gmane.text.xml.cellml.general

[Combine-announce] Update on COMBINE 2013

Nicolas Le Novere — 2013-05-24T08:31:48

Dear Colleagues,

Now that HARMONY has ended, and the developers have been fed, it is time to 
turn to the other side of our activity and talk about standard development. 
The plans for COMBINE forum 2013 are shaping up nicely, thanks to the local 
organisers - the bioinformatics unit of Institut Curie - and in particular 
Eric Bonnet.

The meeting will start on Monday 16th September, with a scientific 
conference. The theme will be the different modelling approaches used in 
biology. There will be invited talks, short talks selected from abstracts 
and poster sessions. So far, we have confirmation of lectures by:

Vincent Danos (CNRS, Paris-Diderot, Univ Edinburgh, rule-based modelling)
Marc Lavielle (INRIA, Paris-sud, pharmacometrics)
Benjamin Ribba (INRIA, multi-scale modelling of tumours)
Denis Thieffry (ENS, logical modelling)
Andrei Zinovyev (Curie, network analysis)

We are waiting for a couple more confirmations.

This meeting should give us an overview of what we cover or not, and fuel 
the dicussio

Harmony 2013

David Nickerson — 2013-05-07T21:15:58

Hi all,

HARMONY 2013 is coming up in a couple of weeks
(http://www.co.mbine.org/events/HARMONY_2013). Two of the CellML
editors will be present (Jonathan Cooper and myself) at the meeting,
so if any of you are planning on attending and have any CellML-related
topics you would like to discuss, please let us know so we can
schedule some time for such discussions.


Cheers,
David.

Fwd: [Combine-discuss] ICSB Tutorial: Modelling and Simulation of Quantitative Biological Models on September 4th, 2013

David Nickerson — 2013-04-29T13:54:07

---------- Forwarded message ----------
From: "Golebiewski, Martin" <martin.golebiewski-b2lVGzS7aqTYtjvyW6yDsg< at >public.gmane.org>
Date: Apr 29, 2013 8:22 AM
Subject: [Combine-discuss] ICSB Tutorial: Modelling and Simulation of
Quantitative Biological Models on September 4th, 2013
To: "combine-discuss-BqG7eWgmHKDYtjvyW6yDsg< at >public.gmane.org" <combine-discuss-BqG7eWgmHKDYtjvyW6yDsg< at >public.gmane.org>
Cc:

Dear colleagues,

We cordially invite you to this full-day COMBINE (http://co.mbine.org/)
tutorial workshop:

            Modelling and Simulation of Quantitative Biological Models
            Wednesday, September 4th, 2013 (9:30 - 17:30)
            Copenhagen (at the Technical University of Denmark)

This workshop is a satellite of the 14th International Conference on
Systems Biology (ICSB). You can sign in for the tutorial (free of charge)
when registering for the conference at http://www.icsb2013.dk.


Participants will learn setting-up quantitative computer models of
biological networks using experimental

Fwd: [Combine-announce] HARMONY travel funds

David Nickerson — 2013-04-25T15:25:21

---------- Forwarded message ----------
From: Moraru,Ion <moraru-/otbM0cIFQZKCnpzQd/jlA< at >public.gmane.org>
Date: Mon, Apr 22, 2013 at 9:17 AM
Subject: [Combine-announce] HARMONY travel funds
To: "combine-announce-BqG7eWgmHKDYtjvyW6yDsg< at >public.gmane.org" <combine-announce-BqG7eWgmHKDYtjvyW6yDsg< at >public.gmane.org>


Dear Colleagues,



This is a reminder that HARMONY 2013 is just one month away.  If you
plan to attend, please make sure to book your hotel and, if needed,
apply for financial support as soon as possible.  See travel info and
details at http://www.co.mbine.org/events/HARMONY_2013



Ion





----------------------------------------------------------
Ion I. Moraru, MD, PhD
Director, High Performance Computing Facility
Associate Professor of Cell Biology
Center for Cell Analysis and Modeling

Cell and Genome Sciences Building, R1635

University of Connecticut Health Center

400 Farmington Ave.

Farmington, CT 06030-6406



Tel: 860-679-2908
Fax: 860-679-1039
Cell: 860-978-8528
Video: 155.37.201.72##16

[Combine-announce] HARMONY travel funds

Moraru,Ion — 2013-04-22T13:17:44

Dear Colleagues,

This is a reminder that HARMONY 2013 is just one month away.  If you plan to attend, please make sure to book your hotel and, if needed, apply for financial support as soon as possible.  See travel info and details at http://www.co.mbine.org/events/HARMONY_2013

Ion


----------------------------------------------------------
Ion I. Moraru, MD, PhD
Director, High Performance Computing Facility
Associate Professor of Cell Biology
Center for Cell Analysis and Modeling
Cell and Genome Sciences Building, R1635
University of Connecticut Health Center
400 Farmington Ave.
Farmington, CT 06030-6406

Tel: 860-679-2908
Fax: 860-679-1039
Cell: 860-978-8528
Video: 155.37.201.72##1635 (H.323) or 1635-Hr+IzL1bVFc< at >public.gmane.org<mailto:1635-Hr+IzL1bVFc< at >public.gmane.org> (SIP)
Email: moraru-/otbM0cIFQZKCnpzQd/jlA< at >public.gmane.org<mailto:moraru-/otbM0cIFQZKCnpzQd/jlA< at >public.gmane.org>

_______________________________________________
Combine-announce mailing list
Combine-announce-jcUp+/l53Jxaa/9Udqfwiw< at >pub

Re: OpenCOR 0.1.1 released

Audette, Michel A. — 2013-04-17T20:15:30

Congratulations, Alan. I may have a student play with this release. 

Cheers, 

Michel

Michel Audette, Ph.D.
Assistant Professor,
Department of Modeling, Simulation and Visualization Engineering,
Old Dominion University,
Norfolk, VA.
________________________________________
From: cellml-discussion-bounces-+N4dcC6UsuQdnm+yROfE0A< at >public.gmane.org [cellml-discussion-bounces-+N4dcC6UsuQdnm+yROfE0A< at >public.gmane.org] on behalf of Alan Garny [alan.garny-MZpvjPyXg2s< at >public.gmane.org]
Sent: Wednesday, April 17, 2013 4:09 PM
To: cellml-discussion-+N4dcC6UsuQdnm+yROfE0A< at >public.gmane.org; 'A list for the developers of CellML tools'
Subject: [cellml-discussion] OpenCOR 0.1.1 released

Dear all,

This is to let you know that OpenCOR 0.1.1<http://www.opencor.ws/download.php> has just been released.

A few useful links:

-          What is new?<http://www.opencor.ws/user/whatIsNew.html>

-          Supported platforms<http://www.opencor.ws/user/supportedPlatforms.html>

-          Report issues, make suggestions, etc.<http

OpenCOR 0.1.1 released

Alan Garny — 2013-04-17T20:09:45

Dear all,

 

This is to let you know that OpenCOR 0.1.1
<http://www.opencor.ws/download.php>  has just been released.

 

A few useful links:

-          What is new? <http://www.opencor.ws/user/whatIsNew.html> 

-          Supported platforms
<http://www.opencor.ws/user/supportedPlatforms.html> 

-          Report issues, make suggestions, etc.
<https://github.com/opencor/opencor/issues> 

 

Best regards, Alan.

_______________________________________________
cellml-discussion mailing list
cellml-discussion-+N4dcC6UsuQdnm+yROfE0A< at >public.gmane.org
http://lists.cellml.org/mailman/listinfo/cellml-discussion

OpenCOR 0.1 Released

David Nickerson — 2013-04-04T03:16:30

Hi all,

OpenCOR (http://opencor.ws) is an open source cross-platform modeling
environment which can be used to organise, edit, simulate and analyse
CellML files on Windows, Linux and OS X
(http://opencor.ws/user/supportedPlatforms.html). OpenCOR version 0.1
is now available from http://opencor.ws/download.php.

This first public release of OpenCOR enables users to annotate and
simulate CellML 1.0 and 1.1 models, including models containing ODE
and/or DAE systems which may require non-linear systems to be solved.

The source code for OpenCOR is available via the github opencor
repository: https://github.com/opencor/opencor. Also on github is the
issue tracker (https://github.com/opencor/opencor/issues) showing the
features that will become available in future releases
(https://github.com/opencor/opencor/issues?labels=Feature&page=1&state=open).


Cheers,
Andre.

Re: interested in a simple model to couple with SOFA

Randall Britten — 2013-03-23T23:16:17

Hi Michel

Mechanical constitutive laws perhaps? Many are likely to be able to be
simulated fast enough for interactivity, I'm guessing.  (I'm sure there
will be some other good suggestions.)

Regards,
Randall

On 23/03/13 3:08 AM, "Audette, Michel A." <maudette-6aBHAdl9KXI< at >public.gmane.org> wrote:

interested in a simple model to couple with SOFA

Audette, Michel A. — 2013-03-22T14:08:50

Dear members of the CellML community, 

I have a undergraduate student researcher who is interested in combining CellML models with SOFA-based interactive macroscopic visualization, possibly in conjunction with OpenCOR, and we are looking for suggestions on simple models that are conducive to such a visualization. In other words, a simple model that is compatible with integration with SOFA (e.g. derived from a SOFA Behavior model) through a series of baby steps. 

My student has an interest in cardiovascular applications, but if this area turns out to be too complex to couple with a macroscopic simulation, especially at interactive rates, we will certainly consider other areas. 

Can any of you, with broad knowledge of CellML models, make a suggestion? 

Thanks for your kind consideration. Best wishes,

Michel

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

CellML Workshop coming up next week

David Nickerson — 2013-03-22T03:12:35

Hi all,

The 7th International CellML Workshop will be running Monday and
Tuesday next week in Auckland, New Zealand. Details for the workshop
are available at:
http://www.cellml.org/community/events/workshop/2013/, including the
workshop programme. We will be using Google Hangouts On Air to
broadcast the workshop live on the Internet, so if you see any talks
in the programme that you would like to watch please feel free to tune
in and hangout with those of us there in person. Details will be
available on the workshop website as the broadcast for each session
comes online, and the recordings will be available via youtube soon
after.


Cheers,
Andre.

Modular Modeling: Standards and Tools. LucianSmith, Caltech

David Nickerson — 2013-03-02T00:03:26

Hi all,

Lucian Smith will be delivering web-presentation next week on the topic:

Modular Modeling: Standards and Tools. Lucian Smith, Caltech

Friday March 8, 2013 2pm EST (8am Saturday 9th, NZDT)

Model exchange and re-use has been greatly enhanced over the last
decade by the emergence of standard model exchange languages such as
SBML and CellML. Model design and re-use becomes even more tractable
with modularity: larger, more complex models can be built using
well-understood smaller models. CellML has long been modular, and SBML
now has a modularity 'package' which allows modular model
construction. We will present an overview of the capabilities of the
modeling standards and tools that facilitate modular modeling.
(http://antimony.sf.net).


Connection details will be available at:
http://www.imagwiki.nibib.nih.gov/mediawiki/index.php?title=Model_and_Data_Sharing_Working_Group#Presentations


Cheers,
Andre.

Re: Java error on Mac OSX10.8.2

Randall Britten — 2013-02-27T20:30:12

Hi Mark

If you send a bit more detail about the model structure change, perhaps we
can solve it.

Regards,
Randall

On 27/02/13 9:32 PM, "Mark Cannell" <mark.cannell-PMBdYf0mooE2EctHIo1CcQ< at >public.gmane.org> wrote:

Re: Java error on Mac OSX10.8.2

Mark Cannell — 2013-02-27T08:32:14

On 26/02/2013, at 9:43 PM, Andrew Miller <ak.miller-1/NbpDiVQt6SYBAHRPvY1A< at >public.gmane.org> wrote:


Yes, that's right, I think it must be something to do with code generation. Initial value chnages under the blue circle seem OK. Edits under the model structure pane can lead to the java error.

Cheers Mark

Re: Java error on Mac OSX10.8.2

Andrew Miller — 2013-02-26T21:43:38

So just to clarify: you are loading a model, running a simulation by 
clicking the Integrate button, cloning the model by right clicking on it 
in the left pane, editing an initial condition in OpenCell, and clicking 
Integrate, without leaving OpenCell in the interim, and the first time 
you click Integrate, it works and you get results, but the second time 
you get the Javascript error about it failing in 
"cellml_servicesICellMLIntegrationService.compileModelODE"?

This is not something I have seen before, the only possibility I can 
think of is that the edit you are making might be introducing a change 
that is tripping a bug in the code generator - what edit are you making, 
and does it happen if you only make a simple change like changing an 
initial condition?

Best wishes,
Andrew

Re: Java error on Mac OSX10.8.2

Mark Cannell — 2013-02-26T21:09:35

Hi Randall

I installed the tools and the repository code does runs in OpenCell. However when I clone the distribution and edit anything I get the same java error I got before the Xcode tools were installed. I have no idea what I could be doing wrong..

Cheers Mark

On 26/02/2013, at 8:36 PM, Randall Britten <r.britten-1/NbpDiVQt6SYBAHRPvY1A< at >public.gmane.org> wrote:


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.Cannell-PMBdYf0mooE2EctHIo1CcQ< at >public.gmane.org

Re: Java error on Mac OSX10.8.2

Randall Britten — 2013-02-26T20:36:47

Hi Mark

I use Mac OS X 10.8.2.  OpenCell v0.8 runs fine, as far as I can tell.  As
Andre said, you need to install Xcode and the Xcode command line tools
(they are free from the Apple App store).  (This is all just an interim
measure until the imminent release of OpenCOR.  Development and
maintenance of OpenCell ceased after the v0.8 release in 2010, in favour
of the OpenCOR project.  We will nevertheless try support you if you
decide to use it.)

Regards,
Randall



On 26/02/13 8:08 PM, "Mark Cannell" <mark.cannell-PMBdYf0mooE2EctHIo1CcQ< at >public.gmane.org> wrote:

Re: Java error on Mac OSX10.8.2

Alan Garny — 2013-02-26T08:53:11

Dear Mark,


This is correct, OpenCOR can't currently save edits. I am hoping to have the
editing of CellML file in OpenCOR within the next few weeks. However, it
will initially be possible to do so by editing the CellML file directly.
This is not ideal, I agree, but we have to start somewhere. Then, the next
step will be to allow the authoring of CellML files using a format similar
to the one used in COR which, I believe, is much more user-friendly.

there a

This is also correct. The development version of OpenCOR addresses that
issue, but it's not yet available as a  download. Talking of downloads, I
tend to upload new snapshots of OpenCOR on a regular basis (weekly roughly;
see http://www.opencor.ws/downloads.html). The snapshots are usually
relatively safe to use. They may just not have certain features you are
after.

Finally, and as Peter mentioned, I will be releasing a first official
version of OpenCOR late next month (including, compared to the current
snapshot, improved simulation capabilities and

Re: Java error on Mac OSX10.8.2

Mark Cannell — 2013-02-26T08:16:27

Hi Peter

This tool looks great. I can't save any edits tho', and in the simulation widow if I change a parameter the change is lost when I run the simulation. Is there a work around beyond editing the file externally and reloading?

Cheers Mark

On 26/02/2013, at 3:35 AM, Peter Hunter <p.hunter-1/NbpDiVQt6SYBAHRPvY1A< at >public.gmane.org> wrote:


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.Cannell-PMBdYf0mooE2EctHIo1CcQ< at >public.gmane.org

Re: Java error on Mac OSX10.8.2

Mark Cannell — 2013-02-26T07:08:37

Hi All, Peter

Could not seem to get OpenCell to run but OpenCor works and looks like a great tool. I look forward to version 1.0 and will see how 0.0 runs in the meantime, 

Thanks, Mark

On 26/02/2013, at 3:35 AM, Peter Hunter <p.hunter-1/NbpDiVQt6SYBAHRPvY1A< at >public.gmane.org> wrote:


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.Cannell-PMBdYf0mooE2EctHIo1CcQ< at >public.gmane.org

Re: Java error on Mac OSX10.8.2

Peter Hunter — 2013-02-26T03:35:55

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: