A list targeted at those interested in contributing to or providing feedback on the development of the CellML language. Members of the CellML team will endeavour to answer questions posted to the mailing list as promptly as possible. Posts are unmoderated, but subscription is.

David Nickerson | 9 Jul 2012 22:33

Fwd: [sysbio] Reminder: please register for COMBINE 2012

---------- Forwarded message ----------
From: Michael Hucka <mhucka@...>
Date: Tue, Jul 10, 2012 at 6:53 AM
Subject: [sysbio] Reminder: please register for COMBINE 2012
To: sysbio@...

Greetings, all you systems-oriented, biologically-inclined people:

With COMBINE 2012 only a month away, we encourage all attendees to
register as soon as possible so that the hosts can plan appropriately.
 Please also submit abstracts for talks and/or posters.

The Computational Modeling in Biology Network (COMBINE) is an initiative to
coordinate the development of the various community standards and formats,
initially in Systems Biology and related fields. The Annual COMBINE forum
is a workshop-style event with oral presentations, posters and breakout
sessions. The meeting provides an opportunity for those involved in many
related standardization and software efforts in systems biology to meet and
discuss their efforts, with the aim of working more closely together to
ensure smooth interoperability between systems.

http://co.mbine.org/events/COMBINE_2012

COMBINE 2012 will take place at The Donnelly Centre building at the
University of Toronto from Wednesday August 15 to Sunday Aug. 19, 2012,
immediately preceding the 13th International Conference on Systems Biology
(http://icsb2012toronto.com/). The COMBINE conference location is a short
walk from ICSB events and COMBINE 2012 is an official satellite meeting of
ICSB, so you can follow the same travel and accommodation instructions for
ICSB and use the same hotel discounts. Registration for COMBINE is $125

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Audette, Michel A. | 15 Aug 2012 21:07

naive questions about modeling blood-brain barrier and its disruption

Dear CellML developers and users, 

I would like to write a white paper to the US Dept of Defense that describes how CellML might be combined with
SOFA and OpenRave-based robotic therapy simulation, where in particular I would like to leverage your
toolkit to model an increase of porosity of the blood-brain barrier, which can be triggered  by ultrasonic
energy delivery, as well as the uptake of a drug. 

My knowledge of CellML is almost nil, and I'm open to any suggestion.

Best wishes, 

Michel

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

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David Nickerson | 16 Aug 2012 01:23

Re: naive questions about modeling blood-brain barrier and its disruption

Hi Michel,

Thanks for the enquiry. Just because this is a completely new type of
application, to me at least, could you please provide a couple of
pointers to some more information. A quick google shows
http://openrave.org/ - is that the simulation tool that you are
referring to? But I can't find anything obvious for SOFA... And do you
know of any introductory papers or other documents which might provide
a bit of detail as to the mathematics you would like to encode in
CellML for this particular application.

Cheers,
David.

On Thu, Aug 16, 2012 at 7:07 AM, Audette, Michel A. <maudette@...> wrote:
> Dear CellML developers and users,
>
> I would like to write a white paper to the US Dept of Defense that describes how CellML might be combined with
SOFA and OpenRave-based robotic therapy simulation, where in particular I would like to leverage your
toolkit to model an increase of porosity of the blood-brain barrier, which can be triggered  by ultrasonic
energy delivery, as well as the uptake of a drug.
>
> My knowledge of CellML is almost nil, and I'm open to any suggestion.
>
> Best wishes,
>
> Michel
>
> Michel Audette, Ph.D.
> Assistant Professor,

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Audette, Michel A. | 16 Aug 2012 04:50

Re: naive questions about modeling blood-brain barrier and its disruption

Hi David, 

thanks for your kind reply. The link for OpenRave is the correct one. The SOFA link is
http://www.sofa-framework.org/ . What SOFA does well is provide a suitable architecture for
interactive medical simulation at the organ level. Where CellML will complement it is modeling
processes at the cell and tissue levels, thereby complementing what SOFA has already in the development
of multi-scale interactive medical simulation, especially if it is possible to distribute the
computation, either over several cores, or over several GPUs. 

I don't have a mathematical expression for this change in porosity of the BBB. You could say that I'm still
dipping my toe in the pool, in terms of my immersion in computational biology. I imagine that if there is a
model for diffusion of molecules accross a tissue layer, that would be a place to start, but ideally, I
would like something that is well adapted to the blood-brain barrier itself. I guess Google is my friend,
and I can report back if I find such an expression. 

Cheers, 

Michel

The basic idea that I have is to pursue the development of 
Michel Audette, Ph.D.
Assistant Professor,
Department of Modeling, Simulation and Visualization Engineering,
Old Dominion University,
Norfolk, VA.
________________________________________
From: cellml-discussion-bounces@...
[cellml-discussion-bounces@...] On Behalf Of David
Nickerson [david.nickerson@...]
Sent: Wednesday, August 15, 2012 7:23 PM

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