Hi.
I just saw BioXSD’s poster on F1000 which describes their own ‘BioJSON’ format. From the abstract, it looks to accomplish pretty much exactly what I and Charles wanted for our own BioJSON spec.
Charles - It would be really useful if you could take a look at their poster / docs to see whether we are ‘compatible’:
http://f1000research.com/posters/5-2213
The University of Dundee is a registered Scottish Charity, No: SC015096
I’ve run off an A3 print (just about legible!).
Mungo Carstairs
Jalview Computational Scientist
The Barton Group
Division of Computational Biology
School of Life Sciences
University of Dundee, Dundee, Scotland, UK.
www.jalview.org
www.compbio.dundee.ac.uk
From: jalview-dev-bounces@jalview.org jalview-dev-bounces@jalview.org on behalf of James Procter (Staff) J.Procter@dundee.ac.uk
Sent: 12 September 2016 10:31:26
To: Jalview Development List
Subject: [Jalview-dev] BioXSD’s BioJSON - review/comparison with Jalview’s 2.9’s BioJSON needed
Hi.
I just saw BioXSD’s poster on F1000 which describes their own ‘BioJSON’ format. From the abstract, it looks to accomplish pretty much exactly what I and Charles wanted for our own BioJSON spec.
Charles - It would be really useful if you could take a look at their poster / docs to see whether we are ‘compatible’:
http://f1000research.com/posters/5-2213
The University of Dundee is a registered Scottish Charity, No: SC015096
The University of Dundee is a registered Scottish Charity, No: SC015096
Yes, important to look at this in detail. I examined Matus Kalas’ thesis last year which included bioXSD and I know Inge Jonassen and his group well.
They are major long-term users and supporters of Jalview so I am pretty sure will be keen to see their work on representation being relevant to Jalview.
We can certainly work with these people to get a common representation that works well for Jalview.
Geoff.
Hi.
I just saw BioXSD’s poster on F1000 which describes their own ‘BioJSON’ format. From the abstract, it looks to accomplish pretty much exactly what I and Charles wanted for our own BioJSON spec.
Charles - It would be really useful if you could take a look at their poster / docs to see whether we are ‘compatible’:
http://f1000research.com/posters/5-2213
The University of Dundee is a registered Scottish Charity, No: SC015096
_______________________________________________ Jalview-dev mailing list [Jalview-dev@jalview.org](mailto:Jalview-dev@jalview.org) [http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-dev](http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-dev)
The University of Dundee is a registered Scottish Charity, No: SC015096
On 12/09/2016 10:31, James Procter (Staff) wrote:
--
Geoff Barton | Professor of Bioinformatics | Head of Division of Computational Biology
School of Life Sciences | University of Dundee, Scotland, UK | [g.j.barton@dundee.ac.uk](mailto:g.j.barton@dundee.ac.uk)
Tel: +44 1382 385860 | [www.compbio.dundee.ac.uk](http://www.compbio.dundee.ac.uk) | twitter: @gjbarton
The University of Dundee is registered Scottish charity: No.SC015096
Yes - this is exactly our idea with BioJSON. I’ve had a look at their schema, it is quite different from ours but we should certainly collaborate with them since we share the same vision.
Charles
Ofoegbu Tochukwu Charles
Jalview Visual Analytics Developer/Scientist
The Barton Group
Division of Computational Biology
School of Life Sciences
University of Dundee, Dundee, Scotland, UK.
Skype: cofoegbu
www.jalview.org
www.compbio.dundee.ac.uk
On 12/09/2016 10:31, James Procter (Staff) wrote:
--
Geoff Barton | Professor of Bioinformatics | Head of Division of Computational Biology
School of Life Sciences | University of Dundee, Scotland, UK | [g.j.barton@dundee.ac.uk](mailto:g.j.barton@dundee.ac.uk)
Tel: +44 1382 385860 | [www.compbio.dundee.ac.uk](http://www.compbio.dundee.ac.uk/) | twitter: @gjbarton
The University of Dundee is registered Scottish charity: No.SC015096
Lets take a closer look when 2.10 is released, and we’ve taken stock of the next milestones.
BioXSD has different, and somewhat broader aims than jalview’s BioJSON. At a pinch they could interoperate, but we lack use cases.
FYI: See twitter conversation:
https://twitter.com/matuskalas/status/775296888870408192
From: jalview-dev-bounces@jalview.org jalview-dev-bounces@jalview.org on behalf of Charles Ofoegbu (Staff) t.c.n.ofoegbu@dundee.ac.uk
Sent: 12 September 2016 14:41:43
To: Jalview Development List
Subject: Re: [Jalview-dev] BioXSD’s BioJSON - review/comparison with Jalview’s 2.9’s BioJSON needed
Yes - this is exactly our idea with BioJSON. I’ve had a look at their schema, it is quite different from ours but we should certainly collaborate with them since we share the same vision.
Charles
Ofoegbu Tochukwu Charles
Jalview Visual Analytics Developer/Scientist
The Barton Group
Division of Computational Biology
School of Life Sciences
University of Dundee, Dundee, Scotland, UK.
Skype: cofoegbu
www.jalview.org
www.compbio.dundee.ac.uk
On 12 Sep 2016, at 10:57, Geoff Barton <gjbarton@dundee.ac.uk> wrote:
Yes, important to look at this in detail. I examined Matus Kalas’ thesis last year which included bioXSD and I know Inge Jonassen and his group well.
They are major long-term users and supporters of Jalview so I am pretty sure will be keen to see their work on representation being relevant to Jalview.
We can certainly work with these people to get a common representation that works well for Jalview.
Geoff.
On 12/09/2016 10:31, James Procter (Staff) wrote:
Hi.
I just saw BioXSD’s poster on F1000 which describes their own ‘BioJSON’ format. From the abstract, it looks to accomplish pretty much exactly what I and Charles wanted for our own BioJSON spec.
Charles - It would be really useful if you could take a look at their poster / docs to see whether we are ‘compatible’:
http://f1000research.com/posters/5-2213The University of Dundee is a registered Scottish Charity, No: SC015096
_______________________________________________ Jalview-dev mailing list [Jalview-dev@jalview.org](mailto:Jalview-dev@jalview.org) [http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-dev](http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-dev)-- Geoff Barton | Professor of Bioinformatics | Head of Division of Computational Biology School of Life Sciences | University of Dundee, Scotland, UK | [g.j.barton@dundee.ac.uk](mailto:g.j.barton@dundee.ac.uk) Tel: +44 1382 385860 | [www.compbio.dundee.ac.uk](http://www.compbio.dundee.ac.uk/) | twitter: @gjbarton The University of Dundee is registered Scottish charity: No.SC015096The University of Dundee is a registered Scottish Charity, No: SC015096 _______________________________________________
Jalview-dev mailing list
Jalview-dev@jalview.org
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The University of Dundee is a registered Scottish Charity, No: SC015096
The University of Dundee is a registered Scottish Charity, No: SC015096