gmane.text.xml.cellml.general

HARMONY 2012 communication

Nicolas Le Novère — 2012-05-18T09:41:43

Dear COMBINE community,

HARMONY 2012 starts in a few days. The main point of information is the 
webpage:
http://co.mbine.org/events/HARMONY_2012

A Google+ page is also available.
https://plus.google.com/118242948876683323405

The official twitter hashtag is #harmony2012
https://twitter.com/#!/search/%23harmony2012

The program is being designed and will evolve through a Google doc. More later.

As usual the presentations, video recording, and any material available 
will be made up available through the webpage.

I am looking forward to this second HARMONY

trouble building on Ubuntu: for opencell build, told to build CellML API with XPCOM, but CellML API does not CMake with XPCOM support

Audette, Michel A. — 2012-05-09T04:43:36

Dear CellML users, 

I have a recent version of Ubuntu, and when I try to build opencell, configure tells me 

configure: error: The CellML API directory /usr/local did not contain interfaces/ICIS.xpt. Give the path to the CellML API with --with-cellml_api=/path/to/cellml_api. Ensure you built the API with XPCOM, Context, CCGS, CIS and CeLEDS support.

When I download the source tarball of cellml-api-1.10 or 1.11, in either case, when I set XPCOM support to ON with CMake, I get 

CMake Error at build/xpcom.cmake:1 (MESSAGE):
   XPCOM support needs to be ported to cmake; please do this and submit a
   patch if you want to use it!

How can I simply get through the two builds? 

Thanks for your kind support.

Best wishes,

Michel Audette, Ph.D. 
Assistant Professor,
Department of Modeling, Simulation and Visualization Engineering,
Old Dominion University,
Norfolk, VA.

CellML API version 1.11 has been released

Andrew Miller — 2012-05-02T00:53:07

Hi all,

The CellML API release candidate version 1.11rc2 has been released 
unmodified as CellML API version 1.11. It can be downloaded from 
http://www.cellml.org/tools/downloads/cellml_api/releases/1.11

CellML API version 1.11 fixes a number of bugs in the CellML API version 
1.10, including some affecting code generation. It adds a new service, 
the CellML Generics and Reflection Service, and features improved 
documentation.  The C++ interface has changed to allow more idiomatic 
STL-based C++ code to be written. Python support has been separated out 
into a separate package that provides more convenient, more idiomatic 
Python support.

Please report any issues you find with the CellML API version 1.11, or 
direct any requests for support, to the Physiome tracker at 
https://tracker.physiomeproject.org/, to 
cellml-tools-developers-+N4dcC6UsuQdnm+yROfE0A< at >public.gmane.org, or directly to ak.miller-1/NbpDiVQt7jvIOssrGNKg< at >public.gmane.org

Best wishes,
Andrew Miller

Server maintenance

Tommy Yu — 2012-04-27T02:54:55

Hi,

There will be a brief outage following a software upgrade for the CellML website (www.cellml.org) and the model repository (models.cellml.org).  The outage is to be occur on 2012-04-29 between the hours of 18:30-20:00 UTC (or Monday morning 7:30am to 9:00am for the people in Auckland).  The length of the outage on each of the server is expected to last no longer than a few minutes.

As according to ITS, this one should actually happen as final approval have been granted; the maintenance windows previous announced was never used.

Regards,
Tommy.

Announcing CellML API 1.11 release candidate 2

Andrew Miller — 2012-04-18T03:24:58

Hi all,

The second release candidate for the CellML API 1.11 (1.11-rc2) has been 
released. This release candidate will become the CellML API 1.11 if 
no-one reports any problems with it by next Wednesday (New Zealand 
time). Please try out the the API and report any problems on the 
Physiome Tracker at https://tracker.physiomeproject.org/, by e-mailing 
cellml-tools-developers-+N4dcC6UsuQdnm+yROfE0A< at >public.gmane.org (you will need to subscribe to the 
list first using this page: 
http://lists.cellml.org/mailman/listinfo/cellml-tools-developers), or by 
e-mailing ak.miller-1/NbpDiVQt7jvIOssrGNKg< at >public.gmane.org

The files making up this release candidate are available here:
   * http://www.cellml.org/tools/downloads/cellml_api/releases/1.11rc2

This release candidate fixes a few bugs found since the last release 
candidate - thanks to those who reported these bugs.

Additionally, it includes an extra build target on Windows - a Visual 
C++ build linked against MSVCRTD (the Debug CRT), suitable for use with 
code that is linked against the Visual C++ Debug CRT. The build target 
linked against the Visual C++ release CRT will continue to be included.

Best wishes,
Andrew

Announcing CellML API 1.11 release candidate 1

Andrew Miller — 2012-04-11T03:49:57

Hi all,

The first release candidate for the CellML API 1.11 (1.11-rc1) has been
released. This release candidate will become the CellML API 1.10 if
no-one reports any problems with it by next Wednesday (New Zealand
time). Please try out the the API and report any problems on the
Physiome Tracker at https://tracker.physiomeproject.org/, by e-mailing
cellml-tools-developers-+N4dcC6UsuQdnm+yROfE0A< at >public.gmane.org (you will need to subscribe to the
list first using this page:
http://lists.cellml.org/mailman/listinfo/cellml-tools-developers), or by
e-mailing ak.miller-1/NbpDiVQt7jvIOssrGNKg< at >public.gmane.org

The files making up this release candidate are available here:
* http://www.cellml.org/tools/downloads/cellml_api/releases/1.11rc1

New features and bugfixes:
* The CellML Generics and Reflection Service lets you write code that
can access the list of available API services, operations, and
attributes. This can be used to write generic code that works over the
entire API without needing to hard-code the details of the part of the
API being called. This has application for creating certain types of
user interfaces, as well as for creating language bindings.
* The Python bindings have been re-written and are now shipped as a
Python egg, separately from the CellML API itself. The new Python
bindings use the Generics & Reflection service to provide a more
idiomatic and more convenient interface to the CellML API from Python.
* A number of bugfixes have been made, including bugfixes to the code
generation which could have resulted in bad numerical results.
* The C++ interface has been revised to be more idiomatic - strings
are now returned using the STL std::string and std::wstring types, and
sequences are returned as std::vector types. Objects are returned using
the already_AddRefd wrapper so users no longer need to use the
RETURN_INTO_OBJREF macro to manage reference counts easily, instead they
can simply assign into an ObjRef. The RETURN_INTO_OBJREF macros remain
available for legacy code.

Best wishes,
Andrew

Open PhD student position in Rostock, Germany

David Nickerson — 2012-03-29T20:37:25

*Doctoral candidate position (PhD student) in Systems Biology/Database and
Information Systems*

Closing date: 1st of May, 2012

Junior research group „Simulation Experiment Management System“ (SEMS) at
the University of Rostock (Germany), Systems Biology and Bioinformatics
group of Prof. Olaf Wolkenhauer. 3yrs full position (TV-L E13), starting
from June 2012.

Area: Systems Biology, Database and Information Systems

The successful applicant for a PhD position will investigate* methods and
techniques for model version control*. Models are here regarded as XML
encodings of computational models of biological systems, annotated with RDF
meta-data. Today, version changes on these models are not sufficiently
stored, maintained, curated, classified and presented to the users of model
databases. This project will enable model version control to ensure
improved reusability of models in the computational biology field.
Knowing of XML and database management systems as well as having a strong
interest in systems biology are prerequisites for this position. Being an
open person, willing to work in a multi-disciplinary field and enjoying to
discuss ideas with collaborators.... our group will be the perfect
environment


You will find the full job announcement at:
http://www.sbi.uni-rostock.de/jobs/description/13/


Please forward.
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Tutorial model

Neubauer, Andreas — 2012-03-29T12:48:12

Hello,

I tried to build the tutorial model from:

http://www.cellml.org/getting-started/tutorials/opencell-model-building-tutorial

Unfortunately, I get the following messages:

Error: Model is unsuitably constrained (i.e. there were still some variables left to be computed, and some unusable equations left over).
At the time of the error, the following variables were found:
 * Defined: time in component environment
 * Defined: A in component flux
 * Defined: B in component flux
 * Defined: C in component flux

The validation shows no errors and I can't find any differences to the model described on the web. Can you please help me?

Thanks!



Dipl.-Phys. Andreas Neubauer
Computerunterstützte Klinische Medizin
Medizinische Fakultät Mannheim
Universität Heidelberg
Theodor-Kutzer-Ufer 1-3
D-68167 Mannheim

Tel: +49 (0)621 383 5126
E-mail: Andreas.Neubauer-V3WxcplCr2pwSm+/Ar+cQmx2QJW9WDlq< at >public.gmane.org<mailto:Andreas.Neubauer< at >MedMa.Uni-Heidelberg.de>
Web: http://www.ma.uni-heidelberg.de/inst/cbtm/ckm/



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Upcoming server maintenance on www.cellml.organd models.cellml.org.

Tommy Yu — 2012-03-22T23:06:17

Hi,

There will be a brief outage following a software upgrade for the CellML website (www.cellml.org) and the model repository (models.cellml.org).  The outage is to be occur on 2012-03-25 between the hours of 18:30-20:00 UTC (or Monday morning 7:30am to 9:00am for the people in Auckland).  The length of the outage on each of the server is expected to last no longer than a few minutes.

Regards,
Tommy.

CellML Model Repository upgraded to PMR2 v0.5

Tommy Yu — 2012-02-14T22:10:16

Hi,

The CellML model repository underwent a software upgrade and is now running PMR2 v0.5.  If you encountered any issues with this update please file a tracker item that blocks the following tracker item:

https://tracker.physiomeproject.org/show_bug.cgi?id=3211

New features that were added for this release includes more CellML specific searching (for models.cellml.org) and updated the CellML API to version 1.11.  Some internal code changes were made also to support some future features.

Regards,
Tommy.

21st release of BioModels Database

Camille Laibe — 2012-02-08T19:14:51

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.


Moreover, after consultation with BioModels Database's Scientific 
Advisory Board and to be more in agreement with the EBI terms of use, it 
was decided that from the next release, the BioModels.net Team will 
abandon its copyright on the encoded form of the models and release them 
in the public domain.


Finally various improvements were made to the underlying software 
infrastructure. The main publicly visible change is the fact that a bug, 
dealing with the handling of annotations in the non-curated branch, has 
been discovered and subsequently fixed. This results in an major 
increase in the number of annotations from models in the non-curated 
branch. However, we would like to emphasise that those annotations were 
provided during submission and are not checked by our curators.

For more information about this release, please refer to the release notes:
http://www.ebi.ac.uk/biomodels-main/static-pages.do?page=release_20120208


We would like to thank all our collaborators, founders and submitters. 
We also want to thank the SBML community for their support and the tools 
they develop and provide.

BioModels Database is the result of numerous current and past 
collaborations and has received funding from multiple sources. Please 
refer to our acknowledgements page for up-to-date details: 
http://www.ebi.ac.uk/biomodels-main/acknowledgements

Camille Laibe
on behalf of the BioModels.net team.

(forw) JSim 2.06 released

Lucian Smith — 2012-02-02T18:17:14

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-qLvuPTP23hPW8SybPu4tS7K6bRJNSFrb< at >public.gmane.org> -----

From: Erik Butterworth <butterw-qLvuPTP23hPW8SybPu4tS7K6bRJNSFrb< at >public.gmane.org>
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-3s7WtUTddSA< at >public.gmane.org>, "Huhns, Michael" <huhns-g1XBJVYGBE6Vc3sceRu5cw< at >public.gmane.org>,
        Melissa Krueger <krueger< at >u.washington.edu>,
        Max Neal <mneal< at >u.washington.edu>,
        David Nickerson <d.nickerson-1/NbpDiVQt6SYBAHRPvY1A< at >public.gmane.org>,
        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-Re5JQEeQqe8AvxtiuMwx3w< at >public.gmane.org>, "Dash, Ranjan" <rdash-gYfhEnJJ71g< at >public.gmane.org>,
        Richard Ward <wardrc1-1Heg1YXhbW8< at >public.gmane.org>, Herb Sauro <hsauro< at >u.washington.edu>,
        Andreas Schwab <andreas.schwab-DsQM18LqTu1UaViMSvqUEg< at >public.gmane.org>,
        Shiva Ayyadurai <vashiva-DPNOqEs/LNQ< at >public.gmane.org>,
        Gary Ynvge <gyngve-GmWTxIRN22iJaUV4rX00uodd74u8MsAO< at >public.gmane.org>,
        Adam Alessio <aalessio< at >u.washington.edu>
Subject: JSim 2.06 released
Date: Thu, 2 Feb 2012 10:01:48 -0800 (PST)
Message-ID: <Pine.LNX.4.64.1202020955210.4336-t/SwAM/BdqT1P/v8h3QXrO0m/0PqwlaelXN7HHkbuXM< at >public.gmane.org>

  Highlights:

  o  new Monte-Carlo analysis module;

  o  CellML output is now available;

  o  various bug fixes,  including one in SBML import which previously
mishandled time-varying compartment volumes.

  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?"

  Note to QPP users:  JSim 2.06 should not be used with the previous
QPP release (0.913).  A new QPP release, 0.914, will be made later today
that is compatible with JSim 2.06.

Erik Butterworth    butterw-lfcS8c3Mqgg< at >public.gmane.org    206-685-2007
Software Engineer, University of Washington Bioengineering
http://physiome.org/~butterw/

----- End forwarded message -----

Registration for the 2012 CellML Workshop isnow open

David Nickerson — 2012-01-17T21:58:48

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.

COMETS 2012 - 3rd IEEE Track on Collaborative Modeling and Simulation - Call for Papers

Daniele Gianni — 2012-01-17T19:54:40

(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,
manufacturing, emergency management, biomedical systems and
sustainable future. However, as the complexity of the
investigated systems increases and the types of investigations
widens, the cost of M&S activities increases for the more
complex models and for the communications among a wider number and
variety of M&S stakeholders (e.g., sub-domain experts, simulator
users, simulator engineers, and final system users). To address
the increasing costs of M&S activities, collaborative
technologies must be introduced to support these activities by
fostering the sharing and reuse of models, by facilitating the
communications among M&S stakeholders, and more generally by
integrating processes, tools and platforms.

Aside from seeking applications of collaborative technologies to
M&S activities, the track seeks innovative contributions that
deal with the application of M&S practices to the design of
collaborative environments. These environments are continuously
becoming more complex, and therefore their design requires
systematic approaches to meet the required quality of
collaboration. This is important for two reasons: to reduce
rework activities on the actual collaborative environment, and to
maximize the productivity and the quality of the process the
collaborative environment supports. M&S offers the methodologies
and tools for such investigations and therefore it can be used to
improve the quality of collaborative environments.

A non–exhaustive list of topics of interest includes:

* collaborative environments for M&S
* collaborative Systems of Systems M&S
* workflow modelling for collaborative environments and processes
* agent-based M&S
* collaborative distributed simulation
* collaborative component-based M&S
* net-centric M&S
* web-based M&S
* model sharing and reuse
* model building and evaluation
* modeling and simulation of business processes
* modeling for collaboration
* simulation-based performance evaluation of collaborative networks
* model-driven simulation engineering
* domain specific languages for the simulation of collaborative environments
* domain specific languages for collaborative M&S
* databases and repositories for M&S
* distributed virtual environments
* virtual research environment for M&S
* collaborative DEVS M&S

To stimulate creativity, however, the track maintains a wider
scope and invites interested researchers to present contributions
that offer original perspectives on collaboration and M&S.

+++++++++++++++++++++++++++++++++++
On-Line Submissions and Publication
+++++++++++++++++++++++++++++++++++

CoMetS'12 intends to bring together researchers and practitioners
to discuss key issues, approaches, open problems, innovative
applications and trends in the track research area.

This year, we will accept submissions in two forms:

(1) papers
(2) poster and industrial presentations

(1) Papers should contain original contributions not published or
submitted elsewhere. Papers up to six pages (including figures,
tables and references) can be submitted. Papers should follow the
IEEE format, which is single spaced, two columns, 10 pt
Times/Roman font. All submissions should be electronic (in PDF)
and will be peer-reviewed by at least three program committee
members.

Accepted full papers will be included in the proceedings and
published by the IEEE Computer Society Press (IEEE approval pending).
Please note that at least one author for each accepted paper should
register to attend WETICE 2012 (http://www.wetice.org) to have the
paper published in the proceedings.

(2) Posters should describe a practical, on-the-field, experience in
any domain area using collaborative M&S. The poster submission
requires the submission of an abstract for evaluation from the
organizers. Accepted abstract must be followed by the submission of
a poster which will be displayed at conference time.
With the poster submission, a short (15 minutes) slot might be
allocated for oral presentation illustrating the industrial case.
The presentation may also include a live demo, but it should not
include commercial details.

Interested authors and participants may contact the organizers for
expression of interests and content appropriateness at any time.

Papers and posters can be submitted in PDF format at the submission
site (https://www.easychair.org/conferences/?conf=comets2012),
which is supported by the EasyChair conference management system.
Please feel free to contact the track chairs (comets2012-bC77Qfv0vuxrovVCs/uTlw< at >public.gmane.org)
if you experience problems with the EasyChair Web site.

+++++++++++++++
Important Dates
+++++++++++++++

* Submission Deadline: March 16, 2012
* Decision to paper authors: April 16, 2012
* Camera Ready to IEEE: April 30, 2012
* Conference dates: June 25 - June 27, 2012


++++++++++++++++++++
Organizing Committee
++++++++++++++++++++

* Andrea D'Ambrogio, University of Roma TorVergata, Italy
* Daniele Gianni, European Space Agency, The Netherlands
* Joachim Fuchs, European Space Agency, The Netherlands
* Giuseppe Iazeolla, University of Roma TorVergata, Italy

+++++++++++++++++
Program Committee
+++++++++++++++++

* Santiago Balestrini, Georgia Institute of Technology, USA
* Massimo Bandecchi, European Space Agency, The Netherlands
* Joseph Giampapa, SEI, Carnegie Mellon University, USA
* Alain Kerbrat, CollESys - AFIS, France
* Axel Lehmann, Universitaet der Bundeswehr Muenchen, Germany
* Cristiano Leorato, Rhea, The Netherlands
* Steve McKeever, University of Oxford, UK
* David Nickerson, Auckland Bioengineering Institute, NZ
* Alfred Park, Oak Ridge National Laboratory, USA
* Wolfgang Prinz, Fraunhofer FIT and RWTH Aachen, Germany
* José L. Risco-Martin, Universidad Complutense de Madrid, Spain
* Jean-Francois Santucci, University of Corsica, France
* Gabriel Wainer, Carleton University, Canada
* Quirien Wijnand, European Space Agency, The Netherlands
* Heming Zhang, Tsinghua University, China

*** Contact Information ***
Daniele Gianni (track co-chair)
Email: danielegmail-comets-whZMOeQn8C0< at >public.gmane.org

Summary of the inaugural CellML Editorial Boardmeeting

David Nickerson — 2011-12-20T01:57:32

*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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Improved CellML support in latest version ofJSim

David Nickerson — 2011-12-19T19:35:26

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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Announcing the 2012 CellML Workshop

David Nickerson — 2011-12-19T11:48:22

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.

Independent variables, and delay

Lucian Smith — 2011-12-16T18:53:34

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. 

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

Cancelled: 14 and 21 December Auckland meetings about CellML API and Specification

Randall Britten — 2011-12-13T04:29:37

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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CellML website brief maintenance period

Randall Britten — 2011-11-21T03:00:38

Hi

I have been informed by the ABI IT department that the CellML website will be unavailable for a short time period tomorrow for infrastructure maintenance.  This will also affect the CellML mailing lists.  Apologies for any inconvenience this may cause.

Regards,
Randall
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IEEE e-Science 2011 WISC Call for Participation

David Nickerson — 2011-11-16T03:30:43

IEEE e-Science 2011 WISC Call for Participation
-----------------------------------------------
The 7th IEEE International Conference on e-Science (e-Science 2011),
to be held in Stockholm, Sweden, during 5-8 December 2011, will bring
together leading international and interdisciplinary research
communities, developers, and users of e-Science applications and
enabling IT technologies. The Workshop on Interoperability in
Scientific Computing will be held on the morning of Monday 5th of
December, and is co-located with the main conference.

We have selected three high-quality papers for presentation at the
workshop. They are:

* Requirements Engineering for Scientific Computing: a Model-based
Approach by Yang Li, Matteo Harutunian, Nitesh Narayan, Bernd Bruegge
and Gerrit Buse.
* Achieving Semantic Interoperability Between Physiology Models and
Clinical Data by Bernard de Bono, Stephen John Sammut and Pierre
Grenon.
* A Profile of Today's SBML-Compatible Software by Michael Hucka,
Frank T. Bergmann, Sarah M. Keating and Lucian P. Smith.

The workshop is scheduled to take place from 09:00am to 10:30am on
Monday December 5, 2011, in Breakout Room 1 of the Stockholm City
Conference Centre. See http://www.cs.ox.ac.uk/david.johnson/wisc11/
for details of the workshop, and http://www.escience2011.org for full
conference details and to register.

========================
WORKSHOP ORGANISATION
========================

Organisers/Chairs
-----------------
David Johnson, Steve McKeever (University of Oxford, UK)

Programme Committee
-------------------
David Nickerson (University of Auckland, New Zealand)
Herbert Sauro (University of Washington, USA)
Steve Harris (University of Oxford, UK)
Jonathan Cooper (University of Oxford, UK)
Rutger Vos (University of Reading, UK)
Dagmar Waltemath (University of Rostock, Germany)
Daniele Gianni (European Space Agency)
Mike Stout (University of Nottingham, UK)