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Camille Laibe | 8 Feb 20:14
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21st release of BioModels Database

Dear colleagues,

We are pleased to announce the twenty-first release of BioModels 
Database (http://www.ebi.ac.uk/biomodels/).

Important changes are happening or announced in this message, so please 
read further.

In this release, 68 new models have been published and numerous existing 
models have been updated. The public version of BioModels Database now 
contains 409 models in the curated and 420 in the non-curated branch. 
Together, these 829 models comprise 130800 species, 151274 relationships 
(which include reactions, rate rules, events and assignment rules), and 
106210 cross-references.

Along with the data release, we would like to announce several important 
changes.

First of all, in addition to the SBML version of each model with 
annotations encoded with MIRIAM URNs, BioModels Database now provides a 
second SBML file with annotations encoded using Identifiers.org URLs. 
Those files can be accessed from the "Download SBML" menu displayed on 
the top left of any model page and from the models archives (now 
provided from the EBI FTP server).

BioModels Database will serve the URN form as the default until the next 
release of the database. Then the URL form will be provided as the 
default. The files with the URN annotations will still be available for 
a while. We encourage software developers to consider the 
Identifiers.org version of MIRIAM URIs for any new development.
(Continue reading)

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Lucian Smith | 2 Feb 19:17
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(forw) JSim 2.06 released

Some of you might be interested in this--JSim now has CellML output as 
well as CellML input.  Since JSim models themselves are not modular, 
everything gets put into a single component; there is hope that in the 
future when JSim itself is modular, it will be able to produce modular 
CellML output.  A few more details at 

http://physiome.org/jsim/docs/MML_CellML.html#exporting

-Lucian

----- Forwarded message from Erik Butterworth
<butterw@...> -----

From: Erik Butterworth <butterw@...>
Reply-To: Erik B <butterw <at> u.washington.edu>
To: JSim Development -- Adam Alessio <aalessio <at> u.washington.edu>,
        "Dr. James Caldwell" <jcald <at> u.washington.edu>,
        Forbes Dewey <cfdewey@...>, "Huhns, Michael" <huhns@...>,
        Melissa Krueger <krueger <at> u.washington.edu>,
        Max Neal <mneal <at> u.washington.edu>,
        David Nickerson <d.nickerson@...>,
        Bart Jardine <barthj <at> u.washington.edu>,
        Gary Raymond <garyr <at> u.washington.edu>,
        "Dr. James Bassingthwaighte" <jbb2 <at> u.washington.edu>,
        Lucian Smith <lpsmith <at> u.washington.edu>,
        Rebecca Rowe <rebikah17@...>, "Dash, Ranjan" <rdash@...>,
        Richard Ward <wardrc1@...>, Herb Sauro <hsauro <at> u.washington.edu>,
        Andreas Schwab <andreas.schwab@...>,
        Shiva Ayyadurai <vashiva@...>,
        Gary Ynvge <gyngve@...>,
(Continue reading)

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David Nickerson | 17 Jan 22:58
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Registration for the 2012 CellML Workshop is now open

Hi all,

Registration for the 2012 CellML Workshop is now open. Please see
http://www.cellml.org/community/events/workshop/2012 for information
on how to register. Registration for the workshop is free and remote
attendance at the workshop will be possible.

Cheers,
David.
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Daniele Gianni | 17 Jan 20:54
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COMETS 2012 - 3rd IEEE Track on Collaborative Modeling and Simulation - Call for Papers

(Please accept our apologies if you receive multiple copies of this message)

#################################################################
                       IEEE WETICE 2012
     3rd IEEE Track on Collaborative Modeling and Simulation
                        (Comets 2012)

                      in cooperation with
                  AFIS (INCOSE France Chapter)
               MIMOS (Italian Association for M&S)

                       CALL FOR PAPERS

#################################################################

June 25-27, 2012, Toulouse (France)
http://www.sel.uniroma2.it/comets12

#################################################################
# Papers Due: March 16, 2012
# Accepted papers will be published in the conference proceedings
# by the IEEE Computer Society Press and indexed by EI.
#################################################################

Modeling and Simulation (M&S) is increasingly becoming a central
activity in the design of new systems and in the analysis of
existing systems because it enables designers and researchers to
investigate systems behavior through virtual representations. For
this reason, M&S is gaining a primary role in many industrial and
research fields, such as space, critical infrastructures,
(Continue reading)

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David Nickerson | 7 Jan 05:41
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Fwd: [sbml-discuss] Draft Distrib Package Proposal

Possibly of interest to some...

---------- Forwarded message ----------
From: Stuart Moodie <moodie-jcUp+/l53Jxaa/9Udqfwiw@public.gmane.org>
Date: Sat, Jan 7, 2012 at 12:47 AM
Subject: [sbml-discuss] Draft Distrib Package Proposal
To: SBML Discussion List <sbml-discuss-7GExONQZ6ZKVc3sceRu5cw@public.gmane.org>


Dear All,

I have been pulling together the current thoughts on the distrib package into a draft proposal document. The document is heavily based on the outcome of discussions at the Statistical models workshop which took place in Hinxton on Jun 2011. You can get the document from here: http://sbml.org/images/1/11/Sbml-level-3-distrib-package-proposal.pdf.

For those of you who are unaware of it the distrib package or "Distributions and Ranges" to give it its full name provides:
"an extension to SBML Level 3 that supports models that supports variables that cab take many values, for instance random variables obtained from a statistical distribution. Applications of the package include for instance descriptions of the alternative values based on prior knowledge (e.g. experiments), encoding of uncertainty of value and mostly statistical model or models that require the use of random values, such as PK/PD models."

There is still a bit or work to do not least because some important issues remain unresolved (mainly because there has been little discussion about them). My hope is that this draft will instigate further discussion about distrib and will lead to the production of a final draft of the proposal in the coming weeks or months.

As with all the Level 3 package proposals, distrib has its own mailing list (sbml-distrib <at> lists.sourceforge.net) and I would urge you to sign up for it as this will be the main forum for discussion about the package specification. If you are unsure whether you are subscribed, then I posted an email to the list at 9:30 GMT today. It's stating the obvious, but if you didn't receive it then you are probably not subscribed.

Best wishes,

Stuart.
---------------------------------
Stuart Moodie
Biomodels Team
EMBL-EBI
Hinxton, UK
moodie-jcUp+/l53Jxaa/9Udqfwiw@public.gmane.org

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To manage your sbml-discuss list subscription, visit
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For questions or feedback about the sbml-discuss list,
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Poul Michael Fonss Nielsen | 20 Dec 21:09
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Re: Dear Professor Nielsen, this is Weiwei, a PhD student in Cornell University

Dear Weiwei Wang

Thanks for your email. CellML is an exchange format for describing lumped parameter models - those that
consist of systems of differential algebraic equations (DAEs). If your models of platelet aggregation
consist only of DAEs, and not partial differential equations, then CellML should be able to represent
them. CellML uses XML to structure the representation. This is primarily to facilitate computer
processing and is not intended to produce human readable representations of models. Although it is
possible to write CellML models directly using a text editor, it is not for the faint-hearted and
certainly not recommended for those unfamiliar with the language. Model editing applications, like
OpenCell or COR, are the preferred tools for creating, composing, and solving CellML models. The res
 ulting CellML files can then be exchanged directly with collaborators and/or uploaded to the model
repository to be read in by CellML-aware applications. If you have further questions, it is recommended
that you direct them to the CellML Discussion List <cellml-discussion@...>.

Best wishes
Poul

On 2011-12-21, at 08:09, Weiwei Wang wrote:

> Dear Professor Nielsen,
> 
> I am currently a PhD student working on computational simulation of platelets aggregation in Cornell
University, USA. All my computation work is written in Fortran, but I want to share the modules with other
researchers. CellML seems is a good platform. However, I have no experience in XML programming. 
> 
> Cruising throught the CellML website, I am kind of confused about the general method. I downloaded the
OpenCell software and I learned the tutorials about modeling under OpenCell. I think I can transfer my
fortran code manually into OpenCell. However, when I tried to download those sample models, I got pages of
XML scripts which I cannot understand at all. 
> 
> So if I want to share my model on the CellML platform, do I just make models in OpenCell? What do I have to do
with those XML scripts?
> 
> Thanks a lot,
> -- 
> Weiwei Wang
> 3rd year PhD student in BioMedical Engineering
> 203 Weill Hall, Cornell University, Ithaca, NY, 14850
> 626-348-9786
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David Nickerson | 20 Dec 02:57
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Summary of the inaugural CellML Editorial Board meeting

The CellML Editorial Board (consisting of Jonathan Cooper, Edmund Crampin, Alan Garny, David “Andre” Nickerson and Poul Nielsen) had their inaugural meeting on the 8th of December 2011. All members of the board were present.

David Nickerson was unanimously elected chairman of the editorial board. At this meeting we discussed the purpose of the CellML editorial board and all agreed that while there is certainly a role in the guardianship of the CellML specifications, we are also responsible for growing the CellML community. To this end, we agreed that it is best to focus immediate efforts on identifying any barriers preventing adoption of CellML. As such, the editorial board is embarking on a review of the CellML API and the CellML model repository in order to identify any existing issues and to provide guidance for future development of these projects. Establishing the process by which the CellML specifications will develop was deferred to the next meeting of the editorial board.

The CellML Editorial Board aim to meet monthly with the next meeting currently scheduled for the 12th of January 2012.



Cheers,
The CellML Editors.
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David Nickerson | 19 Dec 20:35
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Improved CellML support in latest version of JSim

Hi all,

JSim 2.05 has just been released and now has improved support for CellML models. See the release announcement below.


Cheers,
Andre.



Highlights:

o JSim now uses Java 6 rather than Java 5,  resulting in various minor improvements.  If you're running JSim applets in your browser,  but sure to update your Java to version 6.

o JSim's CellML importer has been substantially improved (thanks to LS).
JSim now runs 95% of the CellML 1.0 models in the CellML archive out of box (no editing required).

o Parameter set functionality has been substantially improved, including the addition of loops, sensitivity and optimization configuration to parameter sets.

o Various minor fixes and feature improvements.

See the JSim home page for complete information on JSim, including documentation, downloads, documentation and model repositories:

http://physiome.org/jsim/

For complete details on the latest release, click on "What's New?"
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David Nickerson | 19 Dec 12:48
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Announcing the 2012 CellML Workshop

Hi all,

On behalf of the Auckland Bioengineering Institute and the CellML
Editorial Board, I am pleased to announce that the 2012 CellML
Workshop (http://www.cellml.org/community/events/workshop/2012/) will
be held March 12 & 13 2012 at Goldwater Estate, the University of
Auckland vineyard on Waiheke Island. Please save the date and stay
tuned for further updates.

Cheers,
David.
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Lucian Smith | 16 Dec 19:53
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Independent variables, and delay

A couple questions.  One:  is there a defined way in CellML to find the 
independent variables?  The spec says (about 'initial_value'):

  This attribute provides a convenient means for specifying the value of a 
  scalar real variable when all independent variables in the model have a 
  value of 0.0. Independent variables are those whose values do not depend 
  on others. 

>From that definition, it would seem that if you defined 'pi' in your 
model, the initial value would apply when pi was equal to 0.

But more generally, if you have a single equation in your model:  

u = sin(t)

That's a single equation with two variables--how do you decide that you 
want to vary t and not u?  Do you just apply heuristics, so if you see 
'dx/dy' you assume y is the independent variable?  Is it part of what you 
do *with* a CellML model, that you present the user with t and u as 
possible options, and they pick one?

My second question is a bit simpler:  is there a way to define a delay 
equation in CellML and if so, how do you do it?  (A delay being 
something like 'x, 2 seconds ago'.)

-Lucian
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Randall Britten | 13 Dec 05:29
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Cancelled: 14 and 21 December Auckland meetings about CellML API and Specification

Hi all

 

The weekly above meeting for 14 December and 21 December will be cancelled, due to conflicts with other ABI events.

 

Regards,

Randall

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