Re: [cellml-discussion] Java error on Mac OSX10.8.2

[Peter Hunter]

Hi Mark,

FYI, there is a new CellML simulation tool called OpenCOR being 
developed by Alan Garny that is becoming our primary platform for 
CellML-based modelling (see 
http://www.cellml.org/getting-started/tutorials/opencordemo for download 
instructions). This will shortly have CellML authoring capability and is 
a more robust environment than OpenCell, although I currently use both - 
OpenCell for authoring models and OpenCOR for running simulations. 
OpenCOR has facilities for annotating models against bio-ontologies such 
as GO, although access to the Ricordo webservices for providing the 
ontologies is a wee way off (hopefully achieved by the time of the 
CellML workshop in Auckland in a few weeks).


Rgds, Peter


On 26/02/2013 4:37 a.m., Mark Cannell wrote:

Hi All

I've been trying to test the new open cell 0.8 on a mac but all I get is a java 
runtime error and I have no idea how to get over it:

[Exception... "Component returned failure code: 0x80004005 (NS_ERROR_FAILURE) 
[cellml_servicesICellMLIntegrationService.compileModelODE]"  nsresult: "0x80004005 
(NS_ERROR_FAILURE)"  location: "JS frame :: chrome://opencell/content/util/Integration.js :: 
StartCollectingResults :: line 18"  data: no]

Has anyone run open cell on a mac? I used cor0.8 under a windows emulator and 
that worked Ok but trying to use an integrated platform/interface for student 
teaching is not working…

Any ideas?

Thanks

Mark  B. Cannell Ph.D. FRSNZ
Professor of Cardiac Cell Biology
School of Physiology&  Pharmacology
Medical Sciences Building
University of Bristol
Bristol
BS8 1TD UK

mark.cann...@bristol.ac.uk




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Re: [cellml-discussion] Solicitation of feedback on CellML 1.2

[Peter Hunter]

Hi Andre,

Support for models with parameter uncertainty is pretty urgent in relation to 
grants but I'm in your hands re optimal strategy for getting there.

Cheers,
Peter
--
Sent using BlackBerry


From: David Nickerson [mailto:david.nicker...@gmail.com]
Sent: Monday, October 29, 2012 10:36 PM
To: CellML Discussion List 
Subject: [cellml-discussion] Solicitation of feedback on CellML 1.2

Dear all,

At the 5th International CellML 
Workshop, we discussed 
the main list of features that were desirable to have in CellML 1.2. The CellML 
Editorial Board has been discussing the implementation of these features in 
regard to the next version of the CellML standard. Early on, we decided that 
the entire list of features arising from the workshop was too broad and far 
reaching to accommodate an easy transition from CellML 1.1 to CellML 1.2 in a 
timely manner. We have therefore selected a subset of these features which we 
feel address immediate shortcomings in the CellML 1.1 specification and 
introduce a minimal set of often requested new features.

Tracker item 
55 shows a 
detailed overview of our current plans. This is by no means meant to be the 
final composition of CellML 1.2, but it reflects the current view of the 
editorial board as to the types of models users wish to encode in CellML and 
what is possible to implement in both the specification and software tools.

Jonathan Cooper presented our thoughts on CellML 1.2 at the recent COMBINE 2012 
meeting. Please see the slides 
and video of the presentation to get a more consumable view of the proposed 
changes.

This email is to solicit specific feedback from the community regarding the 
subset of changes that we have selected for inclusion in CellML 1.2. The CellML 
1.2 specification will mark a significant change in the way the CellML standard 
is specified, and we hope that this change will enable a more rapid process for 
standardising new features that modellers require in order to encode and share 
their models using CellML.

From tracker item 55, 
we would like to highlight the following main changes that we think should be 
in CellML 1.2:


  *   Remove reaction element (tracker item 
49);
  *   Remove the directional aspect of connections (tracker item 
337);
  *   Replace grouping with a simplified encapsulation-only mechanism (tracker 
item 356);
  *   Delayed variables (introduction of the evaluatedAt operator with reduced 
functionality to allow infinitesimal delays and initial values) (tracker item 
70).

In addition, we specifically ask for feedback on the issue of moving to MathML 
3.0 (tracker item 67) 
and the inclusion of stochastic variation in models (tracker item 
2809). The editors 
generally agree that switching to MathML 3.0 at this time provides too little 
benefit (mathematical clarity) for the cost involved in making the change (tool 
support, interoperability with other exchange formats). While the proposal for 
stochastic variation is fairly mature, we feel that it requires further work to 
meet the requirements for inclusion in the CellML standard. We also think that 
given sufficient impetus from the community this could be one of the first 
proposals to pass through the new development process for CellML.

The editorial board will shortly be releasing our proposed guidelines for the 
development of the CellML standard. As mentioned above, we hope this new 
process will allow new features (such as for stochastic variation in models) to 
move more quickly from feature requests through to changes in the standard 
specifications.

Thanks,
The CellML Editorial Board.
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Re: [cellml-discussion] ABI CellML Meeting Minutes, 25th May 2011

[Peter Hunter]

Thanks Lucian, my mistake I think, I got *Darren *Wilkinson mixed up 
with *Daryl *Shanley - both at Newcastle.

Cheers, Peter

On 27/05/2011 9:43 a.m., Lucian Smith wrote:

For what it's worth, it's 'Darren', not 'Darryl' (the SBML 'distrib'
package guy).

-Lucian

* Dougal Cowan  [2011-05-26 22:32] writes:

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

http://www.cellml.org/community/meeting/minutes/2011/05.25

Cheers,
Dougal

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Re: [cellml-discussion] CellML for R

[Peter Hunter]

Hi Erin,

Yes, definitely - not least because both R and CellML originated in Auckland. 
I'll speak to Ross Ihaka about this to get his thoughts.

Cheers,
Peter
--
Sent using BlackBerry


From: cellml-discussion-boun...@cellml.org 

To: cellml-discussion@cellml.org 
Sent: Wed Sep 15 08:20:22 2010
Subject: [cellml-discussion] CellML for R

Hello,

I sent this message a couple weeks ago, but I don't think it got posted so I'll 
try again.  I'm developing a large-scale model of the pancreatic beta cell as 
part of my dissertation research.  I'm constructing the model in R, the 
open-source statistical software suite (more info here: 
http://cran.r-project.org/).  I was wondering if there is any interest in a 
collaborative project to create a package for R to read/write/edit CellML files 
for use in modeling and simulation?  R has a huge international user base, and 
making CellML available to those users would be beneficial for both the R and 
CellML communities.

I look forward to hearing from you!

Erin

--
Erin Rachael Shellman
The University of Michigan
Bioinformatics PhD Candidate
http://www.erinshellman.com
shell...@umich.edu
(937) 321.1129

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Re: [cellml-discussion] Remote "attendance" at the CellML hackathon and workshop

[Peter Hunter]

Thanks Catherine!
--
Sent using BlackBerry


- Original Message -
From: cellml-discussion-boun...@cellml.org 

To: CellML Discussion List 
Sent: Wed Feb 10 09:03:00 2010
Subject: [cellml-discussion] Remote "attendance" at the CellML hackathon and
workshop

Dear All

We have received a number of requests for an audio-visual connection  
to the CellML hackathon and workshop allowing people to attend  
"remotely".  I have set up meeting rooms on Evo:

http://evo.caltech.edu/evoGate/

If you would like to "remotely attend" the hackathon and/or the  
workshop you will need to pre-register (for free) in advance at Evo.   
The meetings are called CellML Hackathon (Feb 24th 8.30-16.00 NZ  
time), CellML Workshop (Feb 25th 8.30-17.30 NZ time) and CellML  
Workshop (day 2) (Feb 26th 8.30-18.00 NZ time).  The meetings are  
password protected: for the hackathon - cellmlhack, and for the  
workshop (both days) cellmlwork.

We intend to have both audio and visual connections set up.  If the  
connection becomes unstable there are also phone numbers supplied by  
Evo which can be called (for free).

Please trial the software in advance and let me know if you have any  
questions.

Best wishes
Catherine

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Re: [cellml-discussion] ABI CellML meeting minutes 2009-09-30

[Peter Hunter]

Thanks Dagmar. We are committed to SED-ML! Your comments are very helpful. Peter
--
Sent using BlackBerry


- Original Message -
From: cellml-discussion-boun...@cellml.org 

To: CellML Discussion List 
Sent: Fri Oct 09 19:41:19 2009
Subject: Re: [cellml-discussion] ABI CellML meeting minutes 2009-09-30

Dear all,

I'd like to comment on the last meeting minutes, particularly on the 
metadata specification comments made by Andre:

* Andre said that SED-ML does not yet support everything that we
  need to do for simulation and graphing.

I agree that SED-ML still is at quite an early stage and might not cover 
everything needed.
However, even if the structure of SED-ML does not offer particular 
constructs for some of your needs, you are allowed (by definition of the 
SED-ML schema) to attach annotations to *any* SED-ML element. Thus, you 
could "extend" SED-ML towards supporting whatever additional needs you 
might have for information to put in the simulation description file.
Do you think that would be sufficient? As Nicolas mentioned, that would 
actually be a nice benchmark for us to see in what way SED-ML needs to 
be extended (certainly by what you would put in the annotations often).

* Andrew said that we are still trying to convince the SED-ML group
  to separate out graphing and simulation.

I can say that SED-ML is *not* about graphing at all - in the sense that 
I understand graphing. SED-ML should provide the description of the data 
that is used to create the output, and also how these data relate, e.g. 
for a 2 dimensional plot you would have to specify what to plot against 
what (x and y axes). Let me cite Nicolas again from an earlier mail: 
"E.g. we can create a report {time, var1, var2}, but some information 
will only emerge if we "plot" var1 versus var2. In some sense the 
relationship between var1 and var2 representation is part of the 
post-processing."

* Andre said that you might want to change some of the graphing
  metadata to get different graphs from the same simulation, or vice
  versa.

If we are talking about running one simulation and creating a number of 
different graphs (say, many 2D plots) from that simulation, this is 
already possible in SED-ML right now. All you have to do is to define a 
number of (what we call) data generators, referring to the 
variables/parameters you want to use for your output. Then you can 
define as many outputs as you want, referring to the same or different 
data generators and to the same of different simulation setups.
If you look at the example given in the publication of CMSB 2008, on 
page 9/10 (http://www.springerlink.com/content/n67n137071431xt7/), we 
defined a data generator called "time" and we use it to create 2 
different curves from one single simulation (only the x axis is varying 
here, using 2 different models).

If we, however, are talking about producing the same graph one time with 
a red line, one time with a green line - those things are not part of 
SED-ML core information, and they should go to the above mentioned 
annotations.

* Peter said that we want to encourage cooperation, and use accepted
  standards if they exist.

I cannot tell you how much we would like to see CellML using SED-ML :-)
I know that we do progress pretty slowly, and I am very sorry for that.

* Andre said that the minimal information standard should be out soon.

Maybe a word on that: We are currently (and have been for a while... 
slow again, I know) working on writing up the MIASE guidelines. In my 
opinion, we do make good progress and I think that we have come to quite 
a good consensus already. So, there is hope that "soon" won't take too long.

I am happy to answer all the questions you might have!

Many greetings from Rostock,
Dagmar


Dougal Cowan wrote:
> I have put the minutes from this Wednesday's meeting up at:
>
> http://www.cellml.org/community/meeting/minutes/2009/10.07
>
> Dougal
>
>
>
> __ Information from ESET Smart Security, version of virus signature 
> database 4488 (20091007) __
>
> The message was checked by ESET Smart Security.
>
> http://www.eset.com
>
>
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> http://www.cellml.org/mailman/listinfo/cellml-discussion
>
>   

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Re: [cellml-discussion] ABI CellML team meeting minutes 2009-07-22

[Peter Hunter]

Hi Catherine,

The link on the Iribe model page did let me load OpenCell with the session 
file, but gave error messages. I take your point re session files in general - 
we do need to make it easier to create them as the difference between models 
with (including SVG files) & without them is day & night for new users. 

Cheers, Peter
--
Sent using BlackBerry


- Original Message -
From: cellml-discussion-boun...@cellml.org 

To: CellML Discussion List 
Cc: lfen034 lfen034 ; Pulasthi Mithraratne 

Sent: Mon Aug 03 19:59:13 2009
Subject: Re: [cellml-discussion] ABI CellML team meeting minutes 2009-07-22

Hi Peter

With regards to item 2, according to the model status comment James  
has already created a PCEnv session file for Iribe et al:

http://models.cellml.org/exposure/62724a9b65d81c479e484513aa32e9d3

It looks like this already has a session file - but without an  
embedded SVG diagram (I make that comment based on the fact there is  
no image for this model in the repository).

Pulasthi/Linda - would you please be able to create a diagram for this  
model, load it into the repository in the correct folder, and update  
the documentation to link to it please?  The paper is attached.   
Unfortunately there is no schematic in the paper - it's going to be a  
case of creating one from scratch based on the list of currents, etc.  
in the appendix.  Andre and James will be back from Japan next week  
and they will be able to check your diagram for you (sorry to  
volunteer you Andre and James in your absence - but I thought you  
wouldn't mind!!!)

Also, related to number 2 in general - Peter, I know that James is  
reluctant to create a whole lot of OpenCell session files right now -  
there is a valid reason for this - either relating to OpenCell or PMR2  
- he can update you himself.  But creating one-off session files that  
have been requested, for the time being, is fine.

Best wishes
Catherine


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Re: [cellml-discussion] ABI CellML team meeting minutes 2009-07-22

[Peter Hunter]

Hi Justin,

Some agenda items for the next CellML mtg:
1. I noticed a bug on the new website where the 'home page' reverts to the 
models top page instead of the CellML home page. 
2. A plea from users for implementation of more session files. In particular 
the Iribe et al model needs to be setup for OpenCell.
3. Has the implementation of the SBML API been discussed for OpenCell? 
4. A number of comments from people who attended the IUPS workshop about the 
great job you guys did.

Cheers,
Peter
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Sent using BlackBerry


- Original Message -
From: cellml-discussion-boun...@cellml.org 

To: CellML Discussion List 
Sent: Mon Aug 03 09:54:48 2009
Subject: [cellml-discussion] ABI CellML team meeting minutes 2009-07-22

Dear CellML community,

The ABI CellML team meeting minutes for 2009-07-22 are belatedly 
available at:
http://www.cellml.org/community/meeting/minutes/2009/07.22

Kind Regards,
Justin Marsh.
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Re: [cellml-discussion] Using CellML for simplified neuron models? (Alan Garny)

[Peter Hunter]

Thanks Poul.
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- Original Message -
From: cellml-discussion-boun...@cellml.org 

To: CellML Discussion List 
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
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:

>
> 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" 
>> Subject: Re: [cellml-discussion] Using CellML for simplified neuron
>>  models?
>> To: "'CellML Discussion List'" 
>> Message-ID: <001001c9e2aa$9beba840$d3c2f8...@garny@dpag.ox.ac.uk>
>> Content-Type: text/plain; charset="us-ascii"
>>
>> 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
>>>
>>>  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
>>
>> I believe this could easily be done, as long as you are OK with the
>> following:
>> - this would require integrating the model using an integration
>> technique
>> that relies on a fixed time step. In my experience, anything will
>> make your
>> resetting of Vm difficult.
>> - your output signal (Vm?) will always be generated.
>>
>> Attached is a very simple CellML file (based on the van der Pol
>> model) that
>> illustrates the kind of thing I think you are after. You want to
>> plot the x
>> and y parameters (see attached screenshot).
>>
>> Alan
>> -- next part --
>> A non-text attachment 

Re: [cellml-discussion] Opinion on multiple standards

[Peter Hunter]

Dear Michael,

I agree completely with your views. Our combined challenge now is to try to agree on common metadata 
standards that suit both SBML and CellML. The meeting in April will be an opportunity to do this.


Cheers,
Peter

Michael Hucka wrote:

  AT> P.S. regarding different standards or notation
  AT> systems, it will be never irrelevant to have multiple
  AT> standards (domination may be mantra of Microsoft), it
  AT> gives freedom to choose and that's beauty of open
  AT> community based projects.

What follows is personal opinion, not an official position
on behalf of any group I'm involved with.

Agreement on single open standards for single domains or
application areas *is* beneficial and a goal to strive for.
An example of this is today's web.  Would the web be what it
is today if people had not settled on one set of standards
(HTML for describing pages, HTTP for the protocol)?
Agreement on single standards in single application areas is
what enables practical interoperability in those areas.
(Sure, you can have interoperability even in the face of
multiple standards, but it's a lot more expensive to
implement, and thus not practical in the long run.)

Note that my claim is specifically about *single* domains.
Multiple standards are definitely needed for non-overlapping
(or mostly non-overlapping) domains or application areas.

Multiple proposed standards for the same single domain arise
(1) in the early stages when people are still grappling with
understanding their needs on the one hand, and implications
of specific format/notation/whatever choices on the other;
(2) when an established standard is found to be deficient
as a result of experience, evolution, and/or innovation.
For #2, if things have been going well, people will want to
update an existing standard (e.g., version 1->2) rather than
replace it entirely, but in other cases, wholesale
replacement may be called for.

I hypothesize that when people say "multiple standards are
good in open community projects", it's because people
actually are thinking about multiple application areas, or
an area has not settle on common standards, or people are
dissatisfied with the existing standards.

People sometimes bring up Microsoft as a counter-example to
single standards.  The actual problem is not the adoption of
single standards, it's Microsoft's specific approach, which
involves (i) a single entity making top-down decisions for
its own needs without consultation with other groups, (ii)
not documenting the formats, (iii) changing the formats
roughly every time they update their applications without
prior announcement, and (iv) a belligerent business style.
In other words, people's problem with Microsoft is actually
rooted in Microsoft's lack of an open process.  I wager
Microsoft would be viewed much more favorably if they
developed their document formats using a bottom-up community
process.

In summary, I claim that there are reasons why an area might
end up with multiple proposed standards, but it is false
that having multiple standards is better than using one
standard when a single one can be agreed upon.

Agreement on a single standard certainly takes a lot of
effort, exploration, and time, on both the technical aspects
of defining the standard and the social aspects of arranging
community buy-in.  Sometimes it takes decades before
quiescence is reached on a given topic.  But once a
sufficiently good single standard for a given area can be
found, it is far better to stick with it, and spend your
efforts on something else.

MH

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begin:vcard
fn:Peter Hunter FRS
n:Hunter;Peter
org:University of Auckland;Auckland Bioengineering Institute (ABI)
adr:70 Symonds St;;Level 6;Auckland;;;New Zealand
email;internet:[EMAIL PROTECTED]
title:Director
tel;work:+649 373 7599 x88395
tel;fax:+649 367 7157
tel;home:+649 307 6662
tel;cell:+6421 505033
url:http://www.bioeng.auckland.ac.nz/
version:2.1
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Re: [cellml-discussion] in case you haven't seen it | "Why Are Computational Neuroscience and Systems Biology So Separate?"

[Peter Hunter]

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...


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Re: [cellml-discussion] unit conversion

[Peter Hunter]

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 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_fi

Re: [cellml-discussion] ABI CellML team meeting minutes 2008-05-32

[Peter Hunter]

Hi James,

Excellent notes!
Frank Sachse's name is misspelt near the end.

Cheers,
Peter

James Lawson wrote:
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
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Re: [cellml-discussion] Bug in Nygren model

[Peter Hunter]

Title: Bug in Nygren model




Hi Daniel, 

Thanks for figuring that out. Would you mind sending the change (or
corrected model) to James (CC'd) - he is our principal CellML curator
at the moment.

Cheers, 
Peter

[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
findings in the original paper.
  
  After coordinating with the primary
author, the problem was found and I would like to correct the mistake
and submit the correct model.
  How can I do that? It seems one needs
a membership login to edit models? Or would that be handled by a
dedicated curator?
  Cheers,
  
  Daniel
  
  
  Mit
freundlichen Grüßen / Best regards / Cordialement
  
  Dr.
Daniel Ziemek
  
  Sanofi-Aventis
Deutschland GmbH
  
  GS Bioinformatics
Industriepark Hoechst
Bldg. G879, Room 218
D-65926 Frankfurt am Main
t: +49 69 305 22737
w: www.sanofi-aventis.de
  
  **
  Sanofi-Aventis
Deutschland GmbH ·  Sitz der Gesellschaft: Frankfurt am Main ·
Handelsregister: Frankfurt am Main, Abt. B Nr. 40661
  Vorsitzender des
Aufsichtsrats: Hanspeter Spek - Geschäftsführer: Dr. Heinz-Werner Meier
(Vorsitzender),
  
  Dr. Matthias Braun, Hervé
Gisserot, Dieter Kohl, Prof. Dr. Dr. Werner Kramer, Dr. Martin Siewert
  
  **
  
  

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Re: [cellml-discussion] PMR categories

[Peter Hunter]

Dear All, 

Poul and I have looked at the discussion on this thread and to best
encompass the various suggestions we've decided to ask Tommy to do the
following:
1. Include both a category field with predefined terms (Tommy has this
in now) and an additional general 'key word' field. A model can be in
multiple categories. 
2. The sort facility on the repository will have three ways of sorting:
The 1st is the above list of categories, the 2nd is a drop down list
that provides more options (see next point), and the 3rd is the
curation level. 
3. The 2nd sort facility will present several options such as keyword
search, species, cell type, etc, and access to more extensive boolean
searches (author, year, etc).

Cheers, 
Peter

Matt wrote:

  On 6/8/07, James Lawson <[EMAIL PROTECTED]> wrote:
  
  
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?

  
  
Yes.

  
  
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?

  
  
Read the paper I referenced, it has a very simple breakdown of LSID
and the taxonomy naming issue.

  
  

  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.
  


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Re: [cellml-discussion] PMR categories

[Peter Hunter]

Dear All, 

The intention of this discussion was to decide on a list of items for a
drop-down list of predefined terms that would be available when
choosing 'key words' for a new model and which would be the list of
terms used to display models on www.cellml.org/models (together with
the default 'All models' item). The idea was that choosing one or more
of these key words terms would be mandatory when defining model
metadata but that one could also enter additional keywords for more
advanced searching. 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. But I am keen to
keep this first list of terms fairly short. My suggestion is the
following list. I've checked through the repository and less than 10%
of the models would end up solely under 'Other'. I am sure we will need
to expand this list as the repository grows and I suggest we have a
policy of keeping the number that end up solely in the 'Other' category
to less than 10% of the total. We may also later need a policy to
refine the classification when too many models are displayed under one
term. 

Calcium dynamics
Cell cycle
Cell migration
Circadian rhythms
Electrophysiology
Excitation-contraction coupling
Gene regulation
Mechanical constitutive laws
Metabolism
Myofilament mechanics
Signal transduction
Other (the default key word in the list of predefined terms)

Let me know if you can think of other more appropriate terms or
additional ones, then I'll ask Tommy to implement it. I'm happy to then
go through and classify all current models in the repository into these
categories. 

Cheers, 
Peter

David Nickerson wrote:

  One thing I have found useful in other taxonomy/keyword type web 
interfaces (e.g., see drupal) is that when entering such keywords the 
interface dynamically completes the terms and/or presents alternatives 
based on what the user enters. I'd imagine such an interface would work 
well at pulling terms out of the ontologies Matt is talking about.


David.


Tommy Yu wrote:
  
  
Just had a discussion with Peter, Randall and James about this.

The keywords are in the metadata for the models, and there is no limit to what can go in there.  The concern about that is the list could get too big (for minor categories), or variations in the name (electrophysiology vs electrophysiological), or just spelling in general.  What was decided is to have the same category list, but it would act as a "blessed" list of keywords that will serve as a guide to what should be added to the model, and as a broad category filter for the main repository listing.  Users would still be able to add or search by other keywords (from the advance search interface) if they wish.

Tommy.

Matt wrote:


  On 6/6/07, David Nickerson <[EMAIL PROTECTED]> wrote:
  
  
James Lawson wrote:


  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.
  

not sure I like the idea of a separate category, seems to me adding some
special piece of metadata to models just to make a repository dump look
pretty isn't the way to go. It would be nicer to make use of the
keywords (which are genuinely useful metadata to more than just the
model repository), possibly with the addition of a guided part of the
metadata editing workflow which prompts the user to choose at least one
of the predefined "category" keywords and a filter smart enough to put
models without one of the special keywords into an "other" category.
This way the main repository page layout could be easily changed to add
or remove keywords that get pulled out as categories without having to
change the models.

It would also be nice if we can analyse all the repository searching to
keep track of the most popular keywords and adjust the categories on the
main page accordingly :-)

  
  Well, I'm hoping to steal all the keywords and lay them out in the
physiome ontology and then put them back in as bioentities (or math
related) metadata pointing into this. So the long term relationship
between keywords and this "ontology" metadata is where my thinking
lies. I like the idea of reflecting this information into keywords,
e.g. for 'cardiovascular' the bioentity would be some big long uri
pointing into the instance of the term 'cardiovascular' 

Re: [cellml-discussion] Interactions between SVG diagrams and PCEnv.

[Peter Hunter]

Hi Andre, 

The plan is definitely to link up with Sarala's work - we'll
hand-create the svg diagrams only until the output of Sarala's work can
generate these directly from the CellML model. 

Cheers, 
Peter

David Nickerson wrote:

  Hi Andrew,

I'm wondering how (if?) this fits in with the visualisation work that 
Sarala is doing?

While I'm not sure how standard it is, I know inkscape allows you to add 
links to any object in an SVG diagram where you can set xlink properties 
like: href, type, role, arcrole, title, show, and actuate. I would 
imagine that these are plenty to be able to link SVG objects to other 
resources (assuming this is standard SVG, which it seems to be looking 
at plain SVG diagrams exported from inkscape).

In the diagrams I have been creating with Sarala's help I have 
envisioned that these links would be used to link to associated 
graphs/math/etc provided in a "reference description" of the model. I 
guess for an interactive tool like PCEnv you'd probably link to some 
PCEnv specific resource telling the GUI what to do. Maybe you'd simply 
link directly to a graph trace and PCEnv would be able to interpret such 
a request and show the appropriate trace, but that might get a bit 
restrictive.


Andre.

Andrew Miller wrote:
  
  
Hi all,

Peter Hunter has proposed that it be possible to create SVG diagrams 
which interact with PCEnv so that you can click on parts of the SVG 
diagram and have PCEnv update the styles of traces being displayed on a 
graph.

For example, someone might click on a sodium channel in the SVG diagram, 
and have a trace showing sodium concentrations come up on their graph.

There are several possible ways to implement this, and I am looking for 
feedback from potential users on which way they would find the most useful:

1) Create a generic language which describes the relationship between 
elements in an SVG diagram and trace resources in the graph metadata. 
This relationship could describe what happens when the SVG diagram is 
clicked. This would probably be the most useful for tools other than 
PCEnv to process, although it is not clear whether this would actually 
be useful to such tools.

2) Provide an API which _javascript_ in SVG diagrams  can use to 
manipulate PCEnv traces, perhaps by giving the resource URI.

If we choose to use this _javascript_ API, there are several choices as to 
how we could construct the API:
a) Provide an API which allows trace properties to be directly changed, e.g.
  var tc = new TraceController();
  tc.setTraceStyle(graphURI, traceURI, "invisible");
  tc.setTraceColour(graphURI, traceURI, "#ff00ff");

The problem with this approach is that _javascript_ code will often want 
to highlight variables, but if this is done through hiding traces and/or 
changing colours, code would have to keep track of what changes are 
made, and store enough information to be able to reverse the changes.

b) Use the above API style, but provide additional API functions to save 
all trace styles / colours on a graph and restore them again, by name. 
The only problem here is that the use might have changed something, and 
then their change will get reverted.
c) Make some sort of transactional system, where temporary changes can 
be made in transactions, and the transaction can be rolled back. The 
user will see changes, but if they modify the same variable, their 
change will be committed so will not be rolled back.

The problem with option c is that it is very complex both to implement 
and to learn how to use, which means it might end up never being used 
anyway.

d) Create a highly specialised API allowing the 'highlighted variable' 
to be set, such that only one highlighted variable can be set at a time. 
If the user changes the variable, it gets unhighlighted automatically. 
This is more similar to option 1.

Option 1 and 2d would probably the simplest to use, with there being a 
realistic possibility that option 1 could one day be edited in something 
other than a text editor. However, they do not give the same flexibility 
as the other options would.

I welcome any opinions on what approach would be best.

Best regards,
Andrew Miller

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Re: [cellml-discussion] fixed model - "A Model for Human Ventricular Tissue"

[Peter Hunter]

Hi James, 

I'm a bit puzzled - the link you have to version 4 is documented as
shown below - but this looks like a comment on version 1. All stars (on
my webpage anyway) are greyed out - should one be yellow? I think you
should ask Tommy to drop the number of stars back to one.

When I run that model it does run, but not for long enough. All of
these cardiac models should have default stimulus and time integration
parameters to run through about 5 cycles (just copy the stimulus code
& parameters in the Beeler-Reuter model which was set up by Andrew
and Tommy).

Cheers, 
Peter
Model Status
 This is the original unchecked version of the
model imported from the previous CellML model repository, 24-Jan-2006.
Update: Version 3 was fixed by James R. Lawson on 19/03/07. 

Previous version of model produced the following error message when run
in PCenv: "Error message = "Error: Two variables with incompatible
interfaces are connected: d and d"
Added an attribute of private_interface="in" to declaration of variable
"d" in component 'L_type_Ca_current"


Rationale: both the parent ("L_type_Ca_current") and encapsulated
("L_type_Ca_current_d_gate") components contained
public_interface="out", thus disallowing any connection between the two
components. To transfer "d" from encapsulated to parent component, an
attribute of private_interface="in" was required for the variable "d"
as defined in the parent component.




James Lawson wrote:

  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
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Re: [cellml-discussion] Switching between graphs in PCEnv: Opinions sought

[Peter Hunter]

Hi Andrew,

My preference is for Tabs but you could still keep the title bar – just 
use a shorter one (say half the width of the pane) and put the tabs 
after that.
It is important to be able to preserve the layout of windows and which 
traces are displayed so that you can get back quickly to a configuration 
you've set up. It also would allow us to create good default setups to 
suit particular models in the repository.


I’m still inclined to tab the whole RHS window (set of panes) - maybe as 
well as Tabs in individual panes? An example of where this would be 
useful is that when you have a combined electrophysiology and signal 
transduction model and want to display voltages, currents, etc v time in 
one window and the signal transduction pathways laid out in SVG in 
another window.


BTW, in the graphing window if you set time as x-variable then all other 
created traces for that pane should default to time (since it doesn’t 
make sense to display any other variable along a time axis).


Cheers,
Peter


Andrew Miller wrote:

Hi all,

PCEnv currently supports multiple graphs by using splitters - the user 
decides how much vertical space to assign to each graph by dragging the 
splitter with the mouse. Splitters will 'collapse' if they are brought 
close to a window boundary or another splitter. Collapsed splitters take 
up very little screen space. Initially, all but one of the graphs are 
collapsed.


This approach is good for comparing two graphs against each other, 
because both graphs are on the screen at the same time. However, it has 
several disadvantages:
1) There is a finite number of graphs available (currently 3). This 
number is set in advance by the layout designer, and not the end user.
2) The approach is difficult to use if you want only one graph visible 
on the screen, but want to switch between the graphs. In this case, you 
need to spend quite a bit of time collapsing one graph and expanding 
another to get the sizes you want.
3) Because the graphs are potentially displayed at the same time, they 
are each represented by distinct objects in Mozilla's XUL. This means 
that even hidden graphs impose a performance and memory overhead. This 
is not a big problem with only 3 graphs, but as more are added, it will 
become more serious.


It is worth keeping the splitter approach (although perhaps we could 
limit it down to 2 graphs, as graphs get very squashed by the time you 
have three on the screen at once. If you have an opinion on this issue, 
I would like to hear from you), but also adding in a method to switch 
the graph shown in each splitter pane.


There are two obvious ways of laying it out graphically:
1) Tabs
2) A 'combo-box', in which you select the graph to display, and can type 
in titles.


I personally prefer option 2, because the combo-box then doubles as the 
title of the graph.


Any opinions on which option to take (or suggestions of further 
options), as well as opinions on the details of how it should work from 
the user's perspective, would be welcome.


Best regards,
Andrew Miller


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