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

[cellml-discussion] I am leaving the ABI

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, Ja

[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 <>___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/m

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,

[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 <>___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellm

[cellml-discussion] CellML and cmgui tutorials

m for contact details.) Thanks very much, I hope you find this useful, and please feel free to forward it to anyone you know whom it might interest. Kind regards, James Lawson *The cmgui (http://www.cmiss.org/cmgui) introductory tutorial is available from Dougal Cowan - email him at dj.co...@auc

[cellml-discussion] new cellml.org website

Dear CellML community, We have given cellml.org a complete redesign and makeover. We've added some new content and updated old content, and reworked the architecture and design. We hope you like it. Please visit http://www.cellml.org and take a look. With thanks to the cellml.org web working

[cellml-discussion] CellML Metadata 1.0 Specification finalised

, 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

[cellml-discussion] IUPS2009 CellML Workshop Announcement

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

Re: [cellml-discussion] Using CellML for simplified neuron models?

cells that we've coded up - http://www.cellml.org/models/beeler_reuter_1977_version08 is a fairly simple model with a piecewise-based stimulus protocol added. Please let me know if you need any help accessing the models in the repository. Best of luck! Kind regards, James Lawson Dr. Ha

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

[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:J

Re: [cellml-discussion] tools that use and / or work with CellML

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

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 thro

Re: [cellml-discussion] tools that use and / or work with CellML

t 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 /

Re: [cellml-discussion] tools that use and / or work with CellML

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'r

Re: [cellml-discussion] tools that use and / or work with CellML

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

[cellml-discussion] tools that use and / or work with CellML

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 presentation

[cellml-discussion] tools that use and / or work with CellML

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

[cellml-discussion] cellml namespaces

Hi all, I've been snooping around the website and I noticed that if you actually go to the links for our current live namespaces, you don't find anything particularly interesting. See: http://www.cellml.org/cellml/1.0/ http://www.cellml.org/cellml/1.1/ http://www.cellml.org/metadata/1.0/ Th

[cellml-discussion] CellML Metadata 1.1 specification

Hi all, I'm drafting an updated metadata specification. Please have a look at http://github.com/jameslawsonABI/cellml-metadata-1.1-specification/ if you want to follow my work. Cheers, James begin:vcard fn:James Lawson n:Lawson;James org:Auckland Bioengineering Institute;CellML Model Reposito

[cellml-discussion] cellml.org members directories

Dear all, I am currently in the process of migrating data and content from our current cellml.org site to a new build of the redesigned cellml.org site, which we'll be launching in time for the CellML workshop in the first week of April (more on this closer to the time.) Everyone who has a l

[cellml-discussion] SBML Level 2 Version 4 specification released

Hi all, This might interest some people: http://sbml.org/Forums/index.php?t=tree&goto=4893&rid=0 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;int

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 h

Re: [cellml-discussion] HDF5 licensing

ge: 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 Message-ID: <[EMAIL PROTECTED]> Content-Type: text/plain; charset="iso-8859-1"; Format="flow

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 desi

[cellml-discussion] new CellML FAQ

Hi all, I'm writing up some questions for the new CellML FAQ. Are there any questions you can think of that you think ought to be answered in the FAQ? The current FAQ is at: http://www.cellml.org/faq It's a little outdated, to say the least. Thanks, James begin:vcard fn:James Lawson n:Lawso

[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 .

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 Inst

[cellml-discussion] CellML Metadata Specification development

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:

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

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 w

[cellml-discussion] ABI CellML team meeting minutes 2008-09-03

Dear CellML community, The ABI CellML team meeting minutes are now available at: http://www.cellml.org/meeting_minutes/abi-meeting-minutes-2008-09-03/ Kind regards, James Lawson begin:vcard fn:James Lawson n:Lawson;James org:Auckland Bioengineering Institute;CellML Model Repository Curator

[cellml-discussion] ABI CellML team meeting minutes for 2008-08-27

Dear CellML community, Last Wednesday's ABI CellML team meeting minutes are now available at: *http://www.cellml.org/meeting_minutes/abi-meeting-minutes-2008-08-27/ *Kind regards, James Lawson begin:vcard fn:James Lawson n:Lawson;James org:Auckland Bioengineering Institute;CellML

Re: [cellml-discussion] CellML IRC

, 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

[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

Re: [cellml-discussion] OWL

l 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 c

[cellml-discussion] CellML IRC

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... Kind rega

[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://w

Re: [cellml-discussion] New Proposed Structure for the CellML Website

ght 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 misse

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 side

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

[cellml-discussion] ABI CellML team meeting minutes for 2008-08-06

Dear CellML community, The minutes for this week's ABI CellML team meeting are now available at: http://www.cellml.org/meeting_minutes/abi-meeting-minutes-2008-08-06/ Kind regards, James Lawson begin:vcard fn:James Lawson n:Lawson;James org:Auckland Bioengineering Institute;CellML

[cellml-discussion] ABI CellML team meeting minutes 2008-07-30

Dear CellML community, The ABI CellML team meeting minutes for last Wednesday (2008-07-30) are now available at: http://www.cellml.org/meeting_minutes/abi-meeting-minutes-2008-07-30/ Kind regards, James Lawson begin:vcard fn:James Lawson n:Lawson;James org:Auckland Bioengineering Institute

[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 language which allows scientists to build mathematical models of complex systems. The

[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:

[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

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, Jam

[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

[cellml-discussion] ABI CellML team meeting minutes 2008-06-25

Dear CellML community, The ABI CellML team meeting minutes for last Wednesday (2008-06-25) are now up at: http://www.cellml.org/meeting_minutes/abi-meeting-minutes-2008-06-25/ Kind regards, James Lawson begin:vcard fn:James Lawson n:Lawson;James org:Auckland Bioengineering Institute;CellML

[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 migh

[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

[cellml-discussion] ABI CellML team meeting minutes for Wednesday 2008-06-12

Dear all, The ABI CellML team meeting minutes are available at: http://www.cellml.org/meeting_minutes/abi-meeting-minutes-2008-06-11 Kind regards, James Lawson begin:vcard fn:James Lawson n:Lawson;James org:Auckland Bioengineering Institute;CellML Model Repository Curator, CellML Team adr

Re: [cellml-discussion] ontology integration

Hi Roberto, Could you give us a little more information about what sorts of things you're modelling and what the ontology of your model looks like? Thanks, James roberto wrote: hello i am raising my interest in writing my system biology models in cellML and i am wondering if it possible to

Re: [cellml-discussion] in case you haven't seen it | "Why Are Computational Neuroscience and Systems Biology So Separate?"

is 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

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 i

[cellml-discussion] (OT) the nature of 'mole' | Re: unit conversion

uld 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-discus

Re: [cellml-discussion] unit conversion

x27;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_fi

[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

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 awf

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

[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

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 ontolog

[cellml-discussion] ABI CellML team meeting minutes up

Hi all, The meeting minutes for this week's ABI CellML team meeting are now up at: http://www.cellml.org/meeting_minutes/abi-meeting-minutes-2008-05-14/ Kind regards, James Lawson begin:vcard fn:James Lawson n:Lawson;James org:Auckland Bioengineering Institute;CellML Model Repository Cu

Re: [cellml-discussion] Suggestions regarding search and browse utility for CellML Repository

ot the "biological" part. My objective was provide a "high level" view of CellML Models. Unfortunately my dissertation is written only in brazilian portuguese. I've submmited some papers but I didn't get success. However, if there is some curiosity I can try to tr

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

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

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 commenta

[cellml-discussion] differences between CellML and SBML for modelling hepatic glycogenolysis

nd 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

Re: [cellml-discussion] Modularity with CellML

Hey Mike, It appears that I can't get this article - we apparently don't have access to scitation. Do you have a PDF you could send me? Thanks, James Mike Cooling wrote: Hello For those that heard my ‘teaser talk’ at the CellML workshop last Wednesday, and those that didn’t but are intere

[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-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

[cellml-discussion] ABI CellML team meeting minutes 27/02/08

Dear all, The ABI CellML team weekly meeting minutes for this Wednesay's meeting (27/02/08) are now up at: http://www.cellml.org/meeting_minutes/abi-meeting-minutes-2008-02-27/ Cheers, James begin:vcard fn:James Lawson n:Lawson;James org:Auckland Bioengineering Institute;CellML Model Reposito

[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 Inst

[cellml-discussion] [Fwd: [Synthetic Biology] BBF working groups, SB4.0, and standard workshop]

Thought some of you folks might be interested in this: --- Begin Message --- 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

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 poli

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

[cellml-discussion] [Fwd: [Synthetic Biology] SB4.0, 10-12 October 2008, Hong Kong]

--- Begin Message --- The Fourth International Meeting on Synthetic Biology (SB4.0) will be held from 10-12 October 2008 at the Hong Kong University of Science and Technology in Clear Water Bay, Kowloon, Hong Kong. The organization of the event is being led by the BioBricks Foundation in p

[cellml-discussion] [Fwd: Re: application 'ML']

From Steven Niederer (through Gareth): --- Begin Message --- 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 the

Re: [cellml-discussion] cellml on wikipedia

ation about the model." 1.1 has reactions... James Lawson wrote: > Hi folks, > > It strikes me that wikipedia is probably the first place many people > would look for information on CellML. > > We have a wikipedia page which I'd say is between 200-300 words. > >

[cellml-discussion] cellml on wikipedia

Hi folks, It strikes me that wikipedia is probably the first place many people would look for information on CellML. We have a wikipedia page which I'd say is between 200-300 words. I've edited in the past, but I think it would definitely worth the time to add some further information to the s

[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 cr

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 al

[cellml-discussion] looking for comments on curation proposal

y side needs a bit more fleshing out. Now that we have some practical experience in curation, we know a bit more about how to actually design our curation standards to match how the curation work needs to be done. I'm looking forward to your comments. Thanks. Kind regards, James L

[cellml-discussion] cellml poster for ICSB 2007 conference

o mine and will provide a direct example of this capability. Kind regards, James Lawson ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion

[cellml-discussion] [input requested] cellml.org model curation: representing the curation status of models

is as much commentary, as many flames, and as many ideas as the community can come up with on how you would like to see curation information represented. Particularly I need some input for the 'Questions & Considerations' section, and some more pros and cons. Thanks very much. Kind r

Re: [cellml-discussion] Bug in Nygren model

Kind regards, James Lawson [EMAIL PROTECTED] wrote: > Hi, > > I found a bug in the Nygren et al. model of the CellML repository. > > Mathematical Model of an Adult Human Atrial Cell: The Role of K+ Currents in > Repolarization > > As given, it does not reproduce the f

[cellml-discussion] automated connection creation

Hi all, I was sitting in bed last night, and this idea came to me: It would be really easy to create some kind of script / automation process that automatically connects up variables of the same name if they have matching interfaces. Say you have a component A with variables a and b. a is define

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. >> Subje

[cellml-discussion] how to units make a difference to simulation

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 v

Re: [cellml-discussion] Using PCEnv 2.0

change the subject it doesn't make a new thread, it simply continues the old one. This is important because we archive our discussions on the cellml-discussion list. Thanks for posting, it's good to know issues like this that people are having. Kind regards, James Lawson Ely Edison Matos

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 wo

Re: [cellml-discussion] embedded stimulus currents in CellML models

Alan Garny wrote: Still, I have managed to recompile it. >>> Oops, this got sent too early and I have yet to get CellML2Dot to >> compile... >>> In fact, I have given up and I think it does illustrate the point I >> made in >>> a previous message of mine: documentation, documentation, >> docum

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 >>> "mod

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.

Re: [cellml-discussion] information_cellml_simulator

This is the email I sent him: Dear Danilo, My name is James Lawson, I am the curator of the CellML.org repository of models. If you have any questions whatsoever about any of the models, or how to simulate them, please let me know. I am at your service. First I think you will need to download

Re: [cellml-discussion] information_cellml_simulator

I'm going to email this gentleman and help him out on a more intimate basis. Andrew Miller wrote: > danilo roman wrote: >> Dear all >> I'm a master student at federal university of minas gerais, Brazil. >> Actually I've carried out some research at cardiomyocyte >> electrophysiology under superv

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 an

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 tal

Re: [cellml-discussion] [Tracker Item 42]New: CellML1.1.1specification

David Nickerson wrote: > The more this is explained, the more it sounds like this could all be > achieved with some additions to the errata for the CellML 1.1 > specification. What benefit is gained by making a 1.1.1 version? >From what I gather, publicity. We need some way to direct people's at

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