From heiland at indiana.edu  Mon Feb  2 15:06:14 2009
From: heiland at indiana.edu (Randy Heiland)
Date: Sun, 1 Feb 2009 21:06:14 -0500
Subject: [cellml-discussion] CellML & OWL
References: <mailman.34.1220701835.4225.cellml-discussion@cellml.org>
Message-ID: <FACBD5C8-58CE-4927-A7F1-E5D991F82212@indiana.edu>

Hi Sarala,

Since it's been awhile, thought I'd inquire about the status of this  
work and if you might have any draft papers, etc, you'd be willing to  
share yet?

thanks, Randy

Begin forwarded message:

>
> Message: 1
> Date: Sat, 6 Sep 2008 07:50:11 -0400
> From: Randy Heiland <heiland at indiana.edu>
> Subject: [cellml-discussion] CellML OWL work in progress
> To: sarala.dissanayake at auckland.ac.nz
> Cc: cellml-discussion at cellml.org
> Message-ID: <8DDDAA42-0C3C-4B4D-AFC5-DAEF007DFEAB at indiana.edu>
> Content-Type: text/plain; charset="us-ascii"; Format="flowed"
>
> Thanks for the reply, Sarala.  I/we look forward to your drafts.
>
> best, Randy
>
> Begin forwarded message:
>
>> From: cellml-discussion-request at cellml.org
>> Date: September 4, 2008 8:00:01 PM EDT
>> To: cellml-discussion at cellml.org
>> Subject: cellml-discussion Digest, Vol 50, Issue 4
>> Reply-To: cellml-discussion at cellml.org
>>
>> Send cellml-discussion mailing list submissions to
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>> Today's Topics:
>>
>>  1. CellML OWL work in progress (Sarala Dissanayake)
>>
>>
>> ----------------------------------------------------------------------
>>
>> Message: 1
>> Date: Thu, 04 Sep 2008 20:32:33 +1200
>> From: Sarala Dissanayake <sarala.dissanayake at auckland.ac.nz>
>> Subject: [cellml-discussion] CellML OWL work in progress
>> To: CellML Discussion List <cellml-discussion at cellml.org>
>> Message-ID:
>> 	<20080904203233.ui1ruzjkoc4oc00s at webmail.bioeng.auckland.ac.nz>
>> Content-Type: text/plain;	charset=ISO-8859-1;	DelSp="Yes";
>> 	format="flowed"
>>
>> Hi Randy and Ely,
>>
>> I'm developing a framework for annotating and visualizing CellML
>> models. A solution has been developed that involves:
>> - an ontology for storing CellML models in OWL format (CellMLOWL) and
>> a set of rules for binding these CellMLOWL instances to CellML  
>> models.
>> - an ontology which represents biophysical and biological concepts
>> that are covered in CellML models (CellMLBio) and a set of rules for
>> binding these concepts to CellMLOWL models;
>> - a specification for building visual templates that support a visual
>> language that can be used to represent all biophysical and biological
>> processes covered in CellMLBio ontology and the rules for binding the
>> visual language to concepts within the CellMLBio ontology;
>> - a visual editing tool, that combines the visual language and
>> ontologies to visualize CellML models.
>>
>> I'm currently writing up my thesis and 3 papers. I should be able to
>> make these available to you in draft form soon.
>>
>> Cheers,
>> Sarala
>>
>> ----------------------------------------------------------------
>> This message was sent using IMP, the Internet Messaging Program.
>>
>>
>>
>> ------------------------------
>>
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From c.lloyd at auckland.ac.nz  Wed Feb  4 13:57:49 2009
From: c.lloyd at auckland.ac.nz (Catherine Lloyd)
Date: Wed, 4 Feb 2009 13:57:49 +1300
Subject: [cellml-discussion] CellML model translation requests
Message-ID: <57D6641E-EB92-44DF-9CF6-DEDEEF6EAFC8@auckland.ac.nz>

Dear All

As one of the main curators of the CellML Model Repository, I would  
like to approach you - the community - to ask you if there are any  
models, in particular, which you would like to see translated into  
CellML.  I would rather translate models that have been requested by  
the "experts" rather than the alternative, which is for me randomly  
choose models of my own accord from the literature!

Depending on what kind of a response I get, there will be a system for  
assigning priority to the requests.  Priority will be given to papers  
which are pre-publication, especially where the journal has asked that  
the model code be made available online at the time of going to  
press.  Model completeness is also a consideration, and if authors are  
willing to share their original code this will be in the model's  
favour as this makes the translation process much smoother.

In the future we intend to have a "request for model submission" form  
as part of the new repository (PMR2).  But until this happens the best  
way to get your model translated into CellML and loaded into the  
repository is to email me.

I look forward to hearing from some (many?!) of you.

Best wishes
Catherine








From d.cumin at auckland.ac.nz  Wed Feb  4 14:04:21 2009
From: d.cumin at auckland.ac.nz (David Cumin)
Date: Wed, 4 Feb 2009 14:04:21 +1300
Subject: [cellml-discussion] CellML model translation requests
In-Reply-To: <57D6641E-EB92-44DF-9CF6-DEDEEF6EAFC8@auckland.ac.nz>
References: <57D6641E-EB92-44DF-9CF6-DEDEEF6EAFC8@auckland.ac.nz>
Message-ID: <005f01c98664$833f5ff0$89be1fd0$@cumin@auckland.ac.nz>

This would be great! :) 

Particularly the baroreceptor model.



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 Catherine Lloyd
->Sent: Wednesday, 4 February 2009 1:58 p.m.
->To: CellML Discussion List
->Subject: [cellml-discussion] CellML model translation requests
->
->Dear All
->
->As one of the main curators of the CellML Model Repository, I would
->like to approach you - the community - to ask you if there are any
->models, in particular, which you would like to see translated into
->CellML.  I would rather translate models that have been requested by
->the "experts" rather than the alternative, which is for me randomly
->choose models of my own accord from the literature!
->
->Depending on what kind of a response I get, there will be a system for
->assigning priority to the requests.  Priority will be given to papers
->which are pre-publication, especially where the journal has asked that
->the model code be made available online at the time of going to
->press.  Model completeness is also a consideration, and if authors are
->willing to share their original code this will be in the model's
->favour as this makes the translation process much smoother.
->
->In the future we intend to have a "request for model submission" form
->as part of the new repository (PMR2).  But until this happens the best
->way to get your model translated into CellML and loaded into the
->repository is to email me.
->
->I look forward to hearing from some (many?!) of you.
->
->Best wishes
->Catherine
->
->
->
->
->
->
->
->_______________________________________________
->cellml-discussion mailing list
->cellml-discussion at cellml.org
->http://www.cellml.org/mailman/listinfo/cellml-discussion
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From dj.cowan at auckland.ac.nz  Mon Feb  9 08:09:47 2009
From: dj.cowan at auckland.ac.nz (Dougal Cowan)
Date: Mon, 09 Feb 2009 08:09:47 +1300
Subject: [cellml-discussion] Meeting minutes 2009-02-04
Message-ID: <498F2DFB.4080701@auckland.ac.nz>

The minutes for last week's meeting are up at:

http://www.cellml.org/meeting_minutes/abi-meeting-minutes-2009-02-04/

Dougal

From dj.cowan at auckland.ac.nz  Mon Feb 16 09:40:49 2009
From: dj.cowan at auckland.ac.nz (Dougal Cowan)
Date: Mon, 16 Feb 2009 09:40:49 +1300
Subject: [cellml-discussion] Meeting minutes 2009-02-11
Message-ID: <49987DD1.3030404@auckland.ac.nz>

The minutes for last week's meeting are up at:

http://www.cellml.org/meeting_minutes/abi-meeting-minutes-2009-02-11

Dougal

From ak.miller at auckland.ac.nz  Wed Feb 18 13:59:15 2009
From: ak.miller at auckland.ac.nz (Andrew Miller)
Date: Wed, 18 Feb 2009 13:59:15 +1300
Subject: [cellml-discussion] Example models using possible CellML 1.2 lambda
 calculus type system notation
Message-ID: <499B5D63.4050505@auckland.ac.nz>

Hi all,

In response to a request by Poul Nielsen, I have produced a model 
demonstrating how this functionality might be used.

type_library.cellml is the beginnings of a type library, which provides 
a complex number type and some other types needed to support it. The 
complex number type is actually a function which takes a 'base type' and 
returns a type. For example, if you wanted to represent a 'vector' in a 
plane in metres as a complex number, you can call the function which 
returns a type with real_metres as the argument to get a type for 
storing a number of metres. This form implicitly requires that both 
cartesian co-ordinates have the same type.

Also included is a library of utilities for working with these complex 
numbers to get the cartesian and polar co-ordinates.

Writing this up has identified several places where there is room for 
improvement:
  => We require that the type attribute is present on variables in every 
component it is used (not just one of them), and these types are also 
variables which must be present everywhere. If types are all of type 
type, this isn't as bad, because it means that we only require one extra 
variable. However, if we only required that the type attribute was 
present in one of the connected network of variables (but allowed it to 
be present in more as long as the types match) we would reduce the 
burden on model authors.
  => Wildcard types, or even some sort of type inheritance scheme once 
more looks quite helpful. For example, we have a function called 'sign' 
which returns 1, 0, or -1 depending on the sign of the input. But we 
have to explicitly say what the type of the input is (not just 'any kind 
of real number' for instance). There will be many similar cases. 
Sometimes this is a good thing as it provides additional type safety, 
but in other cases, it is bad. We could have a unidirectional concept of 
compatibility as used in inheritance hierarchies (so for example, 
real_metre matches real_anything, but real_anything doesn't match 
real_metre, since real_metre inherits from real_anything). This can be 
worked around by using functions which return types, or by using the 
trick we used in type_utilities of having a variable you connect up to 
correct type, but the cost of having one import or defining a type just 
to call a basic function puts a lot of burden on model authors and makes 
models rather verbose.

Best wishes,
Andrew

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From dj.cowan at auckland.ac.nz  Fri Feb 20 14:40:41 2009
From: dj.cowan at auckland.ac.nz (Dougal Cowan)
Date: Fri, 20 Feb 2009 14:40:41 +1300
Subject: [cellml-discussion] ABI Meeting minutes 2009-02-18
Message-ID: <499E0A19.2080305@auckland.ac.nz>

I have put the minutes for this wednesday's meeting up at:

http://www.cellml.org/meeting_minutes/abi-meeting-minutes-2009-02-18

Thanks
Dougal


From ak.miller at auckland.ac.nz  Wed Feb 25 11:49:52 2009
From: ak.miller at auckland.ac.nz (Andrew Miller)
Date: Wed, 25 Feb 2009 11:49:52 +1300
Subject: [cellml-discussion] CellML 1.2 examples now with succinct infix
 notation comments of math
Message-ID: <49A47990.8040305@auckland.ac.nz>

Hi all,

Based on feedback I received today, I have now created versions of my 
examples of what CellML 1.2 might look like with embedded comments 
describing the MathML in a more succinct infix notation format (included 
in comments in the XML above the corresponding MathML). This should make 
them more readable and make it easier to comment on.

Best wishes,
Andrew
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From j.marsh at auckland.ac.nz  Wed Feb 25 18:28:15 2009
From: j.marsh at auckland.ac.nz (Justin Marsh)
Date: Wed, 25 Feb 2009 18:28:15 +1300
Subject: [cellml-discussion] CellML DOM API 1.6rc1 (release candidate for
 CellML DOM API 1.6) out
Message-ID: <49A4D6EF.7070008@auckland.ac.nz>

Hi all,

The first release candidate for the CellML DOM API, version 1.6, has 
been released. Information about the released files is available at:
http://www.cellml.org/downloads/cellml_api/releases/1.6rc1/

A release candidate will become a release one week from announcement on 
this list if there are no problems identified with it.

Please report any bugs you find at https://tracker.physiomeproject.org/,
or to this list, or directly to j.marsh at auckland.ac.nz

Best regards,
Justin Marsh.

From j.marsh at auckland.ac.nz  Wed Feb 25 19:05:28 2009
From: j.marsh at auckland.ac.nz (Justin Marsh)
Date: Wed, 25 Feb 2009 19:05:28 +1300
Subject: [cellml-discussion] Announcement of PCEnv 0.6rc1 (release
	candidate	for PCEnv 0.6)
Message-ID: <49A4DFA8.9010200@auckland.ac.nz>

Hi all,

The first release candidate for PCEnv version 0.6 has been released.
This is the first version of PCEnv since 0.1 that can run on OS X; there 
are also a number of other improvements since PCEnv 0.5.
More information, and the released files themselves, are available at 
http://www.cellml.org/downloads/pcenv/releases/0.6rc1

A release candidate will become a release one week from announcement on 
this list if there are no problems identified with it.

Please report any bugs you find at https://tracker.physiomeproject.org/,
or to this list, or directly to j.marsh at auckland.ac.nz

Best regards,
Justin Marsh.



From alan.garny at dpag.ox.ac.uk  Wed Feb 25 22:23:01 2009
From: alan.garny at dpag.ox.ac.uk (Alan Garny)
Date: Wed, 25 Feb 2009 09:23:01 -0000
Subject: [cellml-discussion] Announcement of PCEnv 0.6rc1
	(release	candidate	for PCEnv 0.6)
In-Reply-To: <49A4DFA8.9010200@auckland.ac.nz>
References: <49A4DFA8.9010200@auckland.ac.nz>
Message-ID: <000901c9972a$a80b4020$f821c060$@garny@dpag.ox.ac.uk>

Hi Justin,

> The first release candidate for PCEnv version 0.6 has been released.
> This is the first version of PCEnv since 0.1 that can run on OS X;
> there
> are also a number of other improvements since PCEnv 0.5.
> More information, and the released files themselves, are available at
> http://www.cellml.org/downloads/pcenv/releases/0.6rc1
> 
> A release candidate will become a release one week from announcement on
> this list if there are no problems identified with it.

Don't you think that ONE week (?!) might be a bit short? I mean that one of
the biggest changes in PCEnv is that it now works under OS X. So, I would
expect people wanting to test it under that operating system to need a bit
more than one week. Even for those who use Windows and/or Linux in fact...

Alan