Chronological Thread 

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Dear Michael and Nicolas,
Thanks for your comments. Definitely the Figure 5 is not SBGN Process
Diagrams Level 1 (released around Aug '08, parallel with new SBGN
website). When I wrote this proposal (around April '08), there was no
official release for SBGN Process Diagrams, but that time CellDesigner
website mentioned that CellDesigner's Graphical Notation conforms to
SBGN proposal (as of April '08 draft), and thats why I used the image
from CellDesigner's Graphical Notation to give a representative idea
about SBGN, and there was nothing wrong especially when many of
CellDesigner team members are respected authors of the SBGN Progress
Diagrams specification. Meanwhile I will make sure that final version
have updated SBGN notations.

thanks
Abhishek

P.S. regarding different standards or notation systems, it will be
never irrelevant to have multiple standards (domination may be mantra
of Microsoft), it gives freedom to choose and that's beauty of open
community based projects.

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> Today's Topics:
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> 1. Re: [Fwd: Visual model design and editing capabilities for
> CellML] (Michael Hucka)
> 2. Re: [Fwd: Visual model design and editing capabilities for
> CellML] (Nicolas Le Novere)
> 3. Re: [Fwd: Visual model design and editing capabilities for
> CellML] (Nicolas Le Novere)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 29 Oct 2008 20:24:06 -0700
> From: "Michael Hucka" <mhucka at caltech.edu>
> Subject: Re: [cellml-discussion] [Fwd: Visual model design and editing
> capabilities for CellML]
> To: CellML Discussion List <cellml-discussion at cellml.org>
> Message-ID: <18697.10454.173385.204137 at frantic.local>
> Content-Type: text/plain; charset=us-ascii
>
> Whoaaah. The notation shown in Figure 5 of this document as
> the "SBGN" draft is not SBGN. It was CellDesigner notation,
> and is significantly different from what SBGN is now.
>
> The current specification on sbgn.org includes a one-page
> summary of the process diagram notation. Please make sure
> to use that, and not figure 5, when making any evaluation of
> SBGN :-).
>
> (This is not a criticism and I'm not trying to be picky; I
> only want to clarify this one point because it can be
> potentially important in a decision about choice of
> notations. I know it's hard to track what's going on in
> different efforts, and that this document is several months
> old.)
>
> MH
>
> P.S. As far as I'm aware, EPE (Edinburgh Pathway Editor) is
> in the process of switching to SBGN, so the EPN notation may
> be becoming a bit irrelevant.
>
>
>
> ------------------------------
>
> Message: 2
> Date: Thu, 30 Oct 2008 08:00:45 +0000
> From: Nicolas Le Novere <lenov at ebi.ac.uk>
> Subject: Re: [cellml-discussion] [Fwd: Visual model design and editing
> capabilities for CellML]
> To: CellML Discussion List <cellml-discussion at cellml.org>
> Message-ID: <490969AD.2010105 at ebi.ac.uk>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Michael Hucka wrote:
>> Whoaaah. The notation shown in Figure 5 of this document as
>> the "SBGN" draft is not SBGN. It was CellDesigner notation,
>> and is significantly different from what SBGN is now.
>
> Indeed :-)
>
>> P.S. As far as I'm aware, EPE (Edinburgh Pathway Editor) is
>> in the process of switching to SBGN, so the EPN notation may
>> be becoming a bit irrelevant.
>
> You may also be interested in the following software that have
> started to implement SBGN:
>
> VANTED
> http://vanted.ipk-gatersleben.de/
>
> ARCADIA
> http://personalpages.manchester.ac.uk/staff/Alice.Villeger/arcadia.html
>
> --
> Nicolas LE NOVERE, Computational Neurobiology, EMBL-EBI, Wellcome-Trust
> Genome Campus, Hinxton CB101SD UK, Mob:+447833147074, Tel:+441223494521
> Fax:468, Skype:n.lenovere, AIM:nlenovere, MSN:nlenovere at hotmail.com
> http://www.ebi.ac.uk/~lenov/, http://www.ebi.ac.uk/compneur/
>
>
> ------------------------------
>
> Message: 3
> Date: Thu, 30 Oct 2008 08:03:28 +0000
> From: Nicolas Le Novere <lenov at ebi.ac.uk>
> Subject: Re: [cellml-discussion] [Fwd: Visual model design and editing
> capabilities for CellML]
> To: CellML Discussion List <cellml-discussion at cellml.org>
> Message-ID: <49096A50.9050109 at ebi.ac.uk>
> Content-Type: text/plain; charset="iso-8859-1"; Format="flowed"
>
> Michael Hucka wrote:
>
>> The current specification on sbgn.org includes a one-page
>> summary of the process diagram notation. Please make sure
>> to use that, and not figure 5, when making any evaluation of
>> SBGN :-).
>
> Attached is the reference card for SBGN Process Diagram Level 1
>
> You can find examples at:
>
> http://www.sbgn.org/Documents/Examples
>
> Best.
>
> --
> Nicolas LE NOVERE, Computational Neurobiology, EMBL-EBI, Wellcome-Trust
> Genome Campus, Hinxton CB101SD UK, Mob:+447833147074, Tel:+441223494521
> Fax:468, Skype:n.lenovere, AIM:nlenovere, MSN:nlenovere at hotmail.com
> http://www.ebi.ac.uk/~lenov/, http://www.ebi.ac.uk/compneur/
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> End of cellml-discussion Digest, Vol 51, Issue 16
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• [cellml-discussion] cellml-discussion Digest, Vol 51, Issue 16, Abhishek Tiwari, 10/31/2008
  • [cellml-discussion] Visual model design and editing capabilities for CellML, Nicolas Le novère, 10/31/2008
  • [cellml-discussion] cellml-discussion Digest, Vol 51, Issue 16, Michael Hucka, 10/31/2008

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