From jonathan.cooper at comlab.ox.ac.uk Tue Jan 6 01:10:05 2009 From: jonathan.cooper at comlab.ox.ac.uk (Jonathan Cooper) Date: Mon, 05 Jan 2009 12:10:05 +0000 Subject: [cellml-discussion] Looping Cell Cycle Models In-Reply-To: <4957F9AC.1020904@ebi.ac.uk> References: <295D6A23-8FD8-4590-8329-521ACE030A58@auckland.ac.nz> <4957F116.5040901@ebi.ac.uk> <4C270294-9E34-48C1-AF51-C02078ED16A4@auckland.ac.nz> <4957F387.6090205@ebi.ac.uk> <06F9A186-1FCC-45FE-9E02-6EBF0D340C67@auckland.ac.nz> <4957F9AC.1020904@ebi.ac.uk> Message-ID: <4961F89D.7080606@comlab.ox.ac.uk> On 28/12/08 22:11, Nicolas Le nov?re wrote: > Catherine Lloyd wrote: > >> However, we now face a different problem... Although we can easily >> describe the switches as piece-wise equations, if we define a single >> variable more than once in a CellML model the simulation tools tell >> us that the model is over constrained. >> >> For example in this case we already have a differential equation >> describing the change in mass over time, and then we have a second >> equation placing a condition on mass: > > No, no. Events are not assignment rules. In SBML as well, you could > not have a rate rule and an assignment rule on mass. Events are > discontinuous processes taking place in between simulation iterations. > I think this is just a missing concept in CellML. It exists in > simulators like XPP and GENESIS, used for neuronal simulations (e.g. > to reset voltage in spiking neurons). > > (To be absolutely frank, the existence of events as part of the core > SBML has been challenged many times. But I think we can now see why > they are needed :-)) Indeed, I also think this is a missing feature in CellML, and perhaps one that should be included in version 1.2? For the record, there has been a tracker item created for this issue; see https://tracker.physiomeproject.org/show_bug.cgi?id=1543 Jonathan From j.lawson at auckland.ac.nz Fri Jan 9 14:21:10 2009 From: j.lawson at auckland.ac.nz (James Lawson) Date: Fri, 09 Jan 2009 14:21:10 +1300 Subject: [cellml-discussion] SBML Level 2 Version 4 specification released Message-ID: <4966A686.3050405@auckland.ac.nz> Hi all, This might interest some people: http://sbml.org/Forums/index.php?t=tree&goto=4893&rid=0 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 Tue Jan 13 07:49:05 2009 From: dj.cowan at auckland.ac.nz (Dougal Cowan) Date: Tue, 13 Jan 2009 07:49:05 +1300 Subject: [cellml-discussion] Meeting minutes 2009-01-07 Message-ID: <496B90A1.8020201@auckland.ac.nz> The minutes from last week's ABI CellML Team meeting are up at: http://www.cellml.org/meeting_minutes/abi-meeting-minutes-2009-01-07 Sorry these are a bit late. Dougal From vinothbalaji at rediffmail.com Tue Jan 13 15:15:26 2009 From: vinothbalaji at rediffmail.com (NATARAJAN balaji vinoth) Date: 13 Jan 2009 02:15:26 -0000 Subject: [cellml-discussion] (no subject) Message-ID: <20090113021526.24473.qmail@f4mail-235-131.rediffmail.com> ? i want to log in cellml i want to create a new login for me vinoth 9842540928 -------------- next part -------------- An HTML attachment was scrubbed... URL: From ak.miller at auckland.ac.nz Thu Jan 15 18:23:12 2009 From: ak.miller at auckland.ac.nz (Andrew Miller) Date: Thu, 15 Jan 2009 18:23:12 +1300 Subject: [cellml-discussion] Prototype SBML to CellML converter Message-ID: <496EC840.4030702@auckland.ac.nz> Hi all, I have recently coded up a prototype designed to demonstrate how a program to convert from SBML to CellML might work. This prototype is written in Ruby using the REXML XPath parser, which was rapid to develop but makes it very slow to run - the intention is that once the algorithms to used are worked out, it could be re-written in a more efficient language. The code has been pushed onto github - the project page is at http://github.com/A1kmm/sbml2cellml/tree/master Features supported at present: * SBML parameters, compartments, species, rules, and reactions are translated into the equivalent component, variable and math elements in CellML (the reaction element in CellML is not used because this is considered informally deprecated). * Functions are substituted and expanded in the code invoking the function, since CellML doesn't allow them at present. * Units on constants (MathML cn elements) are automatically inferred from the context, where possible. * I have attempted to support all of SBML except events, time delays and other features which don't have a parallel in CellML yet. * The csymbol for time is replaced with a new variable introduced for time. Feedback and comments on this code would be greatly appreciated. Best wishes, Andrew From dj.cowan at auckland.ac.nz Fri Jan 16 14:01:53 2009 From: dj.cowan at auckland.ac.nz (Dougal Cowan) Date: Fri, 16 Jan 2009 14:01:53 +1300 Subject: [cellml-discussion] Meeting minutes 2009-01-14 Message-ID: <496FDC81.7010204@auckland.ac.nz> The minutes from this week's ABI CellML Team meeting are now up at: http://www.cellml.org/meeting_minutes/abi-meeting-minutes-2009-01-14 Dougal From j.lawson at auckland.ac.nz Fri Jan 23 11:38:47 2009 From: j.lawson at auckland.ac.nz (James Lawson) Date: Fri, 23 Jan 2009 11:38:47 +1300 Subject: [cellml-discussion] CellML leadership structures Message-ID: <4978F577.8040103@auckland.ac.nz> Hi all, We're bouncing around some ideas about how we might structure the decision making process within the CellML community. Ideally, we want to make it as transparent as possible and have some kind of executive group that reports directly to the community via a fair, democratic process. I've drafted a document that outlines some of the ideas we've talked about in the Auckland CellML meetings. There are a few holes in it that we need to patch up - namely, how the actual voting system might work. Please let me know what you think. Kind regards, James -------------- next part -------------- A non-text attachment was scrubbed... Name: cellml_leadership_decisions3.doc Type: application/msword Size: 103424 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: j_lawson.vcf Type: text/x-vcard Size: 278 bytes Desc: not available URL: From d.brooks at auckland.ac.nz Fri Jan 23 12:08:19 2009 From: d.brooks at auckland.ac.nz (David Brooks) Date: Fri, 23 Jan 2009 12:08:19 +1300 Subject: [cellml-discussion] CellML leadership structures In-Reply-To: <4978F577.8040103@auckland.ac.nz> References: <4978F577.8040103@auckland.ac.nz> Message-ID: <4978FC63.3060209@auckland.ac.nz> On 23/1/09 11:38 AM, James Lawson wrote: > Hi all, > > We're bouncing around some ideas about how we might structure the > decision making process within the CellML community. Ideally, we want > to make it as transparent as possible and have some kind of executive > group that reports directly to the community via a fair, democratic > process. > > I've drafted a document that outlines some of the ideas we've talked > about in the Auckland CellML meetings. There are a few holes in it > that we need to patch up - namely, how the actual voting system might > work. > > Please let me know what you think. > > Kind regards, > James So far as a voting system goes, what about the one used by the Apache Software Foundation? See http://www.apache.org/foundation/how-it-works.html *Decision Making* Projects are normally auto governing and driven by the people who volunteer for the job. This is sometimes referred to as "do-ocracy" -- power of those who do. This functions well for most cases. When coordination is required, decisions are taken with a lazy consensus approach: a few positive votes with no negative vote is enough to get going. Voting is done with numbers: * +1 -- a positive vote * 0 -- abstain, have no opinion * -1 -- a negative vote The rules require that a negative vote includes an alternative proposal or a detailed explanation of the reasons for the negative vote. The community then tries to gather consensus on an alternative proposal that resolves the issue. In the great majority of cases, the concerns leading to the negative vote can be addressed. This process is called "consensus gathering" and we consider it a very important indication of a healthy community. Regards, Dave -------------- next part -------------- An HTML attachment was scrubbed... URL: From dj.cowan at auckland.ac.nz Fri Jan 30 13:56:39 2009 From: dj.cowan at auckland.ac.nz (Dougal Cowan) Date: Fri, 30 Jan 2009 13:56:39 +1300 Subject: [cellml-discussion] Meeting minutes 2009-01-28 Message-ID: <49825047.5090607@auckland.ac.nz> The minutes from this week's ABI CellML Team meeting are now up at: http://www.cellml.org/meeting_minutes/abi-meeting-minutes-2009-01-28 Dougal