subject: Re: [cellml-discussion] Auto-generate HDF5 from CellML? To: CellML Discussion List cellml-discussion@cellml.org Message-ID: [EMAIL PROTECTED] Content-Type: text/plain; charset=iso-8859-1; Format=flowed Hi Jon Olav, Sounds really interesting - the one reservation I'd have, however, is that HDF5 doesn't appear to be open-source. Cheers, James Jon Olav Vik wrote: Dear all, I'm considering HDF5 for my storage needs in simulating a CellML model under multiple parameter scenarios. HDF5 is designed for efficient storage, retrieval, navigation and subsetting of huge data sets [1], with annotation [2]. I plan on storing both raw and post-processed data, so that if I detect problems at a higher level, I can go back and look at details and possibly re- run those simulations. David Nickerson described a similar approach in an earlier post [3]. However, setting up the data structure with annotations for physical units and such is quite time-consuming. On the other hand, the CellML representation holds all the required information. It would be very helpful to auto-generate an HDF5 data structure to hold output from simulations of CellML models. Such a tool should be fairly easy to write for someone familiar with both HDF5 and CellML, and would apply to all possible CellML models. I guess it would be overly restrictive to make an output format part of the CellML metadata specification. However, offering a standard output format would save duplication of effort and make it easier to share simulation results for further visualization and analysis. I'd like the opinions of the CellML regulars, in particular whether anything similar has been discussed previously. Best regards, Jon Olav Vik [1] http://www.hdfgroup.org/about/hdf_technologies.html [2] http://www.hdfgroup.org/training/HDFtraining/UsersGuide/MF_Annot.fm1.html [3] http://article.gmane.org/gmane.text.xml.cellml.general/234/match=hdf5 ___ cellml-discussion mailing list cellml-discussion@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: http://www.cellml.org/pipermail/cellml-discussion/attachments/2008/ed3ce968/attachment-0001.vcf -- ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion End of cellml-discussion Digest, Vol 52, Issue 5 ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman
[cellml-discussion] SBML is about to release L2v4
Hi all, It looks like SBML is about to release SBML L2v4 From http://sbml.org/Community/Wiki SBML Level 2 Version 4 will address pending issues logged in the SBML specifications issue tracker https://sourceforge.net/tracker/index.php?atid=894711group_id=71971set=custom_category=990156. Due to the editor's current work and travel schedules, and the desire to time the release of L2v4 with a release of libSBML that supports it, we are pushing back the release of L2v4 and libSBML to early-mid November 2008. Regards, James begin:vcard fn:James Lawson n:Lawson;James org:Auckland Bioengineering Institute;CellML Model Repository Curator, CellML Team adr:;;University of AucklandNew Zealand email;internet:[EMAIL PROTECTED] title:James Lawson url:http://www.cellml.org version:2.1 end:vcard ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
Re: [cellml-discussion] [Fwd: Visual model design and editing capabilities for CellML]
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 [EMAIL PROTECTED]: 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 [EMAIL PROTECTED] To: [EMAIL PROTECTED], Andrew Miller [EMAIL PROTECTED], David Nickerson [EMAIL PROTECTED] 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@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion begin:vcard fn:James Lawson n:Lawson;James org:Auckland Bioengineering Institute;CellML Model Repository Curator, CellML Team adr:;;University of AucklandNew Zealand email;internet:[EMAIL PROTECTED] title:James Lawson url:http://www.cellml.org version:2.1 end:vcard ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
[cellml-discussion] CellML Metadata Specification development
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 begin:vcard fn:James Lawson n:Lawson;James org:Auckland Bioengineering Institute;CellML Model Repository Curator, CellML Team adr:;;University of AucklandNew Zealand email;internet:[EMAIL PROTECTED] title:James Lawson url:http://www.cellml.org version:2.1 end:vcard ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
Re: [cellml-discussion] Finalising CellML Metadata 1.0 specification
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. begin:vcard fn:James Lawson n:Lawson;James org:Auckland Bioengineering Institute;CellML Model Repository Curator, CellML Team adr:;;University of AucklandNew Zealand email;internet:[EMAIL PROTECTED] title:James Lawson url:http://www.cellml.org version:2.1 end:vcard ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
Re: [cellml-discussion] Finalising CellML Metadata 1.0 specification
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@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@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion begin:vcard fn:James Lawson n:Lawson;James org:Auckland Bioengineering Institute;CellML Model Repository Curator, CellML Team adr:;;University of AucklandNew Zealand email;internet:[EMAIL PROTECTED] title:James Lawson url:http://www.cellml.org version:2.1 end:vcard ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
Re: [cellml-discussion] CellML IRC
This makes sense, but I actually think it would be good to have a more casual medium for discussion that *isn't* highly linked up and searchable. Logs would certainly be useful, but the current media (mailing list, tracker etc.) are very much public fora. David Nickerson wrote: On Thu, Aug 21, 2008 at 7:02 AM, James Lawson [EMAIL PROTECTED] wrote: Dear CellML community, We have had an IRC channel in the past, but I believe that it fell into disuse. I have been pretty interested in getting it going again for sometime, so I thought I'd canvass interest. Who thinks they'd be interested? I'd suggest we just put it on freenode... If I remember correctly, while it did fall into disuse there was an actual decision made not to continue with that line of community communication. Especially now as the tracker is being proposed as the place to have specific discussions that maybe are not of general interest to the community, it would seem to me to be a bad idea to add one more independent archive that would need to be searched by users in order to ensure they cover all possible previous discussion threads. Perhaps if there was some way to integrate freenode searches into the tracker search engine then this would make more sense? Better yet, provide a single search and respond interface for the tracker, mailing lists, and any other discussion forum and then people can easily choose the most appropriate medium for them to interact on (with?). Andre. ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion begin:vcard fn:James Lawson n:Lawson;James org:Auckland Bioengineering Institute;CellML Model Repository Curator, CellML Team adr:;;University of AucklandNew Zealand email;internet:[EMAIL PROTECTED] title:James Lawson url:http://www.cellml.org version:2.1 end:vcard ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
Re: [cellml-discussion] OWL
Dear Randy, Thanks for asking. Unfortunately that roadmap is somewhat embarrassing for us. We are currently undertaking a major reworking of the website, and once we finish setting out our plans, the roadmap is right at the top of my list of pages to rewrite. In the meantime, let me see if I can explain what we're up to with respect to OWL and ontologies. Unfortunately, the CellML team member who was primarily responsible for this project, and whose commentary you can find under the wiki section of the site on ontologies, is no longer with us. I have begun to take up the rope on this, but I am still really working on upskilling myself. Sarala Dissanayake is working on writing up her PhD thesis, in which she presents her work on developing CellML-OWL. CellML-OWL aims to provide infrastructure for ontologies that can be used for annotation of models with biological and biophysical information. Sarala has developed a tool for visualisation of CellML models using CellML-OWL as well. I'd direct you to Sarala ([EMAIL PROTECTED]) for more information on our current development in OWL and ontologies. Kind regards, James Lawson Randy Heiland wrote: As I continue to try to educate myself on CellML, I thought I'd ask the open-ended question - what are the latest thoughts/plans for OWL? I saw the web page: http://www.cellml.org/cellml_roadmap, but noticed that it was about 4 yrs old, so thought I'd ask the list. thanks, Randy ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion begin:vcard fn:James Lawson n:Lawson;James org:Auckland Bioengineering Institute;CellML Model Repository Curator, CellML Team adr:;;University of AucklandNew Zealand email;internet:[EMAIL PROTECTED] title:James Lawson url:http://www.cellml.org version:2.1 end:vcard ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
[cellml-discussion] ABI CellML team meeting minutes for 2008-08-20
Dear CellML community, The minutes for last Wednesday's meeting (2008-08-20) are now available at: http://www.cellml.org/meeting_minutes/abi-meeting-minutes-2008-08-20/ Kind regards, James Lawson begin:vcard fn:James Lawson n:Lawson;James org:Auckland Bioengineering Institute;CellML Model Repository Curator, CellML Team adr:;;University of AucklandNew Zealand email;internet:[EMAIL PROTECTED] title:James Lawson url:http://www.cellml.org version:2.1 end:vcard ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
[cellml-discussion] Towards a cyberinfrastructure for the biological sciences - progress, visions and challenges
Hi all, I came across this paper today, and I think it outlines some interesting implications for the role of CellML, the CellML Model Repository and cellml.org as a community website in its vision of a holistic cyberinfrastructure for the biological sciences. It can be found here: http://www.nature.com/nrg/journal/v9/n9/pdf/nrg2414.pdf Kind regards, James begin:vcard fn:James Lawson n:Lawson;James org:Auckland Bioengineering Institute;CellML Model Repository Curator, CellML Team adr:;;University of AucklandNew Zealand email;internet:[EMAIL PROTECTED] title:James Lawson url:http://www.cellml.org version:2.1 end:vcard ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
Re: [cellml-discussion] New Proposed Structure for the CellML Website
Hi Catherine, Weren't we going to put this through the meeting on Wednesday first? Ah too late I guess :) Hopefully we don't get bombarded with feedback quite yet. bw, j Catherine Lloyd wrote: Dear All Over the past few weeks a few of us at the ABI have been meeting on a regular basis to discuss the structure and content of the CellML website. We have been through a site content audit, and have put together a proposal for the new site structure (attached). Please note, this is the underlying structure, and although it will be related to the actual look of the new site, the two are not identical. We have identified 6 major categories - plus site help as a necessary feature of any website. We would appreciate it if you could take some time to review the proposed structure, and please get back to us with any comments or opinions that you may have. Best wishes Catherine ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion begin:vcard fn:James Lawson n:Lawson;James org:Auckland Bioengineering Institute;CellML Model Repository Curator, CellML Team adr:;;University of AucklandNew Zealand email;internet:[EMAIL PROTECTED] title:James Lawson url:http://www.cellml.org version:2.1 end:vcard ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
Re: [cellml-discussion] New Proposed Structure for the CellML Website
Hi all, Just one thing that might be missed here - an acknowledgements section. I would suggest that we create (ala sbml.org - see http://sbml.org/Acknowledgments ) specifically dedicated to our funding sources rather than continue our current approach of showing our funding sources in a sidebar on every page as we currently do. IMO, such a page should come under the 'About CellML' section. Kind regards, James Catherine Lloyd wrote: Dear All Over the past few weeks a few of us at the ABI have been meeting on a regular basis to discuss the structure and content of the CellML website. We have been through a site content audit, and have put together a proposal for the new site structure (attached). Please note, this is the underlying structure, and although it will be related to the actual look of the new site, the two are not identical. We have identified 6 major categories - plus site help as a necessary feature of any website. We would appreciate it if you could take some time to review the proposed structure, and please get back to us with any comments or opinions that you may have. Best wishes Catherine ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion begin:vcard fn:James Lawson n:Lawson;James org:Auckland Bioengineering Institute;CellML Model Repository Curator, CellML Team adr:;;University of AucklandNew Zealand email;internet:[EMAIL PROTECTED] title:James Lawson url:http://www.cellml.org version:2.1 end:vcard ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
Re: [cellml-discussion] New Proposed Structure for the CellML Website
And one more thing, while I think of it - we had a proposal in the ABI meeting a while back to start putting up copies of posters and presentations relevant to CellML on cellml.org, and while (IIRC,) we agreed that this was a good idea, we have not yet formally created a section on the site for this purpose because we were conducting the site review and content audit. So perhaps this would be a category to add under 'About CellML' - perhaps to be grouped with 'publications'? On a related note, if anyone has suggestions for categories / architectures that might be useful in the future (if not right now,) we'd be very interested to hear. One such example might be a prospective 'ontologies' section, which we discussed, but weren't sure where to put. Kind regards, James James Lawson wrote: Hi all, Just one thing that might be missed here - an acknowledgements section. I would suggest that we create (ala sbml.org - see http://sbml.org/Acknowledgments ) specifically dedicated to our funding sources rather than continue our current approach of showing our funding sources in a sidebar on every page as we currently do. IMO, such a page should come under the 'About CellML' section. Kind regards, James Catherine Lloyd wrote: Dear All Over the past few weeks a few of us at the ABI have been meeting on a regular basis to discuss the structure and content of the CellML website. We have been through a site content audit, and have put together a proposal for the new site structure (attached). Please note, this is the underlying structure, and although it will be related to the actual look of the new site, the two are not identical. We have identified 6 major categories - plus site help as a necessary feature of any website. We would appreciate it if you could take some time to review the proposed structure, and please get back to us with any comments or opinions that you may have. Best wishes Catherine ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion begin:vcard fn:James Lawson n:Lawson;James org:Auckland Bioengineering Institute;CellML Model Repository Curator, CellML Team adr:;;University of AucklandNew Zealand email;internet:[EMAIL PROTECTED] title:James Lawson url:http://www.cellml.org version:2.1 end:vcard ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
[cellml-discussion] little b - shared models built from reusable parts
Hi all, Has anyone encountered this before? http://www.littleb.org/ The little b project is an effort to provide an open source http://www.opensource.org/ language which allows scientists to build mathematical models http://en.wikipedia.org/wiki/Mathematical_model of complex systems. The initial focus is systems biology http://en.wikipedia.org/wiki/Systems_biology. The goal is to stimulate widespread sharing and reuse of models. The little b language is designed to allow biologists to build models quickly and easily from shared parts, and to allow theorists to program new ways of describing complex systems. Currently, libraries have been developed for building ODE http://en.wikipedia.org/wiki/Differential_equation models of molecular networks in multi-compartment systems such as cellular epithelia. Little b is based in Common Lisp and contains mechanisms for rule-based reasoning, symbolic mathematics and object-oriented definitions. The syntax is designed to be terse and human-readable to facilitate communication. The environment is both interactive and compilable. Kind regards, James begin:vcard fn:James Lawson n:Lawson;James org:Auckland Bioengineering Institute;CellML Model Repository Curator, CellML Team adr:;;University of AucklandNew Zealand email;internet:[EMAIL PROTECTED] title:James Lawson url:http://www.cellml.org version:2.1 end:vcard ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
[cellml-discussion] ABI CellML team meeting minutes 2008-07-16
Dear CellML Community, The minutes for last week's ABI CellML team meeting minutes are now available at: http://www.cellml.org/meeting_minutes/abi-meeting-minutes-2008-07-17/ Comments are welcome and can be posted at the bottom of the page. Kind regards, James Lawson begin:vcard fn:James Lawson n:Lawson;James org:Auckland Bioengineering Institute;CellML Model Repository Curator, CellML Team adr:;;University of AucklandNew Zealand email;internet:[EMAIL PROTECTED] title:James Lawson url:http://www.cellml.org version:2.1 end:vcard ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
[cellml-discussion] ABI CellML team meeting minutes for Wednesday 2008-07-09
Dear CellML community, The ABI's CellML team meeting minutes for last week (2008-07-09) are now up at: http://www.cellml.org/meeting_minutes/abi-meeting-minutes-2008-07-09/ Kind regards, James Lawson begin:vcard fn:James Lawson n:Lawson;James org:Auckland Bioengineering Institute;CellML Model Repository Curator, CellML Team adr:;;University of AucklandNew Zealand email;internet:[EMAIL PROTECTED] title:James Lawson url:http://www.cellml.org version:2.1 end:vcard ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
Re: [cellml-discussion] About guicellml
Hey Ely, Sorry this email was ages ago but I didn't see it. I had never seen guiCellML before, but I do know now that it was made by a guy called David Cumin who works at the Auckland Bioengineering Institute with us. You're welcome to give him an email at [EMAIL PROTECTED] Kind regards, James Ely Edison Matos wrote: Hello, I found this video about guicellml. Do someone knows about that? Some site, some download...? http://nz.youtube.com/watch?v=NowuAlSsUus Thanks, Ely ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion begin:vcard fn:James Lawson n:Lawson;James org:Auckland Bioengineering Institute;CellML Model Repository Curator, CellML Team adr:;;University of AucklandNew Zealand email;internet:[EMAIL PROTECTED] title:James Lawson url:http://www.cellml.org version:2.1 end:vcard ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
[cellml-discussion] ABI CellML team meeting minutes
Dear CellML community, The ABI CellML team meeting minutes for Wednesday 02/07/08 are now available at: http://www.cellml.org/meeting_minutes/abi-meeting-minutes-2008-07-02/ Kind regards, James Lawson begin:vcard fn:James Lawson n:Lawson;James org:Auckland Bioengineering Institute;CellML Model Repository Curator, CellML Team adr:;;University of AucklandNew Zealand email;internet:[EMAIL PROTECTED] title:James Lawson url:http://www.cellml.org version:2.1 end:vcard ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
[cellml-discussion] from Wired: The end of theory: the data deluge makes the scientific method obsolete
Hi all, Thought I'd see what you guys and girls think of this article, and its relevance to CellML, systems biology etc. http://www.wired.com/science/discoveries/magazine/16-07/pb_theory This is a world where massive amounts of data and applied mathematics replace every other tool that might be brought to bear. Out with every theory of human behavior, from linguistics to sociology. Forget taxonomy, ontology, and psychology. Who knows why people do what they do? The point is they do it, and we can track and measure it with unprecedented fidelity. With enough data, the numbers speak for themselves. Some of my thoughts: when we have bioinformatics servers processing similar amounts of information to the Google servers, then we'll need to rethink how we do things. The question is, how long will that be? And is information that encodes a model more useful than information that just codes data, considering that the model can produce more information? Kind regards, James begin:vcard fn:James Lawson n:Lawson;James org:Auckland Bioengineering Institute;CellML Model Repository Curator, CellML Team adr:;;University of AucklandNew Zealand email;internet:[EMAIL PROTECTED] title:James Lawson url:http://www.cellml.org version:2.1 end:vcard ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
[cellml-discussion] ABI CellML team meeting minutes 2008-06-18
Dear CellML folk, The ABI CellML team meeting minutes for 2008-06-18 are now available at: http://www.cellml.org/meeting_minutes/abi-meeting-minutes-2008-06-18/ Kind regards, James Lawson begin:vcard fn:James Lawson n:Lawson;James org:Auckland Bioengineering Institute;CellML Model Repository Curator, CellML Team adr:;;University of AucklandNew Zealand email;internet:[EMAIL PROTECTED] title:James Lawson url:http://www.cellml.org version:2.1 end:vcard ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
Re: [cellml-discussion] unit conversion
Thanks Erik, I managed to fix the issue before receiving your email, but this clears things up for me very concisely. I would venture to say that the reason that so many CellML models in the CellML repository do not pass Jsim's units checking is not because of CellML, or any tools used to create CellML models. Rather it is often because the models themselves contain unit inconsistencies. It does not help that units are irrelevant to most modelling tools, but I think the modelling community is starting to raise the bar with regards to this issue. Unfortunately it is often quite difficult to 'fix' inappropriate units (both quantitatively and qualitatively,) in a model without breaking it. FYI I've uploaded the model in question, which now runs in Jsim, COR and PCEnv, at: http://www.cellml.org/models/sachse_moreno_abildskov_2008_version02 The 'auto' setting for the integrator in Jsim will not run the model - the CVode integrator must be selected manually. Kind regards, James Lawson Erik Butterworth wrote: On Thu, 29 May 2008, Andrew Miller wrote: I think James had something more along the lines of: I_inter_fibro = 10^6 * (V_fibro - V) / R_mf (where 10^6 is marked as a dimensionless number). In this case the intention of the modeller is that the expression being equated to I_inter_fibro is already in nanoamps, and this will give the correct results in PCEnv and COR, I believe. I agree that it would be better modelling practice to mark 10^6 as being in units nanoamps per milliamps, and in this case PCEnv and COR will give correct results of 1E6 nanoamperes (and I presume also JSim?). Short answer: yes. Long answer: JSim has two unit conversion modes, on and off. With conversion on, the simplest correct formation in MML is 1. I_inter_fibro = (V_fibro - V) / R_mf; With unit conversion off, the simplest correct formation is: 2. I_inter_fibro = 10^6 * (V_fibro - V) / R_mf; With either unit conversion on or off, a dimensionalized constant will produce correct results, at the expense of conciseness: 3. I_inter_fibro = (10^6 nanoamp/milliamp) * (V_fibro - V) / R_mf; To be compatible with (my understanding of) the CellML units spec, JSim's CellML - MML converter creates MML with unit conversion on. However, due the the historically large (although perhaps decreasing) number of CellML models that didn't pass JSim unit balance, the JSim WWW site provides (for CellML models not passing unit balance) an imperfect MML translation with unit conversion off. This allows the models to be compiled and run, even if they may need conversion factor editing. Even if the CellML model doesn't pass JSim unit balance, it would still run correctly if all needed conversion factors were in the CellML in form #3 above. Hope this helps, Erik B. At least my reading of the CellML specification is that tools should not be automatically inserting conversion factors like this when processing CellML models, although they may optionally warn the user that a conversion factor may be missing and / or offer to insert it for them. Best regards, Andrew Erik Butterworth[EMAIL PROTECTED]206-685-2007 On Thu, 29 May 2008, Andrew Miller wrote: Date: Thu, 29 May 2008 11:29:50 +1200 From: Andrew Miller [EMAIL PROTECTED] To: James Lawson [EMAIL PROTECTED] Cc: James Lawson [EMAIL PROTECTED], [EMAIL PROTECTED] Subject: Re: unit conversion James Lawson wrote: Hi Andrew, Justin, Thanks for your help. Basically, I've had to multiply a current by a scaling factor of 1 million to get the model to run in PCEnv. It was made in Jsim and worked fine, but now I have a model that will run in PCEnv but not Jsim. Do you guys have any idea about what I could do to get it running in both? Would showing you the model help? I could email the Jsim guys and ask them if I knew what to ask.. It seems like Jsim doesn't really convert nanoamps into 10e-6 amps and work with the value from there, whereas PCEnv does. Would this be right? Basically the issue that I have addressed is that units for the variables in the equation for I_inter_fibro aren't dimensionally equivalent: The equation is: I_inter_fibro =(V_fibro - V) / R_mf Where I_inter_fibro is in nanoamperes, V_fibro and V are in millivolts and R_mf is in ohms. So the equation says that nanoamps = millivolts / ohms. Thus I have changed the equation to say I_inter_fibro = 1e+06 * (V_fibro - V) / R_mf Hi James, What are the units on the 1E6 scaling factor? If you put them in nanoamps_per_milliamp or something like that, then I think all software should do the right thing. Automatically inserting the conversion factor is not the correct software behaviour however; at most software should be flagging the problem and helping the user to insert the factor if they decide there is an actual problem. Best regards, Andrew So at the moment I do not know how to get the model to run in both PCEnv and Jsim
[cellml-discussion] (OT) the nature of 'mole' | Re: unit conversion
Hi guys,
This is a little OT for CellML-discussion, IMO.
Although you can technically talk about a mole of anything,
I take issue with this. You can talk about 6.23e26 of anything, but when
you talk about a mole of something it *MUST* be atoms or molecules. It
is not just a term like 'score' where you can have a 'score' of anything.|
Wikipedia explains this pretty succinctly.
According to the SI, the mole is not dimensionless, but has its very
own dimension, amount of substance, comparable to other dimensions
such as mass and luminous intensity. (By contrast, the SI specifically
defines the radian and the steradian as special names for the
dimensionless unit one.)
A mole specifically refers to a large number of atoms.
The ampere is a base unit, along with the metre, kelvin, second, mole,
candela and the kilogram: it is defined without reference to the
quantity of electric charge.
So the mole is essentially comprised of a scaling factor applied to
'stuff' where 'stuff' is in the form of 'atom/molecule.' I recognise
that this is 'according to the SI' - but when we're talking about units,
consensus on what the unit means is extremely important.
Kind regards,
James
the way it
is used by the SI system of units, it is always talking about a mole of
some kind of particle, whether that particle is an electron or some
large protein. As such, mole, when used in this sense, truly is a unit
as the term is used in CellML, rather than just a scaling factor (and in
fact, it would make sense to define a 'particle' derived unit in terms
of mole using a multiplier of the inverse of Avogadro's number).
We might also include built-in scaling factors for converting between
prefixes. For example if I have
a variable A in nanomolar and another B in micromolar I might want to say:
A = 1e3 * B
One way to do this is to define a scaling factor unit say (in CORspeak)
def unit nanospermicro from
unit liter {pref: nano};
unit liter {pref: micro, expo:-1};
enddef;
and then have
A = 1e3 {nanospermicro} * B.
Which is slightly clunky.
This is a perfectly valid way of expressing the model, and if necessary,
editing tools could help the user to create such units as required - we
shouldn't complicate the specification substantially for processing
tools based on what might make it easier to do something with current
editing tools, because editing tools will have to change for CellML 1.2
anyway.
(I think the use of 'liter' above should also be replaced with
'dimensionless', but that is a different issue).
It doesn't really make sense to say nanodimensionless per
microdimensionless, I prefer nanolitres per microlitre even though you
need to duplicate it if you have other conversion factors.
We could also include dozen, which would aid the bakery-modelling community
too ;).
If we are talking about dozens of particles, that can already be done in
terms of moles easily using multiplier 12 / nA (i.e. 1.99264653979527 *
10^-23)
Best regards,
Andrew
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Peter Hunter
Sent: Tuesday, 3 June 2008 11:35 a.m.
To: CellML Discussion List
Subject: Re: [cellml-discussion] unit conversion
Hi Mike,
I agree - but there they are in the SI base unit list see
http://physics.nist.gov/cuu/Units/units.html
so probably 150 years too late to do much about it!
Cheers,
Peter
Mike Cooling wrote:
Does it strike anyone else as inconsistent that 'moles' are a unit
when moles are just a scaling factor? Like dozen. Maybe they should be
implemented using 'multiplier' or similar rather than a base unit.
For example, I could have a mole of amps. I couldn't have a second of
amps.
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of James
Lawson
Sent: Tuesday, 3 June 2008 11:07 a.m.
To: Erik B
Cc: cellml-discussion@cellml.org
Subject: Re: [cellml-discussion] unit conversion
Thanks Erik,
I managed to fix the issue before receiving your email, but this
clears things up for me very concisely. I would venture to say that
the reason that so many CellML models in the CellML repository do not
pass Jsim's units checking is not because of CellML, or any tools used
to create CellML models. Rather it is often because the models
themselves contain unit inconsistencies. It does not help that units
are irrelevant to most modelling tools, but I think the modelling
community is starting to raise the bar with regards to this issue.
Unfortunately it is often quite difficult to 'fix' inappropriate units
(both quantitatively and
qualitatively,) in a model without breaking it.
FYI I've uploaded the model in question, which now runs in Jsim, COR
and PCEnv, at:
http://www.cellml.org/models/sachse_moreno_abildskov_2008_version02
The 'auto' setting for the integrator in Jsim will not run the model -
the CVode
Re: [cellml-discussion] in case you haven't seen it | Why Are Computational Neuroscience and Systems Biology So Separate?
Hi folks, Pretty interesting read. I actually came to what I do now through a heavy cellular neurosci background so this disconnect between systems biology and neurosci is something that has really bugged me. They mention in the paper that SBML doesn't provide the spatial support needed for it to be useful to computational neuroscientists. CellML with its emphasis on multiscalar integration and modularity along with FieldML to describe the geometric information could address these issues. Also, I'm always interested in how CellML is represented in these kinds of publications. It is usually seen (as in this paper,) by systems biologists as a competing language for describing systems biology, which is understandable but only partly true. I think we need to seriously market CellML as a Physiome language, a lot more than we do. This will be a topic in the upcoming paper about the CellML repository I'm starting to put together - that is: the name of the software is Physiome Model Repository 2 - what has it got to do with the Physiome Project then? Kind regards, James David Nickerson wrote: Why Are Computational Neuroscience and Systems Biology So Separate? http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.178 some interesting comments, although not totally accurate... begin:vcard fn:James Lawson n:Lawson;James org:Auckland Bioengineering Institute;CellML Model Repository Curator, CellML Team adr:;;University of AucklandNew Zealand email;internet:[EMAIL PROTECTED] title:James Lawson url:http://www.cellml.org version:2.1 end:vcard ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
Re: [cellml-discussion] in case you haven't seen it | Why Are Computational Neuroscience and Systems Biology So Separate?
Hi Peter, I guess I framed it as a question to the community, but it was more of a leading question that I'd like to address in the paper on the repository. What I'm really talking about is the common preconception that SBML and CellML are designed to fill the same niches. The niches overlap but are not the same; I see the idea of CellML as part of the Physiome Project as being quite a powerful way of explaining its niche. With respect to the existence of multiple standards, I would go even further: it is essential to have more than one standard for representing this kind of information, lest the standard define the field, rather than the field defining the standard. Cheers, James Lawson Peter Hunter wrote: Hi James, Re your final question - the Physiome Project at the moment is largely about (i) the development of the markup languages CellML and FieldML ( maybe ModelML for the physics) and their associated model repositories and software tools, and (ii) strategies for bridging spatial and temporal scales. I see no reason at all not to include neuroscience in this picture - in fact there are a number of initiatives relating to a 'brain physiome' just getting underway. The essence of the Physiome is the recognition of the need to link models of structure and function across spatial scales from nm to m and temporal scales from brownian motion to human lifetime turnover of proteins. Easy to say ... While CellML and SBML are in some way competing standards, both communities are helping one another greatly by promoting the idea of modelling standards .. and provided we can convert between them, there's no particular disadvantage in having two standards. Cheers, Peter James Lawson wrote: Hi folks, Pretty interesting read. I actually came to what I do now through a heavy cellular neurosci background so this disconnect between systems biology and neurosci is something that has really bugged me. They mention in the paper that SBML doesn't provide the spatial support needed for it to be useful to computational neuroscientists. CellML with its emphasis on multiscalar integration and modularity along with FieldML to describe the geometric information could address these issues. Also, I'm always interested in how CellML is represented in these kinds of publications. It is usually seen (as in this paper,) by systems biologists as a competing language for describing systems biology, which is understandable but only partly true. I think we need to seriously market CellML as a Physiome language, a lot more than we do. This will be a topic in the upcoming paper about the CellML repository I'm starting to put together - that is: the name of the software is Physiome Model Repository 2 - what has it got to do with the Physiome Project then? Kind regards, James David Nickerson wrote: Why Are Computational Neuroscience and Systems Biology So Separate? http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.178 some interesting comments, although not totally accurate... ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion begin:vcard fn:James Lawson n:Lawson;James org:Auckland Bioengineering Institute;CellML Model Repository Curator, CellML Team adr:;;University of AucklandNew Zealand email;internet:[EMAIL PROTECTED] title:James Lawson url:http://www.cellml.org version:2.1 end:vcard ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
Re: [cellml-discussion] ModelDB
Thanks Andre, I have seen this before, not sure if they've done a lot of work on it since I last looked or whether I just missed how cool it is :) The individual model pages are excellent. They're well designed and very well populated with useful information, just fantastic. They have an awful lot of neuronal models, which is great - something we're missing on the CellML repository. http://senselab.med.yale.edu/modeldb/FindByRegionList.asp is pretty interesting. I'm actually a little bogged down with other work at the moment but hopefully I should be able to get back to the ontology work next week. Cheers, James David Nickerson wrote: Hi James, Not sure if you have seen it, but ModelDB has an ontology-like interface for browsing the models that they have. http://senselab.med.yale.edu/modeldb/ No idea if it is actually driven by some kind of ontology, but seems kind of useful. Andre. begin:vcard fn:James Lawson n:Lawson;James org:Auckland Bioengineering Institute;CellML Model Repository Curator, CellML Team adr:;;University of AucklandNew Zealand email;internet:[EMAIL PROTECTED] title:James Lawson url:http://www.cellml.org version:2.1 end:vcard ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
[cellml-discussion] ABI CellML team meeting minutes for 2008-05-28
Hi all, The ABI CellML team meeting minutes for this week (2008-05-28) are now up at: http://www.cellml.org/meeting_minutes/abi-meeting-minutes-2008-05-08/* *Kind regards, James Lawson begin:vcard fn:James Lawson n:Lawson;James org:Auckland Bioengineering Institute;CellML Model Repository Curator, CellML Team adr:;;University of AucklandNew Zealand email;internet:[EMAIL PROTECTED] title:James Lawson url:http://www.cellml.org version:2.1 end:vcard ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
[cellml-discussion] ABI CellML team meeting minutes 2008-05-32
Dear all, The ABI CellMl team meeting minutes are now up at: http://www.cellml.org/meeting_minutes/abi-meeting-minutes-2008-05-21/?portal_status_message=Changes%20saved. Kind regards, James Lawson begin:vcard fn:James Lawson n:Lawson;James org:Auckland Bioengineering Institute;CellML Model Repository Curator, CellML Team adr:;;University of AucklandNew Zealand email;internet:[EMAIL PROTECTED] title:James Lawson url:http://www.cellml.org version:2.1 end:vcard ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
Re: [cellml-discussion] ABI CellML team meeting minutes 2008-05-32
Apologies, that link should be http://www.cellml.org/meeting_minutes/abi-meeting-minutes-2008-05-21/ James James Lawson wrote: Dear all, The ABI CellMl team meeting minutes are now up at: http://www.cellml.org/meeting_minutes/abi-meeting-minutes-2008-05-21/?portal_status_message=Changes%20saved. Kind regards, James Lawson ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion begin:vcard fn:James Lawson n:Lawson;James org:Auckland Bioengineering Institute;CellML Model Repository Curator, CellML Team adr:;;University of AucklandNew Zealand email;internet:[EMAIL PROTECTED] title:James Lawson url:http://www.cellml.org version:2.1 end:vcard ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
Re: [cellml-discussion] CelOWS - a draft
Hi Ely, I started reading your pdf yesterday but unfortunately got distracted by other major work, but I will definitely be reading it hopefully will be getting some feedback to soon. Kind regards, James Ely Edison Matos wrote: Hello all, I'm sharing my work to integrate CellML with ontologies. As I said in previous message this is a initial work. This was developed as a Master thesis, at Computational Modeling Program, at UFJF (Federal University at Juiz de Fora). Juiz de Fora is a small town at Minas Gerais, Brazil. From now, I apologize for bad English. I hope that main ideas can be understandable. The attached paper is from a submitted paper (unfortunately it was not accepted) with some additions. But it is just a digest of the main work and many topics is missing. A 3 min. avi file is avaible from http://kenobi.cpd.ufjf.br/celo. It shows a sample use of the application prototype, using atomic components extracted from a Noble model and Hodking-Huxley model. It aims to make the idea more clear, but it is just a simplified sample. I thank for the opportunity for sharing the work and I hope that the ideas could be useful in some level. Ely Edison Matos UFJF/Brazil ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion begin:vcard fn:James Lawson n:Lawson;James org:Auckland Bioengineering Institute;CellML Model Repository Curator, CellML Team adr:;;University of AucklandNew Zealand email;internet:[EMAIL PROTECTED] title:James Lawson url:http://www.cellml.org version:2.1 end:vcard ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
Re: [cellml-discussion] Suggestions regarding search and browse utility for CellML Repository
Hi Abhishek, Good to hear from you, you make some very good points. I apologise if someone has already raised these points, I've just come back after being away for a couple of weeks and I'm going through my many unanswered emails. So at the moment, one of the things I am thinking a lot about is ontological annotation of CellML models. I've just been to visit Neil Wipat's lab at the University of Newcastle, and I talked quite a lot with him and members of his group about ontologies and how they might be of use to the CellML community. So one of the things that the new CellML repository will handle much better than the current one is the manner in which a user can view models and their interrelationships, whether these are based directly on CellML relationships such as import based modularity or whether they are based on relationships inferred from ontological tags. I'll definitely have a look at MeSH - what we're planning to do (I believe) is let the CellML-Bio Ontology import as much as possible from other ontologies, and let Sarala's ontological framework stand as our contribution. Where we conclude that there is no ontology that covers what we are trying to do in a satisfactory manner, we'll create our own. I can see this happening in the area of synthetic biology, which is only just starting to be represented by formats like CellML and SBML. So a tree-like browsing structure as constructed from MeSH tags or similar could be one of a number of different ways of viewing the models. You could also do searching by terms, or construct trees according to terms. For example, you could have 'species' as the top level and 'organ' as a lower level, and 'cell type' as the bottom. So then you'd get a tree sorted first by species, then by organ type, say heart, pancreas, liver, etc. and then by cell type, so within the heart: myocardium, epicardium, etc. etc. The possibilities for how we display fully tagged models are huge, so we do need to form some kind of system of constraints - or at least provide a set of default viewing architectures based on what workflows we anticipate for users. When we decompose models into modular elements, this kind of tagging is going to be absolutely crucial for model reusability and for the process of figuring out what module you want and where to get it. As far as the technology for web services and programmatic access to the repository database, that isn't something we've thought about much until now, but on our travels Mike and I have realised that this is really quite important. In fact, it was often one of the first questions I was asked when I was discussing the CellML repository. A lot of people are seeing the repository not simply as a database containing individual models, but as an dataset in and of itself. We need to work on this - I'm told Mike mentioned it at the Auckland CellML meeting last week. Hope you found this of some interest, James Abhishek Tiwari wrote: As growing no of models in CellML repository I feel that CellML Repository can be made more user friendly by implementing one or more suggestions mentioned below- 1. A Tree like browsing mechanism in which end child node of tree will have model. For that we need to have classification system for the models based on Physiological system or better say using MeSH (Medical Subject Headings,something like http://www.nlm.nih.gov/cgi/mesh/2008/MB_cgi). Models can be in multiple classes and basically model metadata can have details for the classification purpose like keywords. Domain ontologies can be used to give better description for tree like representation. 2. For a given model at the end of overview similar models (basic or improved models or more complex models) can be reported (Similar to model variants). 3. Web services to search and download CellMl models for non ABI tools ( using CellMl API or Web API for CellMl). I don't know if efforts to handle above is under development or already exists so I thought to write you all. abhishek ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion begin:vcard fn:James Lawson n:Lawson;James org:Auckland Bioengineering Institute;CellML Model Repository Curator, CellML Team adr:;;University of AucklandNew Zealand email;internet:[EMAIL PROTECTED] title:James Lawson url:http://www.cellml.org version:2.1 end:vcard ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
[cellml-discussion] differences between CellML and SBML for modelling hepatic glycogenolysis
Hi all, I just came across this essay while looking for commentary on the differences between CellML and SBML. I don't believe it is peer reviewed - rather a graduate student's essay, but it does provide an interesting perspective. http://doi.wiley.com/10.1002/pmic.200600438 Kind regards, James Lawson begin:vcard fn:James Lawson n:Lawson;James org:Auckland Bioengineering Institute;CellML Model Repository Curator, CellML Team adr:;;University of AucklandNew Zealand email;internet:[EMAIL PROTECTED] title:James Lawson url:http://www.cellml.org version:2.1 end:vcard ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
Re: [cellml-discussion] differences between CellML and SBML for modelling hepatic glycogenolysis
How terribly unobservant of me. My apologies to the author of this article if he is reading this. James Edmund J. Crampin wrote: It's a review article in Proteomics - certainly peer reviewed. Edmund James Lawson wrote: Hi all, I just came across this essay while looking for commentary on the differences between CellML and SBML. I don't believe it is peer reviewed - rather a graduate student's essay, but it does provide an interesting perspective. http://doi.wiley.com/10.1002/pmic.200600438 Kind regards, James Lawson ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion begin:vcard fn:James Lawson n:Lawson;James org:Auckland Bioengineering Institute;CellML Model Repository Curator, CellML Team adr:;;University of AucklandNew Zealand email;internet:[EMAIL PROTECTED] title:James Lawson url:http://www.cellml.org version:2.1 end:vcard ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
Re: [cellml-discussion] differences between CellML and SBML for modelling hepatic glycogenolysis
Sorry to spam everyone again - I gave the wrong link. This is the one I meant to refer to: http://www.ucl.ac.uk/~ucbptag/work/tg_essay1.pdf Kind regards, James James Lawson wrote: How terribly unobservant of me. My apologies to the author of this article if he is reading this. James Edmund J. Crampin wrote: It's a review article in Proteomics - certainly peer reviewed. Edmund James Lawson wrote: Hi all, I just came across this essay while looking for commentary on the differences between CellML and SBML. I don't believe it is peer reviewed - rather a graduate student's essay, but it does provide an interesting perspective. http://doi.wiley.com/10.1002/pmic.200600438 Kind regards, James Lawson ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion begin:vcard fn:James Lawson n:Lawson;James org:Auckland Bioengineering Institute;CellML Model Repository Curator, CellML Team adr:;;University of AucklandNew Zealand email;internet:[EMAIL PROTECTED] title:James Lawson url:http://www.cellml.org version:2.1 end:vcard ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
[cellml-discussion] ABI CellML team meeting minutes for 2008-04-02
Hi all, The ABI CellML team meeting minutes for this week (2008-04-02) have been posted at: http://www.cellml.org/meeting_minutes/abi-meeting-minutes-2008-04-02/ Kind regards, James begin:vcard fn:James Lawson n:Lawson;James org:Auckland Bioengineering Institute;CellML Model Repository Curator, CellML Team adr:;;University of AucklandNew Zealand email;internet:[EMAIL PROTECTED] title:James Lawson url:http://www.cellml.org version:2.1 end:vcard ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
[cellml-discussion] ABI CellML group meeting 2008-03-05
Hi all, The ABI CellML group meeting minutes for this week's meeting - 2008-03-05 are now up at: http://www.cellml.org/meeting_minutes/abi-meeting-minutes-2008-03-05/ Kind regards, James Lawson begin:vcard fn:James Lawson n:Lawson;James org:Auckland Bioengineering Institute;CellML Model Repository Curator, CellML Team adr:;;University of AucklandNew Zealand email;internet:[EMAIL PROTECTED] title:James Lawson url:http://www.cellml.org version:2.1 end:vcard ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
[cellml-discussion] Auckland CellML Group Meeting Minutes (2008-02-20)
Hi all, The minutes for this week's ABI CellML meeting have been posted at: http://www.cellml.org/meeting_minutes/meeting-minutes-2008-02-20/?portal_status_message=Changes%20saved. Kind regards, James Lawson begin:vcard fn:James Lawson n:Lawson;James org:Auckland Bioengineering Institute;CellML Model Repository Curator, CellML Team adr:;;University of AucklandNew Zealand email;internet:[EMAIL PROTECTED] title:James Lawson url:http://www.cellml.org version:2.1 end:vcard ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
[cellml-discussion] [Fwd: [Synthetic Biology] BBF working groups, SB4.0, and standard workshop]
Thought some of you folks might be interested in this: ---BeginMessage--- Hello, A quick three part email providing updates on several important synthetic biology activities happening now. *** 1. BBF working groups *** The BioBricks Foundation (BBF) is launching four working groups. The first group is SB4.0 If you want to organize a special topic discussion or session at the Fourth International Conference on Synthetic Biology (October 2008), sign up for this group. The second group is Technical. If you want to wrestle Tom Knight, working to define exactly what the heck a BioBrick standard biological part is, then please join this group. The third group is Legal. If you want to sue everybody then please don't join this group. But, if you want to help with figuring out the specific legal scheme that will keep BioBrick parts free to study, use, and modify, then join up here. The fourth group is Volunteers. If you want to help with the workings, leadership, or activities of the BBF itself, or represent the BBF at meetings around the world, then this is the group for you. Somebody has to keep this thing running! Each working group will bring people like you together to discuss and work on issues important to the synthetic biology community. Note that you can join more than one group. And, if you don't like what you see, you can quit. Join up by subscribing to one or more of the appropriate mailing lists here: http://openwetware.org/wiki/The_BioBricks_Foundation:MailingLists In launching these groups, the BBF is hoping that a diverse community from many countries, schools, companies, and organizations will continue to come together as synthetic biology develops, so that the technology of biology reaches its best constructive potential, and is available for all to use. *** 2. SB4.0 *** The Fourth International Meeting on Synthetic Biology will take place 10-12 October 2008 at HKUST in Hong Kong. Given everything that is happening, and how much there is still to do, SB4.0 is going to be an amazing meeting. The organizers of the meeting, myself included, can't pretend that we understand everything that should be presented or discussed at the conference. Thus, we are asking for your help. If you would like to suggest a topic for discussion, or organize a breakout session, or can suggest whatever would work best for a particular idea, please let me know. We are developing tremendous resources in support of SB4.0 (including significant travel assistance) and will work very hard to make all good ideas happen. If you want to be part of a broader discussion on SB4.0 organization, please join the working group (as per above). Conference website here: http://syntheticbiology.org/Synthetic_Biology_4.0.html *** 3. Legal and Technical Standard Workshop *** The BBF had a great kickoff workshop at MIT last November, discussion the legal scheme for BioBrick standard biological parts, and also defining and launching an open technical standards process for synthetic biology. Building on this success, the next workshop (and our first west coast meeting) will take place on March 1 at UCSF in San Francisco. If you want to attend or call into the meeting, please register (for free) here: http://openwetware.org/wiki/The_BioBricks_Foundation:Workshop2 *** BONUS *** If you want to join the BBF as a member, that's free too. Sign up here: http://openwetware.org/wiki/The_BioBricks_Foundation:Membership Be great! Drew _ Drew Endy http://mit.edu/endy/ http://biobricks.org/ ___ discuss mailing list [EMAIL PROTECTED] http://lists.syntheticbiology.org/mailman/listinfo/discuss ---End Message--- begin:vcard fn:James Lawson n:Lawson;James org:Auckland Bioengineering Institute;CellML Model Repository Curator, CellML Team adr:;;University of AucklandNew Zealand email;internet:[EMAIL PROTECTED] title:James Lawson url:http://www.cellml.org version:2.1 end:vcard ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
Re: [cellml-discussion] Survey on opinions for the backwards compatibility levels for future CellML Specs
Good points. Re: Peter's mention of the European groups taking up CellML as per their funding commitments, and his comment that 2008 promises to be a very busy year indeed for us, I think we can hedge our bets on the latter. Kind regards, James Randall Britten wrote: Hi all I think the policy depends on the answer to these two questions: 1) In terms of how widely CellML has been adopted worldwide, how does the current status compare to what we expect in say 6 months, and say a year from now? 2) How successful have we been in terms of achieving the vision of CellML? If we think CellML is about as popular as it ever will be, and that the current version is essentially good enough, then our emphasis may be on compatibility. However, if we think that the rate of adoption will increase dramatically at some point in the future, and that there is a lot of room for improvement, then it may be better to break compatibility now, while it is still early enough, but we have learnt enough to make one of the next versions a lot better than the current version. My impression is that we are in the latter position. Regards, Randall ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion begin:vcard fn:James Lawson n:Lawson;James org:Auckland Bioengineering Institute;CellML Model Repository Curator, CellML Team adr:;;University of AucklandNew Zealand email;internet:[EMAIL PROTECTED] title:James Lawson url:http://www.cellml.org version:2.1 end:vcard ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
Re: [cellml-discussion] Survey on opinions for the backwards compatibility levels for future CellML Specs
Andrew Miller wrote: Hi all, Hi, thanks for providing a nice intro to this issue Andrew. There have recently been some discussions of changes which would drastically break forwards or backwards compatibility of CellML (for example, changing the way that connections work). I think that it is important that we come to some consensus on what the policy for inter-version compatibility in CellML should be quite soon, because this drastically affects decisions that need to be made in CellML specification development. It doesn't really make sense to be inconsistent with respect to version compatibility - it would be quite unfortunate if we worked hard to keep compatibility for one part of CellML, and then broke it in another major part such as by changing the way connections work, and so I think we need a policy on this. I certainly agree with you that we need to keep policy consistent. However the possibility that immediately came to mind is that we could group versions of the specification with respect to interversion compatibility. If we have major decisions to make regarding the continuing integrity of the language that might break compatibility, I think we must reserve the right to do this, giving careful consideration of the impact to the community of course. For example, if we were to break compatibility of 1.0 and 1.1 with 1.2, but have 1.3 and 1.4 compatible with 1.2, this would reduce development workload compared with a policy of not requiring version compatibility between successive versions at all. Perhaps this is an approach we might want to take between, say CellML 1.X and CellML 2.X - that is, we reserve major changes that will break compatibility for major versioning events. I have come up with a number of different potential policy statements on when backwards compatibility should be broken and when it should be kept. It might help us to reach consensus if members of the CellML community could rank the policies in order of preference (1 is the most preferable policy, 2 the next most, and so on), and suggest any good policies that may be missing. Option A) Future versions of CellML should aim to solely express the intention of previous versions better and more clearly. They should aim to keep full compatibility with an implementation of the specification according to the rules of the specification as they were interpreted by implementors. Option B) Future versions of CellML should try to be mostly compatible with existing implementations of previous versions of CellML. They may remove functionality that does not have an established base of software which correctly implements that functionality. They may also add in new functionality, if that new functionality significantly increases the expressiveness of the language. However, in normal circumstances, compatibility should be maintained, so that when a model not using new features is saved in the new version's most preferred format, it can still be correctly loaded into software only supporting the old version. Likewise, a model not using any removed features should be able to be loaded in software supporting only the new version of the specification. Option C) Future versions of CellML should make any changes which make it conceptually cleaner, even if there is a less clean compromise available that would have lesser compatibility implications. Software will need to explicitly support more than one version as a completely separate format. My preferred choice is Option B. Despite being apparently at opposite ends of the spectrum, Option A and Option C are, in my opinion, fairly similar, because if we adopted Option A, larger changes would appear in a new specification called something other than CellML. Although there could be advantages of coming up with a more meaningful name than CellML, I think that this would also set us back in terms of community awareness of the specification, and so I think that Option C is marginally better than Option A (i.e. my personal order of preference is currently B:1, C:2, A:3). I would have to concur - out of those three possibilities, B would be preferable. Kind regards, James I look forward to any feedback on this you may have. Best regards, Andrew ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion begin:vcard fn:James Lawson n:Lawson;James org:Auckland Bioengineering Institute;CellML Model Repository Curator, CellML Team adr:;;University of AucklandNew Zealand email;internet:[EMAIL PROTECTED] title:James Lawson url:http://www.cellml.org version:2.1 end:vcard ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
[cellml-discussion] [Fwd: Re: application 'ML']
From Steven Niederer (through Gareth): ---BeginMessage--- Hi everyone, this from Steven in Oxford, via the CellML Webmaster account. Please let me know if there is a more appropriate contact I can forward this mail to. thanks, Gareth Steven Niederer wrote: Hi guys, Just checking if there was any work been done on the following: 1) creating maps of variable names to allow a user (me) to define a variable that I want to change in a one file and have that mapped onto the corresponding variable in a model. (I am batch processing analysis of 20+ models at the moment) ie I wish to set value for intracellular calcium. I want to call the variable Cai but in the models that I have it is called cai, Cai and Ca_i etc. so I wish to create a wrapper for each model to map the variables to a standard name. Is there any work been done on things like this and if so is their a recommended format for the mapping wrapper? 2) Defining virtual experiment protocols. After defining the model variables that I wish to set as model outputs or inputs I would like to define how the input variables are set and if I want any post processing to be done on my output signals. Again I wondered if there was a proposed format for these types of descriptions. Any suggestions would be great. cheers Steven Niederer begin:vcard fn:Gareth de Walters n:de Walters;Gareth org:University of Auckland;Auckland Bioengineering Institute adr:Auckland;;Level 6, 70 Symonds StNew Zealand title:Webmaster and Database Administrator tel;work:+64 9 373 7599 extension 85360 x-mozilla-html:FALSE url:www.bioeng.auckland.ac.nz version:2.1 end:vcard ---End Message--- ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
[cellml-discussion] cellml in synthetic biology
Here's a really interesting project (IMO) that seems to be pretty keen on using Cellml. http://openwetware.org/wiki/Talk:Registry_of_Standard_Biological_Models http://openwetware.org/wiki/Registry_of_Standard_Biological_Models/Registry_organization Openwetware is a big MIT based initiative to create a forum for and standardise synthetic biology. Seems to me they need some info on CellML... and some support. The first link talks about SBML (Mike Hucka is quoted,) but also mentions that multiscale modelling will be essential, which isn't something that SBML could call its forte. We, however, can. So don't mind if I do... ;) James ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
Re: [cellml-discussion] Physiome Project issue tracker now available
Hi all, I'd just like to recognise Andrew and Randall, amongst others, for all their hard work on this. Since we got the tracker running internally a couple of months ago we've generated over 200 tracker items, and dealt with many of them. Good work guys :) James Andrew Miller wrote: Hi all, We have now got an issue tracker for the CellML and other physiome-related projects available at https://tracker.physiomeproject.org/ . This tracker is open to the public, and will accept 'tracker items', which could be questions, reports of bugs or feature suggestions for CellML / Physiome related software / web services / websites, problems or suggestions related to repository models, issues relating to the CellML specifications, and a wide range of other similar items (essentially, anything piece of information related to the physiome project that needs to be tracked and will eventually be marked as 'resolved' at some definite point in time). The tracker allows anyone to create an account and add themselves to the CC lists of existing tracker items - this provides a convenient way to follow the progress of issues you are interested in. After creating an account, anyone is also able (and encouraged) to submit new tracker items, comment on existing tracker items, and make other similar changes to the tracker item database. If you find any problems with the tracker itself, then please submit a tracker item (log in, then choose Submit Bug Report [navigation area on the left] = cellml.org site = Choose 'CellML Tracker' as the component and fill in the rest of the form). If you are unable to create a tracker item, then you can let me know of the issue by e-mail. Best regards, Andrew ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
Re: [cellml-discussion] how to units make a difference to simulation
Alan Garny wrote:
-Original Message-
From: [EMAIL PROTECTED] [mailto:cellml-discussion-
[EMAIL PROTECTED] On Behalf Of James Lawson
Sent: 06 August 2007 00:40
To: For those interested in contributing to the development of CellML.
Subject: [cellml-discussion] how to units make a difference to
simulation
Hi all,
Recently Catherine said that she had a model that was running but not
producing the right output. Instead of producing a train of spikes, it
was just producing some kind of curve flattening off at an asymptote.
Then when she changed some units on a relevant variable from
dimensionless to the right units, she got the nice spiking output.
As for myself, I've been looking at a model which has both a normal
version and a scaled/non-dimensionalized version. When I consulted him
about the output I was getting and which equations I should be using
from his paper, the model author suggested that I use the
non-dimensionalised set of equations, since the model describes a very
stiff problem, and as such, that is what the ND'd equations are there
for. Wheras before I was just getting curves that looked nothing like
I
want, I am now getting trains of spikes.
I realise the first example might be slightly different from the first
(damn I am sick of people who don't know how to write English, the
Americans, that is, telling me I need a 'z' everywhere!) but...
The point/question I want to raise here, is how does PCEnv / other
simulators treat units? Is it possible that some of the models in the
repository simply don't run or produce the right outputs because of
the
units? If so, this would be news to me! It would also be frustrating
given the number of times we have to guess or spend hours poring over
equations trying to work out the units of a variable.
Hi James,
As you know we (Catherine, you and I) spent a bit of time this morning
trying to understand some models. One of the models that Catherine has been
working on had problems with units. My understanding is that PCEnv didn't
pick those problems up, while COR did. Correcting the problems, Catherine
was able to get the model to work (I believe there might still be another
problem, but not related to units this time).
Anyway, the view we have now taken in Oxford is that models shouldn't have
any problem related to units.
I absolutely agree that models should not have units problems. The
problem is that many of them do, and, speaking for myself, I do not have
the skills or the knowledge to know how to rearrange someone else's
model to fix the units. Especially with big models, it can just get too
complex. I'd like to see unit checking in PCEnv, but I wouldn't want a
model with bad units to not run - I'd just want error messages telling
me there is a problem.
This means that, dimensional equivalences,
which are allowed in the CellML specification, are not acceptable to us.
We should always have strict equivalences. E.g. A = B+C (with A and B in mV,
while C in V) would be seen as being dimensionally equivalent and OK in
regards to the CellML specification (and therefore COR, since it will only
generate a warning). Yet, we would modify the equation so that it now reads:
A = B+1000{millivolt_per_millivolt}*C. This may not be a great example, but
I think you got the gist of it.
The idea is, therefore, to have models that have no unit issues *at all*. I
appreciate that this may seem a bit restrictive, but we have had so many
issues with units over the years that we believe it will be worth it in the
long term.
This would be great. I think it needs to start with the model authors
though, which is where standards such as MIRIAM come in.
Alternatively, we could have the software doing units conversion for the
user... but that's another issue... and I understand that some are against
that idea.
Again, this is a feature that it would be useful to be able to turn on
and off. However I think in most cases the software will not be smart
enough to figure out what the units should be.
Alan.
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[cellml-discussion] how to units make a difference to simulation
Hi all, Recently Catherine said that she had a model that was running but not producing the right output. Instead of producing a train of spikes, it was just producing some kind of curve flattening off at an asymptote. Then when she changed some units on a relevant variable from dimensionless to the right units, she got the nice spiking output. As for myself, I've been looking at a model which has both a normal version and a scaled/non-dimensionalized version. When I consulted him about the output I was getting and which equations I should be using from his paper, the model author suggested that I use the non-dimensionalised set of equations, since the model describes a very stiff problem, and as such, that is what the ND'd equations are there for. Wheras before I was just getting curves that looked nothing like I want, I am now getting trains of spikes. I realise the first example might be slightly different from the first (damn I am sick of people who don't know how to write English, the Americans, that is, telling me I need a 'z' everywhere!) but... The point/question I want to raise here, is how does PCEnv / other simulators treat units? Is it possible that some of the models in the repository simply don't run or produce the right outputs because of the units? If so, this would be news to me! It would also be frustrating given the number of times we have to guess or spend hours poring over equations trying to work out the units of a variable. Thanks, James Lawson ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
Re: [cellml-discussion] Using PCEnv 2.0
Alan Garny wrote: Hi Ely, I have the feeling that this might a locale issue. In Brazil, the decimal separator is ,, while it is . in New Zealand (where PCEnv 0.2 is being developed). So, while 0.3 will be a valid floating point number in, at least, English speaking country, it won't be in Brazil (and a few other countries for that matter!). So, for things to work for you, you would need to have 0,3 instead. This being said, PCEnv should maybe force the use of . as a decimal separator and , as a thousand separator, independent of the locale. COR, for examples, does that. Anyway, a quick fix for you would be to switch to an English-based locale whenever you use PCEnv, at least until a fix for PCEnv is available (assuming I have properly diagnosed the problem!). Best wishes, Alan. I saw this and I thought I ran that model not more than a few days ago... - it would never have crossed my mind that he might have been using the wrong separator. I hope you're right and it isn't something more obscure. Good work :) James -Original Message- From: [EMAIL PROTECTED] [mailto:cellml-discussion- [EMAIL PROTECTED] On Behalf Of Ely Edison Matos Sent: 25 July 2007 21:01 To: CellML Discussion List Subject: [cellml-discussion] Using PCEnv 2.0 Hello, My name is Ely Matos. I'm studying CellML Models in a academic project. I've downloaded PCEnv 2.0 and some models from repository. But my first use, loading the file hodgkin_huxley_1952_version06.cellml show a strange error: Error: Variable g_L has initial_value 0.3 which isn't a valid floating point number, nor a valid variable name within that component. How can I fix it? The Integrate button don't appear. Sorry, if here is not the right to place to this question (if so, plz, indicate the right place..:-)) Thanks, Ely Matos Federal University of Juiz de Fora - Brazil ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
Re: [cellml-discussion] CellML 1.1.1 specification
David Nickerson wrote: Matt wrote: It seems there is some misunderstanding as to whether we are discussing a proposal to remove the reaction element from CellML or a proposed new specification. I thought it was the latter but you seem to be talking about the former... Both. I think. So I will try another explanation. If we had our specification in a version control system and tagged out releases and release candidates etc, and if we followed a protocol of releasing at least one stable minor release that marks depreciation only, then the following would be the result (in my mind) - The current trunk is the development version of cellml 1.2 (i.e. unreleased-dev). - This current trunk look likes CellML 1.1 and the associated definitions in DTDs etc. - We update this to mark out that reaction elements are going to be depreciated, this includes comments in DTDs etc. We don't remove reaction elements from the specification at this stage because that's where we hang the depreciation notices. - We tag this as 1.1.1 and release it - We then delete reaction elements from the specification that is on trunk. Now, this is the kind of process I think covers the steps you have been talking about and at the end makes available a trunk version of 1.2-dev-unreleased that doesn't have reaction elements that people can check out an play with (this is essentially the proposal page the Andrew wrote up - though I think there are issues remaining now with the absence of biology from a Cell ML standard. yep - thats how I would see the specification evolving over time, subject, of course, to the various proposals being accepted and assigned to an appropriate version. I think the absence of biology from the core specification is probably a good thing, It might be worth adding an editorial comment or similar to note that the metadata is where the vast majority of biological information is defined. but there needs to be clear annotation of the specification describing how reactions should now be represented in a world without reactions - another best practice recommendation and examples in the model repository at the least, I would hope. Yep, the 'signal transduction' tutorial will no longer be needed, since its main purpose is to describe the best practice for use of reaction elements to describe biochemical pathways. The question will be, do we just remove it, or do we create a new tutorial that is biochem specific, but doesn't talk about reaction elements. For example, there are two main ways to code up a biochem model: either you can use equations that describe, for example, the rate of change of conc. of species A, where species A might have a few different processes acting on it, so this equation would be a summation of the effect of these processes, OR, you can split the equation into 'fluxes,' which represent just the effect of one process on a species at a time. I think it would be worth writing a best practice guide for writing biochem models, even if it is relatively short, since there are a few things that are different from how an ephys model should be coded up. But what I am also saying is that this is still just an idea, so it should be put forward as a proposal that has not been accepted. I.e. that the steps I described above are purely hypothetical at the moment, since we haven't had the chance to hear arguments from people about it - it might turn out to be a silly proposal. definitely. Your steps describe the process for how the specification may be updated, developed, etc., but each release will be the result of a set of proposals being accepted and assigned to that particular release. this is why the proposal to remove the reaction element should have first been put forward independently of any specific future version of CellML. Perhaps we could start by formalising the actual proposal to get rid of the rxn element. Why are we doing it? How will we replace the purpose it served, using metadata for example? I realise that this has been discussed a lot in an informal manner, and was in fact decided well before my time, but I guess if we're going to do something as major as create a new spec version, we should build the foundations first. In this discussion forum we could then debate the merits of this proposal and, if deemed suitable, develop a schedule for the implementation of the proposal (i.e., mark reaction element for deprecation in 1.1.1 and then remove the reaction element in 1.2). Other proposals would also be similarly evaluated and possibly assigned to the same or different releases of the CellML specification. It definitely should not, at this stage, be a forgone conclusion that the reaction element should be removed in 1.2 (or some specific future version of CellML) - that is still open to discussion in my mind, It would be good to see a thorough list of pros and cons for the rxn element. If we do write a
Re: [cellml-discussion] embedded stimulus currents in CellML models
Matt wrote: On 7/19/07, David Nickerson [EMAIL PROTECTED] wrote: Of course. And in the same sense you could simply delete the stimulus protocol component if you didn't want it. I think the issue is in fact a curation issue - we are specifying one of our curation 'levels' as model is the same as is described in the paper. If there is a stimulus protocol that isn't in the paper in the CellML model, then this curation standard is invalidated. This is fine, as it (hopefully) moves the model up to the next 'level,' which requires that the model be able to produce the appropriate output, but doesn't necessarily require that the model be identical to that described in the paper. So the solution is that we should really have both. So there is validation in the sense that there is a true representation of a publication - which more often than not is pretty useless, and there is validation in the sense that the model can demonstrate what we think was intended by the publication (most obviously produces the right results) but perhaps many changes in the underlying formulation. Is it ok to only offer the former as a historical version? I guess it depends if you define all versions that are not the most recent version as 'historical.' What does historical mean here exactly? But essentially, I think it's okay if it's noted in the model documentation - perhaps a note on why the model won't run in a simulator, and that this particular version might be better for multicellular networks where the stimulus is externally defined? It's a pretty simple matter to get a model to the point where it is complete except for a stimulus protocol, upload it as version x, then add the stimulus protocol and upload that as version y. To be honest, if people are wanting to fiddle around with multicellular systems they probably know what they're doing enough to be able to identify and delete an extraneous stimulus component they don't want. The documentation will identify it as 'foreign.' and should it be necessary to actually do the former if we can easily see where the math needs to be written out differently? Hmm, if it doesn't really take any effort to do, then the only reason (besides the above,) I can think of not to do this, is that it just creates extra versions that aren't particularly useful. ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
Re: [cellml-discussion] embedded stimulus currents in CellML models
Alan Garny wrote: Shouldn't we therefore offer at least two different sets of CellML 1.0 files? One that only contains the model itself and another that also includes some simulation specific information? I actually replied to this somewhere else - I'll repeat it... We just talked about this issue in the meeting. We decided that it was probably worth providing one with and one without. Obviously the one without would not be able to be simulated in PCEnv or COR. You could still easily modify the model for your own purpose in COR (and the same in PCEnv, I believe). Of course. And in the same sense you could simply delete the stimulus protocol component if you didn't want it. I think the issue is in fact a curation issue - we are specifying one of our curation 'levels' as model is the same as is described in the paper. If there is a stimulus protocol that isn't in the paper in the CellML model, then this curation standard is invalidated. This is fine, as it (hopefully) moves the model up to the next 'level,' which requires that the model be able to produce the appropriate output, but doesn't necessarily require that the model be identical to that described in the paper. So the solution is that we should really have both. This is the kind of issue that really needs to go in a tracker. Though CellML 1.1 is the obvious way to go, we have to accept the fact that most CellML users probably only use CellML 1.0. But is that because they a.) don't need 1.1, b.) don't know how to use 1.1 or c.) want to use 1.1 but don't because the repository doesn't support it? I suspect it is either a or c, since most people would find out how to use 1.1 if it was a tool they thought would be useful. Depending on the end-user, it could be a, b and/or c, as well as the fact that apart from PCEnv, no other CellML-capable software that I am aware of can deal with CellML 1.1 models. This emphasises my view that we have to make the CellML API easy to use and provide several examples of its use. This is a good point. There is no point simply criticising other software because it doesn't make use of 1.1. We need to ask why this is, and if there is anything we can do to make it easier for developers to make their software 1.1-capable. I think this is definitely an area where you could be very useful, since you can take a fresh look at the API, whereas it is much harder for someone like Andrew to take a step back from it. Alan. ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
Re: [cellml-discussion] embedded stimulus currents in CellML models
Alan Garny wrote: Depending on the end-user, it could be a, b and/or c, as well as the fact that apart from PCEnv, no other CellML-capable software that I am aware of can deal with CellML 1.1 models. This emphasises my view that we have to make the CellML API easy to use and provide several examples of its use. http://cellml.sourceforge.net :-) That is a good start indeed. Now, I am waiting for you to write the documentation... :) Alan. ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion I was actually trying to get CellML2Dot running. I didn't try very hard... It's in the cellml-discussion archives (or if not the team-cellml, but I think the former.) It would definitely be cool to get some basic documentation for these tools. If you have a go at installing CellML2Dot in Linux Alan, let me know. I'd like to see Andre's simulator too. How does it differ from PCEnv or COR Andre? ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
[cellml-discussion] CellML2Dot
Hi Andre, In the workshop you showed us a slide of a program you'd made for debugging models that showed all the connections etc. Is this that program? I tried to get the source off subversion but it didn't work. Do you have any tips on getting this tool to work? Thanks, James ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
Re: [cellml-discussion] Proposal: Local CellML team e-mail addresses
Andrew Miller wrote: Hi, There has been some discussion recently about how best to handle local CellML addresses (which can be used by local groups with an interest in CellML to arrange meetings and hold other discussions which are purely local in scope and not of interest to the broader CellML community). Something I didn't think of before... surely most other groups already have a mailing list that serves their group's interest anyway... What would make it worthwhile for them to actually swap over to an official cellml list? At the University of Auckland, we have a list for the Auckland CellML team. However, I feel that some of the discussion on that list would probably better occur on the cellml-discussion mailing list (or another more public forum). After discussing this at our Auckland CellML group meeting, it was suggested that perhaps similar issues are arising at other localised groups working on CellML. To this end, we came up with a rough proposal (which I expand on below) which I hope will help both the Auckland group and other groups using CellML to collaborate. Please note that this is just a proposal, and I would welcome feedback on how we can improve it. I would be especially interested to hear opinions from other groups outside Auckland using CellML. Proposal: 1) Groups can request location@cellml.org mailing lists. a) Any group which is working on a CellML related project may [follow some procedure which needs to be decided] to request a mailing list for discussion of location specific matters related to their CellML project. b) The e-mail address requested shall follow the format location@cellml.org, where location is replaced with a short word, phrase, or abbrevation which describes the geographical location of the group concerned. c) The location name should be sufficient to uniquely distinguish the group from other separate groups that may wish to work on CellML. List names are subject to review to ensure that they are unlikely to conflict with another group or cause confusion. 2) Location-specific mailing lists to have open membership and be publicly archived. a) Any person may join any location-specific mailing list without moderator approval, regardless of their actual geographic location. b) All location-specific mailing lists shall have a publicly readable archive, hosted at cellml.org. 3) Scope and posting rules for location-specific mailing lists. a) All messages posted to location-specific mailing lists must be related in some way to CellML, or to tools which process CellML, or to the operation of groups with an interest in CellML. Some degree of leeway should be afforded by cellml.org administrators here, as long as the list is not being used as a free hosting service for work not even vaguely related CellML. b) Message posters are strongly encouraged to send messages which may be of broader interest to the cellml-discussion list rather than to the location-specific address. c) The location-specific mailing lists must not be used for information which is of a private or confidential nature (after all, it is an open membership list with a public archive). d) All posters to location-specific mailing lists agree that their messages may be further distributed (with attribution to them), including by forwarding to the cellml-discussion list or by inclusion in public bug-trackers (and also agree to the translation of their messages into another language). e) The location-specific groups may establish their own additional posting rules by their normal decision-making process, as long as these posting rules do not conflict with the general rules described here. These posting rules may include (without limitation) the scope of the list, who is allowed to post to the list (but not who can subscribe) and how often, and the permitted language(s) of any posts to the list. 4) Administration and moderation of location-specific mailing lists. a) Each location-specific group shall determine their own process for the control of their own mailing lists, and their nominated administrator will be provided with a password allowing them access to the administrative interface. b) Group designated administrators are free to change the settings of the groups location-specific CellML mailing list (after changes are approved through the appropriate local decision-making processes). However, they must not make changes which cause the mailing list archives to be no longer public, or which cause the list to require moderator approval before allowing subscriptions. c) Group designated administrators may also (in accordance with locally determined policies) subscribe and remove people from their mailing lists are a service to the person being added or removed. Administrators may infer that a person wishes to be added or removed from the
Re: [cellml-discussion] [team-cellml] @cellml.org addresses
Matt wrote: This seems like it's going in circles. I'm not really sure why anyone would want to contact us personally with something they didn't want to send to the list. Wasn't this originally your suggestion? Thinking about this more we should probably try: 1) cellml-discussion@cellml.org 2) [EMAIL PROTECTED] - for specific enquiries that you don't want publicly available. It would make sense to have a nominated person or persons that address mail in there - James I would think - who decides if an email should be forwarded to the list because it really is a public issue - or respond and acknowledge the email and seek a response from those in the team that it seems appropriate to. 3) a team page where everyone who is on the team-cellml list has a picture and a small blurb (kind of like http://sbml.org/contacts/) ... which is really just to give a face to those who are quite deeply involved. I would imagine people like Penny Noble to be on that. If someone contacts someone on that page then it will likely be quite personal. On 6/25/07, Andrew Miller [EMAIL PROTECTED] wrote: David Brooks wrote: See below... On 25/06/2007 4:32 p.m., Andrew Miller wrote: James Lawson wrote: Andrew Miller wrote: I don't think we should use the word 'project team' because there is no formal project team. Perhaps we can just have a list of people categorised by their interest in the CellML project, and then a contact page which helps people find certain people (for example, we could have a category for technical issues with cellml.org, which would list Tommy, a category for people with the ability to curate cardiac electrophysiology models, which would list James, and a category for people with an interest in cardiac electrophysiological modelling, which would list anyone who wanted to be on the list). There is then the issue of whether we use our own email addresses or @cellml.org addresses. Andre is keen on the latter, and I agree. Although I am not entirely convinced that it is necessary or beneficial, and I think that we risk harming the community nature of CellML by saying that only certain people can get a cellml.org e-mail address. Surely there's no harm in having a small number of generic @cellml.org email addresses that reflect the roles people play? (eg [EMAIL PROTECTED], [EMAIL PROTECTED], [EMAIL PROTECTED]). I don't think it's a good idea to have lots of these addresses (as this can get confusing), nor should the roles be too specialised. We have tried this in the past, and it resulted in the fragmentation of the community, and it had several negative outcomes: 1) People were sending all messages of a given type to the aliases, instead of to the list. However, because these aliases were closed mailing lists with generally out of date membership, mails sent to the lists were essentially getting forgotten about when there were people on the main list who could have answered the message. 2) There was no archive so there was no way to tell if a question was answered. 3) People often referred to e-mails sent to these lists at the CellML meetings, but it was hard to tell what they were talking about because only some people at the meeting got the messages. 4) Because the aliases were open, they got a lot of spam, which made it hard to see the signal over the noise. 5) Because the traffic was fragmented, it looked to anyone looking at the cellml-discussion archives like there was nothing happening with the CellML project. As a result of this, we decided over a year ago to get rid of info, tools and other lists like that and consolidate them all into cellml-discussion. I don't really think we want to go back to the way it was before without addressing all the problems it caused last time. Best regards, Andrew Regards, Dave ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
Re: [cellml-discussion] model upload problems
Sounds like this is something we should broadcast with a megaphone. There is probably nothing that would irk someone more than uploading a file and it not working. James Tommy Yu wrote: David Nickerson wrote: Hi, I just tried to load the attached model into the model repository to use as an example with the graphing metadata specification but am having some problems. Firstly, it didn't pick up some of the model metadata during the upload process. At least there were some empty text boxes presented to me that I would have expected to be filled with the metadata from the model. Not sure if that is an error in the upload process or an error in my model metadata? These boxes are still empty later when I got to the metadata editor. Hi Andre, Your metadata is fine, it did get picked up. However, the namespace is CellML 1.1 which the XSLT that generates the documentation (from the tmp-documentation namespace) do not support. Ditto for CellML - MathML XSLT. I see that it is just one file, so I changed it to 1.0 and repository thinks it's okay now. Kind Regards, Tommy. I managed to get it into the repository as http://www.cellml.org/models/sine-approximations_version01 but it doesn't really seem to work. The overview page just says: error occurs during transform. See error log - can I see the error log somewhere or is this just for the site admin to see? The view math tab gives and XML parsing error - a bit strange since I can run simulations of the model fine using my tool based on the CCGS and API and the code generation tab works fine and gives me the expected C code. Anyone have any suggestions? Thanks, Andre. ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
Re: [cellml-discussion] Concerning the CellML Model Repository | version/variant metadata?
My $0.02 on this is (please forgive me if I get some of the technical stuff mixed up): The current naming scheme is as it translates to the web address is: author(s)_date_versionXX_variantXX I think it should be author(s)_date_variantXX_versionXX instead, since IMO, one should be thinking in terms of versions of variants, rather than variants of versions. Also, I think that if there were perhaps some metadata that could pertain to what version and variant a cellml file is, and also some 'sub'metadata under variant to say what the variant represents, whether it's a particular cell type or what. I realise that metadata isn't supposed to be added to a model for the sake of a repository or for any non-generalised purpose, but I think that version/variant metadata would be useful. E.g. for 1.1 models, a simulator could pick this metadata up. So you could bring up window in which the software could tell you that, for example, you are embedding this version of this markov model of an L-type Ca++ channel, by such and such et al., into a variant 02 - epicardial cell Pandit et al. cardiac cell model, etc. etc. Another example would be working with CellML 1.1 models in an era where we have a library of components that people can use. We might have a GPCR component which has a large number of variants, and it would be crucial for the simulation/editing programs like PCEnv to know, and be able to tell the user, which version and variant of each component they are using. People might want to swap in different variants to see how if affects their model etc. And of course this version/variant metadata would obviously be highly useful (IMO) for the repository. Maybe subversion could automatically write this metadata. What I'm really trying to say is that I think there is justification for version/variant information to be stored in metadata as well as the URI naming scheme, since, unless I'm missing something, there is useful information (both for repositories and simulator software) that can't be stored in the URI. James - Version/Variant It already clogged up the system. There is no proper revision control mechanism, what we have now is an ad-hoc emulated system. I don't think it has clogged the system I just think it has been improperly used both by authors and by the user interface. Ideally the users and authors shouldn't be presented the option to make mistakes like this, should they? Most people, I would imagine, don't care about the versions of a model unless they are actually working on/with it. This is no fault of the authors, there is simply a specification for versioning that is missing. The hope is that subversion applies well to this. ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
Re: [cellml-discussion] model upload problems
Loading http://www.cellml.org/models/sine-approximations_version01 in PCEnv, the graph has three traces, but only one of them shows (sin1). Is this supposed to happen? So the idea of this graphing metadata is to fulfil a similar function to that of session files? I had a look at the spec but it's a bit technical for me to completely grasp it. David Nickerson wrote: James Lawson wrote: Sounds like this is something we should broadcast with a megaphone. There is probably nothing that would irk someone more than uploading a file and it not working. or perhaps, if possible without too much effort, to detect XML files uploaded which don't have a document element of model in the CellML 1.0 namespace and give the user an error and not accept the model? Andre. James Tommy Yu wrote: David Nickerson wrote: Hi, I just tried to load the attached model into the model repository to use as an example with the graphing metadata specification but am having some problems. Firstly, it didn't pick up some of the model metadata during the upload process. At least there were some empty text boxes presented to me that I would have expected to be filled with the metadata from the model. Not sure if that is an error in the upload process or an error in my model metadata? These boxes are still empty later when I got to the metadata editor. Hi Andre, Your metadata is fine, it did get picked up. However, the namespace is CellML 1.1 which the XSLT that generates the documentation (from the tmp-documentation namespace) do not support. Ditto for CellML - MathML XSLT. I see that it is just one file, so I changed it to 1.0 and repository thinks it's okay now. Kind Regards, Tommy. I managed to get it into the repository as http://www.cellml.org/models/sine-approximations_version01 but it doesn't really seem to work. The overview page just says: error occurs during transform. See error log - can I see the error log somewhere or is this just for the site admin to see? The view math tab gives and XML parsing error - a bit strange since I can run simulations of the model fine using my tool based on the CCGS and API and the code generation tab works fine and gives me the expected C code. Anyone have any suggestions? Thanks, Andre. ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
Re: [cellml-discussion] [team-cellml] @cellml.org addresses
Andrew Miller wrote: James Lawson wrote: David Nickerson wrote: I see the project team is being the core management team for the CellML project - essentially the group that should be making the decisions when consensus can't be reached and setting the goals for the future of the CellML project. Although I'm really not too sure who would be included in such a group. At present, CellML meetings are open to anyone who wants to attend (although obviously the fact that they are held in Auckland limits that set from a lot of people who want to attend), and 'final' decisions are made at the meetings by whoever turns up. Just the management team? Perhaps I'll get a list of who exactly is on the 'team-cellml' list and that can be the initial list. Plus Penny, on Peter's request. The team-cellml list is not intended to be a list of people involved in the management of CellML, and membership on that list is not supposed to imply any sort of increased status with the CellML project (it is merely supposed to be an Auckland-local list for meeting notifications and so on). I don't think we have ever refused to subscribe anyone who wanted to be on that list from being on there (subscription requests only require approval to keep spammers off and to ensure that people realise that it is not the main CellML list). In terms of the policy for allocating addresses, we don't want to become a free e-mail redirection host for anyone on the Internet, but I think as long as someone at least has some connection with CellML, they should be allowed an alias (subject to review of what that alias is to ensure it is unlikely to cause confusion or conflict with future lists / aliases we might want to assign). I suggest that we simply give an @cellml.org alias to anyone who asks for one and has a demonstrated interest of some kind in the CellML project (whether they are a modeller using CellML, a tool developer, or interested in some of the theoretical or mathematical aspects of CellML). Simply providing a form to fill out providing details to list, and having someone briefly review them should be sufficient to keep out people who just want the e-mail alias. So perhaps we could have two groups - the main cellml team, and then the cellml community. We'd probably want those on different, linked pages. P.S. Peter is away from today until the 20th July, getting back to the office on the 23rd, if you didn't get the email. I would like to see this mailing list used as more of place for decision making so that things like this shouldn't affect the project. I think cellml-discussion@cellml.org is much more appropriate for such discussions than the team-cellml list, to which only e-mails which are unlikely to be relevant outside of the Auckland group should be sent. This has been agreed on at CellML meetings (before you were working on the CellML project), and unless that decision is revisited I think we should all try to abide by it to ensure that no-one outside of Auckland who wants to contribute to CellML is unable to post (the list is publicly indexed so others could read it if they wanted to, but if they are not on the list they might be unaware that discussions are taking place). Well, it does get a fair amount of traffic. Although it seems to mainly just be you, Matt, Tommy and I, and occasionally Andrew. It was nice to see some others like Winfred Li and Jonathan Cooper posting on the Having high traffic on the list does at least demonstrate that the CellML project is still active. That said, I agree that being on a moderate traffic mailing list when you are only interested in one thing is probably a little bit annoying (I have to manage how many mailing lists I get on because it does add up once you are getting a few messages a day from dozens of lists). We can't make the list completely open for posting by non-subscribers (because we would get a lot of spam, as has been a problem with previous open @cellml.org lists). However, we could have a system were users have to confirm their own message to ensure they use a valid sender address. The only problem would be ensuring that we copy people on the threads that they started (although with a bit of coding we could make mailman do this automatically as long as the thread header got kept correctly by the UA). Best regards, Andrew cellml-discussion list the other day. Maybe you could go for a compromise Andre and use [EMAIL PROTECTED] or something :) I like the sound of that :-) ___ team-cellml mailing list [EMAIL PROTECTED] http://list.bioeng.auckland.ac.nz/mailman/listinfo/team-cellml ___ team-cellml mailing list [EMAIL PROTECTED] http://list.bioeng.auckland.ac.nz/mailman/listinfo/team-cellml
Re: [cellml-discussion] curation status of models in the repository
No, there are no stars, anywhere, that are on by default. They are all off by default until someone, probably me, certifies that the model meets the requirements to get itself a star, or two. Or maybe three. its more whether that one star is on or off by default? ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
Re: [cellml-discussion] a detailed curation specification
I have been thinking about this and I think it's worth proposing formally. But is having a whole level all about units consistency justified? Perhaps there are other things we could add to this level that could similarly require the intervention/expertise of the model author? I can't think of anything off the top of my head right now. David Nickerson wrote: Just one comment here. That is, if you look at the level 2 curation requirements, the only one that isn't satisfied by most of the models I've given two stars is the unit checking. So what this means is that we have a bunch of models which are much better curated than the level 1 curated models, but there isn't any way to actually show that if we aren't going to let them be level two. This is related to your point about splitting up the curation levels, and there are many models which would require actually reformulating the model completely to get units consistency (which would probably require the author getting involved.) If we did move units consistency up to level three, I think it would make things more straight forward. Rather than moving units consistency up to level 3 it would probably be better to move what is currently level 3 up to 4 and make level 3 all about units consistency. I think for the time being I'm going to take a left-wing approach and spend more time fixing the models that are completely broken. which I think is the right thing to be doing, I just think we need to be careful that the status advertised for a given model matches the definition of that status. Yep. I feel like biting off something I can chew right now. David. ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
Re: [cellml-discussion] a detailed curation specification
David Nickerson wrote: I have been thinking about this and I think it's worth proposing formally. But is having a whole level all about units consistency justified? Perhaps there are other things we could add to this level that could similarly require the intervention/expertise of the model author? I can't think of anything off the top of my head right now. Personally I think there is nothing wrong with the current levels and keeping units with getting the model giving correct results. I have little faith in a model which can give the correct results while being defined with inconsistent units. I was simply suggesting moving units to a higher level to try and ease the burden of getting models beyond level 1 curation, as you pointed out a model which does run and gives reasonable results is much better than one which does not run at all, even with inconsistent units, depending upon the task you wish to put it to. The units inconsistency issue is a legacy of the majority of models being written by hand with no way to test them. In most cases the models already in the repository can now be tested with either JSim or PyCML for units consistency, so it would be good to see those tests being done as part of your curation workflow - even if that just ends up as a comment in the model status that the units are not consistent or something. Sure, I'll start doing that. By the way, what exactly is a workflow? ;) David. ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
Re: [cellml-discussion] curation status of models in the repository
Hi David, I haven't been using Jsim, I've mainly been using PCEnv. It is my understanding that I can't use Jsim yet, from what others have told me, but I haven't checked that out myself. Regarding the star system, I agree it is confusing. I'm just using it because it's there. If you have any ideas on a more robust way on presenting curation status to users, I'm all ears. I agree unit checks are really essential to properly validating a model, but often there doesn't seem to be a way of getting everything to check out. For example, take this relatively simple model that I've just fixed. I've given it two stars because it nicely reproduces the figures in the paper it comes from. However, when I run Jonathan Cooper's validator on it, the following result comes up: [EMAIL PROTECTED]:~/Desktop/tools/JC$ python validator.py ~/Desktop/goldbeter3.cellml Validating file /people/jlaw060/Desktop/goldbeter3.cellml against CellML 1.0 Error checking units: Operator plus requires its operands to have dimensionally equivalent units; dimensionless and first_order_rate differ Context: 1st expression in the 1st math element in component M XPath: /*[1]/*[4]/*[8]/*[1]/*[3]/*[2]/*[3] Error checking units: Operator plus requires its operands to have dimensionally equivalent units; dimensionless and first_order_rate differ Context: 1st expression in the 1st math element in component X XPath: /*[1]/*[5]/*[8]/*[1]/*[3]/*[2]/*[3] Unrecognised namespaces used: http://cellml.org/tmp-documentation http://imc.org/vCard/3.0# http://www.cellml.org/metadata/simulation/1.0# File is NOT valid CellML 1.0 The first equation it has a problem with is: d(M)/d(time) = V1 * M_ / (K1 + M_) - V2 * M / (K2 + M) where it doesn't like adding K1 to M_ (or K2 to M,) which have units per minute (first order rate) and dimensionless (fraction of concentration of:activated enzyme / total enzyme,) respectively. Because of the way this model is built, getting the units to match would require drastically remaking it, and I don't think I'd know how to do it. I have some ideas, but only because this is a particularly simple model, with 3 differential equations and two algebraic expressions. In a larger model I would have absolutely no idea where to start. So what is the solution to this? Only code up models in CellML that are perfect? Because technically, this model isn't valid CellML Kind regards, James David Nickerson wrote: Hi all, I am just after a bit of clarification on the use of the stars with the models in the model repository. As I understand the model curation (from http://www.cellml.org/repository-info/info), one star means the model is at curation level 1, two stars for level 2, and three for level 3 curation. For the model simulation tools, there is one star if the model loads in and runs, 2 if the model gives the right results, and 3 stars if the results have been rigorously verified. The first question I have is if the stars next to the Standard link represent the model curation level while those next to specific tools correspond to the running of simulations of that model with that tool? In other words, it is not very obvious what all the stars are implying when looking at a model's page in the repository. Looking at the models with two stars (thanks to Tommy's new filter tool on the main page), I see they generally have two stars for Standard, PCEnv and COR but no stars for JSim. If the Standard stars do reflect the curation level of the model, then my second question is how are the units are being checked (as required for level 2 curation) without using JSim? I was under the impression that JSim was the only tool capable of throughly checking all the units for consistency in a model, but perhaps there is something else? And if so, should it not also be displayed along with PCEnv, COR, and JSim? Thanks, David. ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
Re: [cellml-discussion] curation status of models in the repository
David Nickerson wrote: OK - now I'm really confused by all this talk of stars and simulation tools. Perhaps the key is to separate the model curation status from the simulation tools - i.e., to have a distinct Curation Level field at the top of the model page separate to the current Download options section. I think it is very import to ensure there is a clear distinction between model curation status and how good or bad particular simulation tools are in regard to a specific model. I'm not sure that we want to get rid of the multiple stars for simulation tools, as defined by http://www.cellml.org/repository-info/info. If someone comes along and wants to look into using a particular uncurated model, it would be a good starting point to know which tools can or cannot at least load the model even if it doesn't give the right answers. Sure, but you only need a binary system to describe that - it either loads or it doesn't, one star, either there or not. More stars means confusion. Okay, I have just talked with Peter. He has decided that the units checking of models is a core issue and needs to be dealt with ASAP. I agree. We have decided to reform the current representation of curation levels. Firstly, the three stars for each simulator will go, and be replaced by one star, which represents that the model loads in that simulator. The argument against this is that all models should load in all simulators. This is, however not the case, refer to my comment later. Until it is the case, it is worth having simulator specific stars. Just to point out that this would be much better if it was framed as a proposal rather than an explanation of a decision already reached. Otherwise there is little point seeking comments... Sorry, the decision was for reform, the rest is what we talked about and are points for discussion. I'm a bit worried that you seem to be saying that by default all models will get one star and then that star has to be manually removed? seems the wrong way round to me. Hmm, I'd be worried if I was saying that too :) If that's how it came across I didn't mean that. Let me put it this way the three *possible* stars for each simulator will go, and be replaced by one *possible* star. Is that clearer? Secondly, all models which do not produce the output given in the paper will lose their one star. This first 'curation' star will be given to models which give the correct output. The problem with this, is that it is often not possible to reproduce the figures in a lot of the papers. These figures are often made by varying the initial values of variables or by using log scales etc. which would require adding components to the model or changing it such that it no longer accurately represents the model described in the paper. As such, we need a better way of judging whether our models are giving the right output. Where possible, I think contacting the authors of the paper might help here. This would hopefully then lead on to the model getting a second star. There is nothing to say that the analysis of simulation results has to be performed in the same tool. For example, results can be exported from PCEnv and checked using gnuplot or even Excel...having said that, I am having some good success generating such figures using the graphing metadata (which I really should finish writing up soon!) and imports to look at things like restitution curves and pH dependence...but I think that is for the future, we want to focus on the curation in regard to the current repository features. The second star will be for, as Andre said, I'd be happy with giving a CellML 1.0 model without reactions a curation status of level 2 if and only if it runs in PCEnv and JSim without error and gives identical results (within some numerical tolerance) and passes Jonathan's validation tests without error. (What do you mean identical results? Identical results between simulators or identical to the figures in the paper? If the latter, how do you quantify this?) This second star will in most cases require the author to fix the model so that it satisfies the validation tests, such as unit testing. This obviously presents a problem for the models that were made in the 60's and 70's. Most of these models are pretty seminal though, so hopefully we won't have too many problems with them. Now it gets confusingthis particular second star is for the curation level, right? rather than a specific simulation tool? My suggestion was just one way that could be used to be satisfied that a model passes the requirements for level 2 curation without sitting down and manually checking every variable and equation in a model. Okay, the idea is that: there are two sets of stars. One for curation, one for the simulator. For curation, there are three possible stars, as outlined here. For the simulator, there is one possible star, which is given if
Re: [cellml-discussion] a detailed curation specification
Just one comment here. That is, if you look at the level 2 curation requirements, the only one that isn't satisfied by most of the models I've given two stars is the unit checking. So what this means is that we have a bunch of models which are much better curated than the level 1 curated models, but there isn't any way to actually show that if we aren't going to let them be level two. This is related to your point about splitting up the curation levels, and there are many models which would require actually reformulating the model completely to get units consistency (which would probably require the author getting involved.) If we did move units consistency up to level three, I think it would make things more straight forward. I think for the time being I'm going to take a left-wing approach and spend more time fixing the models that are completely broken. David Nickerson wrote: http://www.cellml.org/repository-info/info essentially lays out the requirements for each level of curation. I think this gives a clear indication of what is required for level 0, 1, and 2 curation and my document you mention below starts to look at what is required for level 3. Just to point out that that document is the combination of discussions with many people, primarily based on a proposal from Jim Bassingthwaighte. I think until there is some progress on defining what level 3 curation is that we don't worry about it for now, especially since it is generally regarded that no existing published models would meet all the requirements for level 3 curation. I think level 3 is something we can aspire to as people start using tools like CellML and decent testing frameworks in the actual development of new models rather than an add-on after the model is already developed (like what Randy was talking about at the CellML workshop). In terms of level 1 and 2 curation, I'm not really sure what more detail you need in the way of a specification? Currently the only way to make sure the math described by a CellML model is equivalent to a published paper is to sit down and look at them both side by side. Whether you do that looking at the content MathML directly or use some utility to render the MathML in a more readable format is a personal preference. Ideally this is best done by the model author, but any model curator can undertake this level of curation. Similarly, how level 2 curation is achieved is really up to the person doing the curation. I've put forward a suggestion on how this could be done, but different people can choose to use whatever tools they prefer as long as there is confidence that the required conditions have been met. Personally, I'd say the more different simulation and validation tools used the better, although the formulation and mathematics used in a given model might restrict which tools can be used and force more manual checking upon the curator. Ideally I think level 2 curation should be undertaken independently of the model author, but can't really see a reason to enforce this as the curation annotation should contain the curator data. In fact, there is no reason curation can't be done by more than one curator, whereby model users might have more confidence in a model that has been stamped level 2 by more than one person... A key point to note is that a model curated to level 2 is not necessarily also curated to level 1 - so we need to be careful about the graphical representation used on in the model repository. i.e., the first two stars being yellow should imply that the model satisfies bother level 1 and 2 curation. In general, at least for the electrophysiology models, none of the models in the repository will satisfy both curation levels 1 and 2. Also, the requirements for each of the curation levels are currently the result of many discussions on what we'd ideally like to see for each level. As people spend more time curating models and using these annotations I'd expect there could be some changes in these definitions required. So if you have any suggestions please put them forward. One that has come up a bit would be breaking level 2 into more pieces, for example pushing the units consistency requirement to a higher level. David. PS - no immediate plans to come back to Auckland, I think the 8th-18th comment was in regard to the April workshop. James Lawson wrote: Dear all, Another thing Peter has asked me to seek input on is the need for a detailed, realistic curation specification that I can follow. Andre's 'thoughts on model curation and model repositories' goes some way towards this but it isn't formalised and this kind of document probably needs the input of more than one person. The proposed document also needs to take into account the current and future state of the repository, and provide guidelines to follow that will result in significant, consistent progress
Re: [cellml-discussion] clarification required?
Hi David/Andre, We decided it was more useful to give the number of individual models in the repository, rather than the number of model files (including versions and variants). Personally I think this is better, but I'd also like to see a few other important stats there too, including the total number of versions that we used to have and perhaps a few other things as well, like curated models. David Nickerson wrote: Hi all, I noticed the other day that on the front page of the model repository at cellml.org, the simple total number of models in the repository has now changed to the number of peer reviewed models in the repository. I was just wondering what this means and why the total number of models in the repository is no longer given? Thanks, David. ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
Re: [cellml-discussion] PMR categories
Peter Hunter wrote: It may be that the additional key words should adhere to terms from an ontology as Matt suggests and should use the predictive completion facility that Andre suggests. Will we use the Physiome ontology for this? It will require changing the current keywords that are defined in the metadata for many of the models so they fit an ontology. Should we be using ontology terms for the major categories as well? A quick flick through the Physiome ontology suggests that we might have trouble finding terms in it that would fit what we want. ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
Re: [cellml-discussion] PMR categories
Actually, I'd venture to say that the majority of them aren't models of human biological systems. A lot of them are animal models or based on experiments done in non-human cell lines (for example Xenopus oocytes (frog) are commonplace for cell cycle experiments,) and there are also a number of bacterial models. I agree, I think the metadata field for species (a lot of the models already have this, I think,) would be a useful value to sort by. Perhaps this should be on the advanced search page rather than on the front page, however. Eventually, the plan is to be able to sort by pretty much any metadata field that is contained in the models. In the future, perhaps we'll actually have specific sections devoted to particular species. For example, the nematode work Caenorhabditis elegans has only ~1000 cells, and every single cell and its function has been mapped. The C. elegans neural system in particular has been mapped in a lot of detail, with work by White, Brenner et al. (1986) mapping all the synaptic connections between all of the neurons. Although I haven't checked, I imagine there are efforts to model the whole organism. While this isn't a human physiome project, animal models like this are really important in developing frameworks to use for modelling/studying larger systems. Randall Britten wrote: A separate phylogeny attribute is probably also needed. It is not clear whether all the models are meant to pertain to human physiology. One example certainly does not: # Baylor, Hollingworth, Chandler, 2002, 'Comparison of Simulated and Measured Calcium Sparks in Intact Skeletal Muscle Fibers of the Frog'. ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
Re: [cellml-discussion] PMR categories
So for example someone's trying to build a large model but the only components (or data to build components) available are from non-matching species? So the LFID (I looked it up but it went over my head) provides a way we can do that which is more precise and flexible than simply referring to NCBI taxonomy? The critical thing for us is that a single model will quite often contain elements that derive their mechanism or parameters from studies on different organisms, so we need to be quite rigorous in looking at all components in a model and identifying their origin. This is obviously one facet where imports should be helping us to put circles around species specific submodels. ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
[cellml-discussion] PMR categories
Hi folks, Tommy is currently working on a sorting function for the main model list of the PMR. Peter is looking for some ideas on what categories people think should be included (with respect to biology, not curation - that will be separate, coming soon!) The old repository obviously has models listed under categories. Do we want to keep those categories? We don't want too many categories, so what is important? As well as just biological function, perhaps the model type is important too. Particularly when the repository goes 1.1 we'll start getting multiscale models. Here's a list I compiled, which represents most of the models we currently have. Multiscale Cardiobiology/Cardiophysiology Neurobiology/Neurophysiology Beta Cells/Insulin Electrophysiology Biomechanics Biochemistry Pharmacology Signal Transduction/Signalling Metabolism Energy Metabolism Cell Cycle Immunology Virology HIV Circadian Rhythms Calcium Dynamics Protein Structure Function Please discuss. Kind regards, James Lawson ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
Re: [cellml-discussion] PMR categories
David Nickerson wrote: Would I be correct in assuming that these terms will be key words added to the model metadata and that the division into categories on the main repository page will be assembled from queries on each of these predefined key words? Well potentially, there could be many many different keywords, so Peter suggested that we might not necessarily want to base the categories on just the keywords. At the moment, Tommy's sorting function is based on keywords but he suggested that we could have both a keyword and a more general category selection system. And if so, I'm gonna further assume that there are no issues with having a model in more than one category, right? right And what are the consequences for a model not fitting into any of these categories? We create an 'other' category? I'd suggest that multiscale is a bit too general to be useful in this sort of setting, as its conceivable that pretty much every model in the repository is multiscale in some sense. Fair enough, multiscale can be a pretty abstracted term. David. Thanks, your comments are always helpful. James ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
[cellml-discussion] 'CAVEman' the future of medicine
Hey folks, Thought you might be interested in this. I really don't know how far they've actually got but they're certainly making some pretty impressive claims. http://www.cosmosmagazine.com/node/1351 'Caveman' the future of medicine OTTAWA: The world's first virtual computer model of a human body has been created, translating a litany of complex medical and genomic data into 4D images to test drugs and surgical techniques. The virtual man has his skin and skeleton removed to display every vein, artery and organ, and consists of more than 3,000 body parts projected from the walls and floor. -James ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
Re: [cellml-discussion] removal of reaction components from models
Andrew Miller wrote: Have you actually looked at what exactly is happening? Is this an overflow where quantities are getting so big they go to infinity because you have a loop which doesn't have any self-regulation? Hi Andrew, Yes, I have looked at what's happening. In some cases the integrator only gets up to the second time point, which isn't that useful. For the models that get further than that, I don't see any evidence of numbers getting absurdly small or absurdly big. Although some of the fluxes in the asthagiri_lauffenburger csv file that I've sent you seem to start off extremely small - like 10E^-38 small. I don't know. That's with the BDF integrator. With most of the other integrators (example Implicit Gear M1) they get up to the second time step and then start producing NaN outputs.] I presume that the model that is being generated from the reactions by my script would be exactly identical to what you would enter if you recreated the model by hand (assuming that the entered rate laws are an accurate representation of the paper). If the rates were specified using one of the common formulae for enzyme rates, you would get product inhibition and these overflows wouldn't happen, but I think that perhaps the entered rate laws are too simple. I would presume that too. Obviously, getting rid of the reactions is the overall goal, but I don't see any reason why you would be better to re-create the models from scratch, rather than starting from the original model with reactions, I am starting from the original model with reactions, not building it totally from scratch. running it through my script to generate equations for this, and then fixing any problems such as rate laws which don't represent what the authors of the paper actually used and/or result in species getting exponential increases to such high concentrations they overflow the floating point representation. I don't think that this process is possible to automate due to the way the models have been coded up using reaction components. Of course, I may be wrong. It's something that's difficult to explain over email. If you want to see what I mean, come see me and I'll show you an example. Then perhaps you might have a better idea about whether the process can be automated or now. Additionally, rebuilding the model provides a really good opportunity for curation. I've been rebuilding the bertram_arnot_zamponi model and I've actually found a few errors and omissions, which I definitely wouldn't have found without looking at the model in the depth required to rebuild it. My script could generate metadata as well if required. However, as Poul suggested at the CellML meeting, feedback from Matt on exactly what metadata we should generate it and where that metadata should be stored (I think it preferably should be in the model, but Matt might have a different opinion). Yep. Kind regards, James ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
[cellml-discussion] removal of reaction components from models
Dear All, This email is aimed at anyone who has comments, but we particularly want to draw Matt's attention. In the CellML meeting yesterday I brought up the issue of replacement of reaction components with straight math. At present PCEnv isn't handling reaction components well - models which use reaction components aren't integrating, for one. There are also issues with math elements not being picked up if they are under role elements. Andrew has written a script to pull these math elements up a level so that they're a direct child of the component, not the role element. The script also defines delta variables as rate * stoichiometry. Running this script on the models which contain reaction components has cleared up most of the errors with undefined delta variables, so now many of the models with reaction components can now be loaded in PCEnv. The problem is that *none of them* will integrate properly. I am making the assumption that this effect is due to the reaction component, not the models, since it is so widespread among many very different models. I'm going to start rebuilding models without reaction components. However, one of the primary issues around this is that the information represented by the attributes defined in the reaction components is, while not essential for computation of the model, definitely something that we want to keep. For example, what species are reactants, products, catalysts, activators, inhibitors (and what kind of inhibitor,) etc. Ideally, these attributes would be recorded as metadata. We don't as yet have this facility, however. So the questions are: 1.) what to do with this data meanwhile 2.) how to redesign reaction descriptions using a combination of math and metadata. One of the reasons we're seeking your input Matt, is that ontologies such as BioPAX could be really useful in providing a framework for how we assign metadata to reactions, in a biological sense. Also, Sarala mentioned in the meeting yesterday that she was using BioPAX to describe reactions in her work. Regarding the first question, some of the ideas that were suggested were: a.) use commenting to describe the attributes of each reaction b.) keep the files (well, we already do anyway,) that describe the models in terms of reaction components and refer back to them later when we have the facilities to enter metadata on reactions to the models which have been rebuilt without the reaction components. So if anyone has any comments on this, they'd be much appreciated. James ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
[cellml-discussion] some repository stats
Hi Folks, I have now checked every model in the repository in PCEnv and recorded whether they run, and if so, whether they integrate, or if they don't run, what the error message is. The great majority contain undefined variables. As of 24/04/07: Out of a total of 250 different models (I only counted once, so make that plus or minus a few,) 58 models are functional in PCEnv and have therefore made it to a one star rating. That's 23.2 %, which isn't too bad. There are 412 files in the repository, so that equates to an average of 1.65 versions/variants per model. Most of the variants got uploaded automatically from the old repository as versions, so that's something I'll fix eventually. As of now, a star next to the model name in the repository list definitively means that at least one version of that model runs and integrates in PCEnv. James ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
Re: [cellml-discussion] CellML Validation, Curation and Model Composition
As for re-usability, again, in my view, implies that you have some CellML model that can be re-used :-) Following the ideas of my best practices this would be a model which contains just math with no parameter values or initial conditions embedded in it such that I can take that math and use it in the way I want without restriction. Practically, there is still use in being able to take models which do have parameters and initial conditions embedded in them and plugging them into another model. The following is rather speculative - perhaps there is a way to do this already that I'm unaware of. I'm just fishing for comments. If you have a model which contains only math, and say you want to use it as a component. It has no parameters, and you need to plug in a whole plethora of initial conditions etc. Is there any way to avoid doing this manually? If you had a file containing all these parameters and values and the variables/components that they pertain to, it would be good to be able to simply import these into the model automatically. The most important use for this parameter importing feature could be in experimentation with the models. If you had a set of parameters that you wanted to change over a range (for example, ligand concentration in a GPCR signalling system,) and take the results that the model outputs (you might want to know cAMP production rates by adenylate cyclase, PKA activation levels, desensitization rates, etc. etc.) you could run this 'experiment file,' and get the results output to CSV. It would probably take an awfully long time to integrate the model several hundred times if you wanted that many data points, but at present, you'd have to manually change the values you wanted to change, integrate, export to CSV, then do it over again. James ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
[cellml-discussion] model variants(?): e.g. where multiple cell types are described by the same model in different files
Hi folks, I'm just fishing for some comments on how to handle cases where there are models which describe, for example, the properties of multiple cell types. Bondarenko et al. 2004 is a good example of this: In the Bondarenko et al. 2004 publication described here, the authors develop a computer model of the mouse ventricular action potential (see below). The model includes parameters for both the apex and the septum regions of the heart (the apex parameters have been substituted into the CellML version of the model described in ), and this helps to illustrate how there are regional differences in myocyte repolarisation in the mouse heart. Penny Noble has just sent me a zip file containing the latest versions of all the models she has curated for COR. I'm currently in the process of comparing these versions to the latest versions we have on the repository. In some cases, she has provided several variants of the same model which describe different cell types, as above. Firstly, are these true 'variants'? If so, then the matter is relatively simple. Unfortunately, if one goes through the repository list, variants simply come up as a duplication of the model listing, with no information concerning what the variant represents. This is something I imagine will be fixed in time, but is presently rather frustrating considering the issue at hand. Does anyone have any comments on this? Should I simply put the files up as different variants, with a note in the documentation? Thanks, James Lawson ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
Re: [cellml-discussion] model variants(?): e.g. where multiple cell types are described by the same model in different files
Addendum: The model in the repository describes the apex cells only. James Lawson wrote: Hi folks, I'm just fishing for some comments on how to handle cases where there are models which describe, for example, the properties of multiple cell types. Bondarenko et al. 2004 is a good example of this: In the Bondarenko et al. 2004 publication described here, the authors develop a computer model of the mouse ventricular action potential (see below). The model includes parameters for both the apex and the septum regions of the heart (the apex parameters have been substituted into the CellML version of the model described in ), and this helps to illustrate how there are regional differences in myocyte repolarisation in the mouse heart. Penny Noble has just sent me a zip file containing the latest versions of all the models she has curated for COR. I'm currently in the process of comparing these versions to the latest versions we have on the repository. In some cases, she has provided several variants of the same model which describe different cell types, as above. Firstly, are these true 'variants'? If so, then the matter is relatively simple. Unfortunately, if one goes through the repository list, variants simply come up as a duplication of the model listing, with no information concerning what the variant represents. This is something I imagine will be fixed in time, but is presently rather frustrating considering the issue at hand. Does anyone have any comments on this? Should I simply put the files up as different variants, with a note in the documentation? Thanks, James Lawson ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
Re: [cellml-discussion] model variants(?): e.g. where multiple cell types are described by the same model in different files
Matt wrote: This scratches a couple of important pending issues: 1) I feel the term 'variant' is odd (even though I originally suggested it). It was intended to mean that the model labelled as a variant is a variation of the one it is a variant of. However, this isn't really a very applicable definition, especially if one may consider a model to be a variant of more than one other model. Since variant is bound up in the URI and name then this makes for dilemmas. My suggestion would be that we drop variants altogether. We can mark relations in a better way through metadata. I am also querying whether the flatness of our URI scheme is appropriate for our uses. e.g. perhaps: http://www.cellml.org/models/bondarenko_szigeti_bett_kim_rasmusson_2004_version01 should be something like http://www.cellml.org/models/bondarenko_szigeti_bett_kim_rasmusson/2004/ventricular?rev=1 (no that is not a formal proposal) But this doesn't really help you now. The technically correct method at the moment would be that the new models that are similar but different only in their parameterisations are added as variants. Right. Another alternative in the short term would to simply name the models as separate models (which they are) That's an interesting proposal. Given the current way that the models are listed, that would be a good way of displaying that the models are variants. If you upload two variants of a model, they come up as duplicate listings (i.e. no information is displayed about the nature of the variant,) so simply making them two different models would get around this. Anyone else have comments on this? and we define now an rdf relation scheme that is very explicitly about how different models at different URIs relate to the one you are editing. This would mean that Tommy needs to update the rendering of the pages for these models to reflect this information. 2) These models should use imports so that we can at least point to the generic model and then the specialised parameterised ones. But that won't work right now because the repository can't handle 1.1 models. In this case there is no generic model available. The model we have on the repository for Bondarenko et al. 2004 is the one describing the apical cells. cheers Matt ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
[cellml-discussion] curation annotation framework
So, for example in http://www.cellml.org/models/tentusscher_noble_noble_panfilov_2004_version01_variant01 I'm guessing you have fixed the model to work in PCEnv (hence the star) but the model status still states This is the original unchecked version of the model imported from the previous CellML model repository, 24-Jan-2006. Given there is still no curation annotation framework I think we still need to be using such a plain text description of the status of each model and thus you should update the documentation to reflect what you actually have done. This would also be the place to justify the use of a variant rather than version. This particular model isn't one I've actually fixed - just one that I've checked and annotated with a star to denote that it runs in PCEnv. As such I don't know exactly where that version has come from - I can only assume that it came from the old repository. The presence of the star means that it shouldn't say that it is unchecked, however. I'll change that now. Of course the star system remains ambiguous because not all of the models that lack stars don't run in PCEnv - they simply haven't been checked, and not all of the models with stars have been fixed by myself personally - I have just certified that they run in PCEnv. In the case that I have in fact created a new version, I have updated the model status. Since there's currently no annotation framework as such, and since I have really just started and am learning what needs to be said etc as I go, some of the annotation I've put to models that I fixed earlier isn't consistent with what I'm doing now. The model documentation can't be changed from the page - the file needs to be downloaded, changed and then reuploaded. At the moment I'm primarily saying what version the current version was updated from, by who, and when (if I know). Some of my earlier annotations included the error that the previous version was producing. This can produce a lot of text though, particularly when it requires listing scores of variables that couldn't be defined etc. I do have all this information (regarding how a particular model was fixed, that is,) documented on my computer, however. Does anyone have any comments or proposals, formal or informal, concerning what information needs to be included in the model status documentation? The more consistent I can be now, the less I'll have to go back and redo in the future. James ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
[cellml-discussion] fixed model - A Model for Human Ventricular Tissue
Fixed version 3 of Ten Tusscher, Noble, Noble, Panfilov, 2003 A Model for Human Ventricular Tissue in CellML repository New file is now version 4 http://www.cellml.org/models/tentusscher_noble_noble_panfilov_2003_version04 Updated PCenv stars to one star (should it be three? indicating that it runs fine?) James Lawson ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
