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Alan Garny | 1 Jun 2009 13:17
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Re: Using CellML for simplified neuron models?

Hi Hans,

> 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
>
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James Lawson | 2 Jun 2009 02:17
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Re: [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-bounces@...
[mailto:team-bounces@...] 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
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James Lawson | 2 Jun 2009 02:25
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Re: Using CellML for simplified neuron models?

Dear Hans,

Further to Alan's email, I thought I'd refer you to some models we have 
in the CellML Model Repository. Have a look at some of Dr Richard 
Bertram's models at http://www.cellml.org/models - most of these are 
models of bursting in pancreatic beta cells, but there are a couple of 
neuronal models there too. You can find them under 'Bertram' in the 
repository listing.

If your simple conditional statements can be covered by piecewise 
equations, it can be done in CellML.

You might do well to look at some of the electrophysiological models of 
heart 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. Hans Ekkehard Plesser wrote:
> 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,
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Alan Garny | 2 Jun 2009 11:17
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Re: [cellmlteam] Contributing CellML models to Wolfram Alpha

> -----Original Message-----
> From: cellml-discussion-bounces@... [mailto:cellml-discussion-
> bounces@...] On Behalf Of James Lawson
> 
> 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.

I must confess that I am not particularly impressed with it either. I did
'play' with it quite a bit when it got released and, yes, it's fun/cool if
you stick to the kind of stuff shown in Wolfram's demo, but otherwise...
it's basically 'useless'. This put aside, I like the concept and no doubt
that it's going to take time to make it worthwhile.

> 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....?

a) and c) I would imagine it's pretty obvious. The sole fact that CellML
models would become 'available' through WA means that people would get to
know about CellML and, from there, might be interested in finding more about
it, etc.

As for your other points, I don't know for certain, but I don't think it
matters: anything that can help people use CellML is a good thing (as long
as it fits the maximum output for minimum input paradigm... :))

Alan
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Edmund J. Crampin | 2 Jun 2009 22:33
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Re: [cellmlteam] Contributing CellML models to Wolfram Alpha

I think this is a good suggestion from Abhishek, which was also raised  
earlier by Richard Simpson (our Business Development Manager) in a  
broader context than just CellML. I wonder if Abhishek is willing to  
explore this a little further?
Edmund

Dr Edmund J. Crampin

Systems Biology Group Leader
Associate Director Postgraduate
Auckland Bioengineering Institute
and
Senior Lecturer
Department of Engineering Science
The University of Auckland
New Zealand

On 2/06/2009, at 9:17 PM, Alan Garny wrote:

>> -----Original Message-----
>> From: cellml-discussion-bounces@... [mailto:cellml-discussion-
>> bounces@...] On Behalf Of James Lawson
>>
>> 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.
>
> I must confess that I am not particularly impressed with it either.  
> I did
> 'play' with it quite a bit when it got released and, yes, it's fun/ 
> cool if
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Dr. Hans Ekkehard Plesser | 4 Jun 2009 14:50
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Re: Using CellML for simplified neuron models? (Alan Garny)


Hi Alan!

[Apologies for breaking the thread, I had subscribed to the list in digest form.]

Thank you for your example. Unfortunately, fixed time-stepping schemes where events (threshold
crossings and membrane potential resets) can occur only on a fixed time grid are one of the big
no-nos in neuronal network modeling, since they can lead to strong synchronization artefacts.
Indeed, quite a lot of research in recent years has focused on algorithms to determine the exact
time of threshold crossings efficiencly. I'd be happy to send you reference if you are interested.

Thus, if we wanted to use CellML to represent neuron models in a general form, we would need a
possibility to represent instantaneous events in continuous time. I believe SBML events provide
this, don't they?

Best,
Hans

> ----------------------------------------------------------------------
> 
> Message: 1
> Date: Mon, 1 Jun 2009 12:17:54 +0100
> From: "Alan Garny" <alan.garny@...>
> Subject: Re: [cellml-discussion] Using CellML for simplified neuron
> 	models?
> To: "'CellML Discussion List'" <cellml-discussion@...>
> Message-ID: <001001c9e2aa$9beba840$d3c2f8c0$ <at> garny@...>
> Content-Type: text/plain; charset="us-ascii"
> 
> Hi Hans,
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Alan Garny | 4 Jun 2009 15:02
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Re: Using CellML for simplified neuron models? (Alan Garny)

Hi Hans,

I can see your point now and agree that the solution I offered is not
suitable. In fact, I wasn't happy with the solution myself, but that was the
best I could come up with with CellML in mind. So, yes, this means that
events are not supported by CellML, unlike in SBML. 

Bottom line: you are out of luck with CellML while SBML is what you are
after, at least with regards to events.

Alan

> -----Original Message-----
> From: cellml-discussion-bounces@... [mailto:cellml-discussion-
> bounces@...] On Behalf Of Dr. Hans Ekkehard Plesser
> Sent: 04 June 2009 13:51
> To: cellml-discussion@...
> Subject: Re: [cellml-discussion] Using CellML for simplified neuron
models?
> (Alan Garny)
> 
> 
> Hi Alan!
> 
> [Apologies for breaking the thread, I had subscribed to the list in digest
> form.]
> 
> Thank you for your example. Unfortunately, fixed time-stepping schemes
> where events (threshold
> crossings and membrane potential resets) can occur only on a fixed time
(Continue reading)

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Poul Nielsen | 4 Jun 2009 23:22
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Re: Using CellML for simplified neuron models? (Alan Garny)

Dear Hans

Thank you for raising this. It s, in fact, one of the issues discussed  
at the recent combined CellML SBGN-SBO BioPAX MIASE Workshop held this  
April on Waiheke Island. There is a clear need to be able to specify  
discontinuous processes and events, such as you have described.  
However, both CellML and SBML use a declarative specification of  
models, described with content MathML. Event handling fits more  
naturally with imperative descriptions of models so there is currently  
no clean way of describing events using content MathML. SBML, which  
also uses content MathML as its underlying mathematical description  
language, has addressed this problem by augmenting the language with  
events and reset rules. After some discussion at the recent workshop,  
the consensus was that the next iteration of CellML (1.2) would  
include facilities for specifying events and applying reset rules in a  
way that is consistent with SBML. There are several reasons for taking  
this approach: it is a method that fits reasonably naturally with  
modellers' notion of describing such models; the solution has been  
tested by the SBML community; the construct will be straightforward to  
handle when translating between SBML and CellML. We are currently  
working on the CellML 1.2 specification and plan to have a draft  
released shortly with the addition of events and reset rules to handle  
problems such as you have described.

Best wishes
Poul

On 2009-06-05, at 00:50, Dr. Hans Ekkehard Plesser wrote:

>
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Dougal Cowan | 5 Jun 2009 05:06
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ABI CellML Meeting minutes 2009-06-03

I have put the minutes from Wednesday's meeting up at:

http://www.cellml.org/meeting_minutes/abi-cellml-meeting-minutes-2009-06-03

Dougal
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Peter Hunter | 5 Jun 2009 07:51
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Re: Using CellML for simplified neuron models? (Alan Garny)

Thanks Poul.
--------------------------
Sent using BlackBerry

----- Original Message -----
From: cellml-discussion-bounces@... <cellml-discussion-bounces@...>
To: CellML Discussion List <cellml-discussion@...>
Sent: Fri Jun 05 09:22:23 2009
Subject: Re: [cellml-discussion] Using CellML for simplified neuron models?     (Alan Garny)

Dear Hans

Thank you for raising this. It s, in fact, one of the issues discussed
at the recent combined CellML SBGN-SBO BioPAX MIASE Workshop held this
April on Waiheke Island. There is a clear need to be able to specify
discontinuous processes and events, such as you have described.
However, both CellML and SBML use a declarative specification of
models, described with content MathML. Event handling fits more
naturally with imperative descriptions of models so there is currently
no clean way of describing events using content MathML. SBML, which
also uses content MathML as its underlying mathematical description
language, has addressed this problem by augmenting the language with
events and reset rules. After some discussion at the recent workshop,
the consensus was that the next iteration of CellML (1.2) would
include facilities for specifying events and applying reset rules in a
way that is consistent with SBML. There are several reasons for taking
this approach: it is a method that fits reasonably naturally with
modellers' notion of describing such models; the solution has been
tested by the SBML community; the construct will be straightforward to
handle when translating between SBML and CellML. We are currently
(Continue reading)

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