Request for Additional Model Formats in SEEK Please

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j....@epcc.ed.ac.uk

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Nov 27, 2018, 5:20:45 AM11/27/18
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Dear SEEK Developers,

I am working on migrating a number of plant systems biology models from a database in our organisation (SynthSys at University of Edinburgh) into SEEK. I am using the API to submit models and ISA entities programmatically; the API is great, working very well and the API documentation has been incredibly helpful!

I have a feature request I would be very grateful if you could consider, which is to allow specification of a couple of additional model formats. We have a number of models using the MathML/Simile (https://www.w3.org/TR/MathML3/), XGMML (http://xml.coverpages.org/xgmml-draft-xgmml-20000315.html) and SBGN-ML PD (https://github.com/sbgn/sbgn/wiki/SBGN_ML) formats. Please could you advise whether it would be possible to add these formats into the list of model format specifications available? Many thanks.

Kind regards,

Johnny Hay
Prof Andrew Millar Group
SynthSys
University of Edinburgh

P.S. I visited https://seek4science.org/tech/reporting-bugs-and-features.html to submit this feature request but I get a page error, so submitted here instead - hope that's okay!

Stuart Owen

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Nov 27, 2018, 5:45:53 AM11/27/18
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Yes I can look into adding these for our next version. If you are using the FAIRDOMHub we can get it updated quite quickly outside of the release schedule.

I'll try and get this done later today or tomorrow.

regards,

Stuart.

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HAY Johnny

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Nov 27, 2018, 5:51:24 AM11/27/18
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Hi Stuart,

That's super, thank you very much! I shall be using the FAIRDOMHub very soon for the final migration; at the moment, I am using the Docker SEEK container to test everything locally before I am completely confident that my migration application is working properly. Many thanks.

Best,

Johnny

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Mr Johnny Hay
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Stuart Owen

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Nov 28, 2018, 8:43:05 AM11/28/18
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Hi,

The new model types have been added, and are now available on the FAIRDOMHub. They will be included as part of the upgrade for the next seek version.

I also noticed and consolidated a couple of differences between the fairdomhub and a default SEEK installation, so they should now be the same.

    "Field Modelling Markup Language (FieldML)" becomes "FieldML",

    "KEGG Markup Language (KGML)" becomes "KGML"

    "VCell" becomes "Virtual Cell Markup Language (VCML)"


If you need to use this immediately in your local docker container, there is a development image  fairdom/seek:1.7-dev . You will need to step into the container and run a small rake command:

> docker exec -it seek bash

> bundle exec rake db:seed:model_formats

hopefully this helps,

Stuart.

HAY Johnny

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Nov 28, 2018, 9:03:58 AM11/28/18
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Hi Stuart,

That's fantastic, thank you very much!

Cheers,

Johnny

HAY Johnny

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Nov 30, 2018, 6:04:46 AM11/30/18
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Hi Stuart,

Thanks again for those updates. I realised I made a mistake with my original request, sincere apologies. Please would it be possible to rename the 'MathML/Smile' format to simply 'MathML' and would it be possible to add another additional format for 'Simile XML v3' please? Very sorry for the confusion, I hope it doesn't cause too much bother. Many thanks.

Best,

Johnny

Stuart Owen

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Nov 30, 2018, 7:51:53 AM11/30/18
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OK.

Stuart Owen

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Dec 3, 2018, 7:56:52 AM12/3/18
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Hi,

I updated this on Friday, and updated the FAIRDOMHub.

regards,

Stuart.

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