Chronological Thread 

< Chronological >      < Thread >

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Hi Peter,

This is a common complaint. IMHO, the best solution is to "decorate" the SBGN
glyphs. See:
http://sbgn.github.io/sbgn/faq/pd#can-i-decorate-my-nodes

You can see other example in this paper:
http://onlinelibrary.wiley.com/doi/10.1002/psp4.12155/full

The extreme version of it is the SBOL visual standard, where the outline of the
activity glyphs is invisible. But the whole diagrams are still "SBGN
compliant".

The issue of standardising the decoration is another topic. Do you know the
Reactome icon library?
http://reactome.org/icon-lib/

It is a bit complicated, but I think a simplified subset could be generated.
Things like receptors, channels etc. are now de facto standards.

On 12/09/17 22:52, Peter Hunter wrote:

Hi Andre,

I'm just about to start building SVG diagrams representing bond graph based
CellML models (for use in our WebGL multiscale GUI). This means I have to
designing glyphs for the ion channels, membrane transporters, pumps, etc,
with a compromise between attractiveness from a biological perspective
(instantly recognisable as an ion channel, etc) and simplicity. The current
SBGN ones are too computer science oriented for a biologist friendly GUI. It
would be nice to have a community standard for these glyphs and a library of
them to draw on. Could that be put on the agenda? A start might be to have a
small working group who could come up with suggestions for community
feedback. I'd be happy to either lead the group or just participate. I'm
guessing there may be an effort underway somewhere for this already. Clearly
it would be good to connect this effort with the SBGN activity if that is
still going.

Cheers, Peter

Sent from my iPhone

On 13/09/2017, at 09:21, David Nickerson
<david.nickerson AT gmail.com>
wrote:

Hi all,

COMBINE is coming up shortly in Milan, October 9-13. The preliminary
agenda is now available at http://co.mbine.org/events/COMBINE_2017,
and we are now asking for poster abstracts.

Please also register as soon as you can to help us plan a great meeting.

Cheers,
David.


---------- Forwarded message ----------
From: Antoniotti Marco
<antoniotti.marco AT disco.unimib.it>
Date: 13 September 2017 at 02:58
Subject: [COMBINE 2017] Call for participation and poster submission deadline
To:
"combine-coord AT googlegroups.com"

<combine-coord AT googlegroups.com>


Apologies for multiple postings…




COMBINE 2017: 8th Computational Modeling in Biology Network Workshop
==============================================================================

Oct. 9th - 13th, 2017, Università degli Studi di Milano Bicocca, Milan, ITALY
http://co.mbine.org/events/COMBINE_2017
------------------------------------------------------------------------------

The "Computational Modeling in Biology" Network (COMBINE) is an
initiative to coordinate the development of the various community
standards and formats in systems biology and related fields. COMBINE
2017 will be a workshop-style event with oral presentations, posters,
and breakout sessions. The five meeting days will include talks about
the COMBINE standards and associated or related standardization
efforts, as well as presentations of tools using these standards. Oral
presentations will be selected from the submitted abstracts. In
addition, poster sessions will allow people to inform each other about
their software and other projects in a setting that fosters
interaction and in-depth discussion.


CONFIRMED SPEAKERS
------------------

Shailesh Appukuttan, UNIC, CNRS, France
James Faeder, University of Pittsburgh, USA
Padraig Gleeson UCL, UK
Martin Golebiewski, Heidelberg Institute for Theoretical Studies (HITS),
Germany
Carlos F. Lopez, Department of Cancer Biology Vanderbilt University
School of Medicine, USA
Marco Nobile, DISCo, Università degli Studi di Milano Bicocca, Italy


PRELIMINARY PROGRAM
-------------------

The preliminary program is available on the COMBINE site,
http://co.mbine.org/events/COMBINE_2017


CALL FOR POSTERS
----------------

The deadline to submit posters for consideration is October 6th, 2017.

Please see the COMBINE website for submission instructions. The
submission process is hosted by Easychair (http://www.easychair.org)


TOPICS OF INTEREST
------------------

Topics include, but are not limited to:
- Data exchange, pipelines and model standards for systems biology
- Graphical notation standards for systems biology
- Standards for sharing and analysing biological pathway data
- Standards for computational biological models

More on the COMBINE standards at http://co.mbine.org/standards


IMPORTANT DATES
---------------

Poster submission deadline: October 6th, 2017.
COMBINE Workshop: October 9-13 2017


REGISTRATION
------------

Registrations are open. The registration fee is set to
300 EUR and it includes breaks and the social event.
"On site" registration will be possible, but only with credit card
payment.


We apologize for the cumbersome procedure; please read carefully the
instructions for payment on the registration form. You can register at
https://goo.gl/forms/omoiLmBda4rElye33


PROGRAM AND LOCAL CHAIRS
------------------------

Marco Antoniotti, Alex Graudenzi, Giancarlo Mauri, DISCo),
(Università degli Studi di Milano Bicocca)

If you have any questions, please contact <marco.antoniotti [.at.] unimib.it>


COMBINE COORDINATORS
--------------------

Gary Bader (Toronto)
Padraig Gleeson (UCL)
Martin Golebiewski (Heidelberg)
Michael Hucka (Caltech)
Nicolas Le Novère (Babraham)
Chris J. Myers (Utah)
David Nickerson (Auckland)
Falk Schreiber (Monash)
Dagmar Waltemath (Rostock)


ACKNOWLEDGEMENTS
----------------

COMBINE 2017 is generously supported by:
- Department of Informatics, Systems and Communication (DISCo),
Università degli Studi di Milano Bicocca (ITALY)
- Centre of Systems Biology, Università degli Studi di Milano Bicocca (ITALY)
- The CHARME COST Action (http://cost-charme.eu)



--
Marco Antoniotti, Associate Professor tel. +39 - 02 64 48 79 01
DISCo, Università Milano Bicocca U14 2043 http://bimib.disco.unimib.it
Viale Sarca 336
I-20126 Milan (MI) ITALY

Please check: http://co.mbine.org/events/COMBINE_2017
Please check: https://sites.google.com/site/troncopackage/

Please note that I am not checking my Spam-box anymore.
Please do not forward this email without asking me first (cum grano salis).





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--


David Nickerson
about.me/david.nickerson

--
Nicolas LE NOVERE, Babraham Institute, Babraham Campus Cambridge, CB22 3AT
Tel: +441223496433 Mob:+447833147074
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• [cellml-discussion] Fwd: [COMBINE 2017] Call for participation and poster submission deadline, David Nickerson, 09/13/2017
  • Re: [cellml-discussion] Fwd: [COMBINE 2017] Call for participation and poster submission deadline, Peter Hunter, 09/13/2017
    • Re: [cellml-discussion] Fwd: [COMBINE 2017] Call for participation and poster submission deadline, Nicolas Le Novere, 09/13/2017

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