From j.lawson at auckland.ac.nz Mon May 4 13:18:10 2009 From: j.lawson at auckland.ac.nz (James Lawson) Date: Mon, 04 May 2009 13:18:10 +1200 Subject: [cellml-discussion] tools that use and / or work with CellML Message-ID: <49FE4252.7040405@auckland.ac.nz> 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 -------------- next part -------------- A non-text attachment was scrubbed... Name: j_lawson.vcf Type: text/x-vcard Size: 278 bytes Desc: not available URL: From j.lawson at auckland.ac.nz Mon May 4 13:40:10 2009 From: j.lawson at auckland.ac.nz (James Lawson) Date: Mon, 04 May 2009 13:40:10 +1200 Subject: [cellml-discussion] tools that use and / or work with CellML Message-ID: <49FE477A.4000403@auckland.ac.nz> 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 -------------- next part -------------- A non-text attachment was scrubbed... Name: j_lawson.vcf Type: text/x-vcard Size: 278 bytes Desc: not available URL: From d.cumin at auckland.ac.nz Mon May 4 14:07:51 2009 From: d.cumin at auckland.ac.nz (David Cumin) Date: Mon, 4 May 2009 14:07:51 +1200 Subject: [cellml-discussion] tools that use and / or work with CellML In-Reply-To: <49FE4252.7040405@auckland.ac.nz> References: <49FE4252.7040405@auckland.ac.nz> Message-ID: <004f01c9cc5d$215da5a0$6418f0e0$@cumin@auckland.ac.nz> 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-bounces at cellml.org [mailto:cellml-discussion- ->bounces at 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 -------------- next part -------------- A non-text attachment was scrubbed... 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Name: fminsearchbnd.m URL: From j.lawson at auckland.ac.nz Mon May 4 14:13:07 2009 From: j.lawson at auckland.ac.nz (James Lawson) Date: Mon, 04 May 2009 14:13:07 +1200 Subject: [cellml-discussion] tools that use and / or work with CellML In-Reply-To: <004f01c9cc5d$215da5a0$6418f0e0$@cumin@auckland.ac.nz> References: <49FE4252.7040405@auckland.ac.nz> <004f01c9cc5d$215da5a0$6418f0e0$@cumin@auckland.ac.nz> Message-ID: <49FE4F33.3060906@auckland.ac.nz> 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-bounces at cellml.org [mailto:cellml-discussion- > ->bounces at 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 at cellml.org > http://www.cellml.org/mailman/listinfo/cellml-discussion -------------- next part -------------- A non-text attachment was scrubbed... Name: j_lawson.vcf Type: text/x-vcard Size: 278 bytes Desc: not available URL: From j.lawson at auckland.ac.nz Mon May 4 15:20:25 2009 From: j.lawson at auckland.ac.nz (James Lawson) Date: Mon, 04 May 2009 15:20:25 +1200 Subject: [cellml-discussion] tools that use and / or work with CellML In-Reply-To: <49FE4252.7040405@auckland.ac.nz> References: <49FE4252.7040405@auckland.ac.nz> Message-ID: <49FE5EF9.2040405@auckland.ac.nz> 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 at 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. Cheers, James -------------- next part -------------- A non-text attachment was scrubbed... Name: j_lawson.vcf Type: text/x-vcard Size: 278 bytes Desc: not available URL: From j.lawson at auckland.ac.nz Mon May 4 15:42:53 2009 From: j.lawson at auckland.ac.nz (James Lawson) Date: Mon, 04 May 2009 15:42:53 +1200 Subject: [cellml-discussion] tools that use and / or work with CellML In-Reply-To: <004f01c9cc5d$215da5a0$6418f0e0$@cumin@auckland.ac.nz> References: <49FE4252.7040405@auckland.ac.nz> <004f01c9cc5d$215da5a0$6418f0e0$@cumin@auckland.ac.nz> Message-ID: <49FE643D.8030607@auckland.ac.nz> Hi David, I think the graphical tool you wrote is up on the CellML website but is not listed in the tools page, so if you could give us a short description of it and perhaps the latest version, I'll put it in the listing. 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-bounces at cellml.org [mailto:cellml-discussion- > ->bounces at 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 at cellml.org > http://www.cellml.org/mailman/listinfo/cellml-discussion -------------- next part -------------- A non-text attachment was scrubbed... Name: j_lawson.vcf Type: text/x-vcard Size: 278 bytes Desc: not available URL: From ak.miller at auckland.ac.nz Wed May 6 12:04:24 2009 From: ak.miller at auckland.ac.nz (Andrew Miller) Date: Wed, 06 May 2009 12:04:24 +1200 Subject: [cellml-discussion] ABI Meeting minutes 2009-04-29 Message-ID: <4A00D408.6030203@auckland.ac.nz> Hi all, I have put the minutes from last Wednesday's meeting up at: http://www.cellml.org/meeting_minutes/abi-meeting-minutes-2009-04-29/ Apologies to those who would have liked to see these sooner. Best wishes, Andrew From rodrigue at ebi.ac.uk Wed May 6 22:19:35 2009 From: rodrigue at ebi.ac.uk (Nicolas Rodriguez) Date: Wed, 06 May 2009 11:19:35 +0100 Subject: [cellml-discussion] tools that use and / or work with CellML In-Reply-To: <49FE5EF9.2040405@auckland.ac.nz> References: <49FE4252.7040405@auckland.ac.nz> <49FE5EF9.2040405@auckland.ac.nz> Message-ID: <4A016437.4040100@ebi.ac.uk> 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 at 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 From dj.cowan at auckland.ac.nz Thu May 7 16:23:55 2009 From: dj.cowan at auckland.ac.nz (Dougal Cowan) Date: Thu, 07 May 2009 16:23:55 +1200 Subject: [cellml-discussion] ABI Meeting minutes 2009-05-06 Message-ID: <20090507162355.n6drxn68pws0k84g@webmail.bioeng.auckland.ac.nz> I have put the minutes from Wednesday's meeting up at: http://www.cellml.org/meeting_minutes/abi-meeting-minutes-2009-05-06/ Dougal ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. From ak.miller at auckland.ac.nz Thu May 7 17:07:54 2009 From: ak.miller at auckland.ac.nz (Andrew Miller) Date: Thu, 07 May 2009 17:07:54 +1200 Subject: [cellml-discussion] ABI Meeting minutes 2009-05-06 In-Reply-To: <20090507162355.n6drxn68pws0k84g@webmail.bioeng.auckland.ac.nz> References: <20090507162355.n6drxn68pws0k84g@webmail.bioeng.auckland.ac.nz> Message-ID: <4A026CAA.8060804@auckland.ac.nz> Dougal Cowan wrote: > I have put the minutes from Wednesday's meeting up at: > > http://www.cellml.org/meeting_minutes/abi-meeting-minutes-2009-05-06/ It is worth noting that the changes I sent earlier today weren't included in the minutes: " Hi all, A few extra things: 4) Andrew will add a tracker item about [alternative graphical platforms] Andrew has done this, and there has been some discussion on the tracker about the issue, including from David Nickerson, Alan Garny, and Carey Stevens. and futher down add two bullet points to: 5) OpenCell development - update Andrew mentioned that he had been looking into some of the options for the graphical platform. He has also continued with the work on refactoring the model tree view so that the metadata support can be implemented more easily. Best wishes, Andrew " I also think we need to consider giving people a bit longer to reply to draft minutes (especially if there is not enough time to ensure that suggested changes get included). It is important that if we are claiming that people have said things, they have a proper chance to review what we claim they said beforehand. Best wishes, Andrew > > Dougal > > ---------------------------------------------------------------- > This message was sent using IMP, the Internet Messaging Program. > > _______________________________________________ > cellml-discussion mailing list > cellml-discussion at cellml.org > http://www.cellml.org/mailman/listinfo/cellml-discussion From j.lawson at auckland.ac.nz Fri May 8 13:01:49 2009 From: j.lawson at auckland.ac.nz (James Lawson) Date: Fri, 08 May 2009 13:01:49 +1200 Subject: [cellml-discussion] tools that use and / or work with CellML In-Reply-To: <4A016437.4040100@ebi.ac.uk> References: <49FE4252.7040405@auckland.ac.nz> <49FE5EF9.2040405@auckland.ac.nz> <4A016437.4040100@ebi.ac.uk> Message-ID: <4A03847D.2010202@auckland.ac.nz> 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 at 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 at cellml.org > http://www.cellml.org/mailman/listinfo/cellml-discussion -------------- next part -------------- A non-text attachment was scrubbed... Name: j_lawson.vcf Type: text/x-vcard Size: 278 bytes Desc: not available URL: From tommy.yu at auckland.ac.nz Wed May 13 12:53:28 2009 From: tommy.yu at auckland.ac.nz (Tommy Yu) Date: Wed, 13 May 2009 12:53:28 +1200 Subject: [cellml-discussion] PMR2 v0.1rc1 Message-ID: <4A0A1A08.6040800@auckland.ac.nz> Greetings, The first release candidate of the v0.1 release of PMR2 can be accessed at http://67.223.234.212:8380/pmr2/. The tracker item for this release is https://tracker.physiomeproject.org/show_bug.cgi?id=1772. Kind Regards, Tommy. From dj.cowan at auckland.ac.nz Fri May 15 11:13:40 2009 From: dj.cowan at auckland.ac.nz (Dougal Cowan) Date: Fri, 15 May 2009 11:13:40 +1200 Subject: [cellml-discussion] ABI Meeting minutes 2009-05-13 Message-ID: <20090515111340.5wctspsntc8s80cg@webmail.bioeng.auckland.ac.nz> I have put the minutes from Wednesday's meeting up at: http://www.cellml.org/meeting_minutes/abi-meeting-minutes-2009-05-13/ Dougal ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. From j.lawson at auckland.ac.nz Mon May 18 17:19:23 2009 From: j.lawson at auckland.ac.nz (James Lawson) Date: Mon, 18 May 2009 17:19:23 +1200 Subject: [cellml-discussion] tools that use and / or work with CellML In-Reply-To: <49FE477A.4000403@auckland.ac.nz> References: <49FE477A.4000403@auckland.ac.nz> Message-ID: <4A10EFDB.90301@auckland.ac.nz> 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 at cellml.org > http://www.cellml.org/mailman/listinfo/cellml-discussion > -------------- next part -------------- A non-text attachment was scrubbed... Name: j_lawson.vcf Type: text/x-vcard Size: 278 bytes Desc: not available URL: From j.lawson at auckland.ac.nz Mon May 25 12:34:59 2009 From: j.lawson at auckland.ac.nz (James Lawson) Date: Mon, 25 May 2009 12:34:59 +1200 Subject: [cellml-discussion] cellml.org publications listing Message-ID: <4A19E7B3.1050403@auckland.ac.nz> 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 -------------- next part -------------- A non-text attachment was scrubbed... Name: j_lawson.vcf Type: text/x-vcard Size: 278 bytes Desc: not available URL: From dj.cowan at auckland.ac.nz Fri May 29 08:27:29 2009 From: dj.cowan at auckland.ac.nz (Dougal Cowan) Date: Fri, 29 May 2009 08:27:29 +1200 Subject: [cellml-discussion] ABI CellML Meeting minutes 2009-05-27 Message-ID: <4A1EF3B1.6070009@auckland.ac.nz> I have put the minutes from Wednesday's meeting up at: http://www.cellml.org/meeting_minutes/abi-cellml-meeting-minutes-2009-05-27/ Dougal From hans.ekkehard.plesser at umb.no Sat May 30 02:28:11 2009 From: hans.ekkehard.plesser at umb.no (Dr. Hans Ekkehard Plesser) Date: Fri, 29 May 2009 16:28:11 +0200 Subject: [cellml-discussion] Using CellML for simplified neuron models? Message-ID: <4A1FF0FB.8070601@umb.no> Hi! We are looking for a good way to describe and share neuron models, and CellML appears a good candidate. The neuron models we are interested in consist mostly of a single compartment, possibly of a small number of compartments. As far as I can see, CellML appears well suited to describe the so-called subthreshold dynamics of model neurons. But I am wondering if CellML can also capture (or be extended to capture) the threshold operation present in most simplified neuron models. Briefly, the model dynamics are integrated according to a set of differential equations. When the membrane potential of the neuron crosses a certain threshold, the neuron is said to "fire": the membrane potential is reset to a certain value instantaneuously, and often clamped at that value for a certain period of time afterwards (refractory period); also, an output signal is generated. In simple pseudocode, this would look like: while ( simulation time not up ) process input update dynamics according to ODE if ( neuron is refractory ) V_m = V_reset count down "refractoriness" if ( V_m > Threshold ) V_m = V_reset emit output signal count up time Best regards, Hans -- Dr. Hans Ekkehard Plesser Associate Professor Dept. of Mathematical Sciences and Technology Norwegian University of Life Sciences Phone +47 6496 5467 Fax +47 6496 5401 Email hans.ekkehard.plesser at umb.no Home http://arken.umb.no/~plesser