SED-ML support in JWS Online

COMBINE 2016

Martin Peters

In an ideal world, you should be able to reproduce any simulation published in a paper. This does happen for some models. You have a website which links the paper from JWS and data from the FAIRDOM hub. Then you can tweak the parameters of a published model and see how the results change. This means that there is a SED-ML database as part of JWS online. Once you’ve made your modifications, you can then re-submit the model back to JWS.

You can also export the COMBINE archive you’ve created in the course of this work and take it away to do more simulations locally. Currently, only time-course simulation is supported (to keep the computational time as low as possible). Excel spreadsheets are used instead of NuML. Further, there is support only for 2d plots. However, they have achieved their goal of being able to go from a paper to the actual simulation of a model from that paper in one click.

Please note that this post is merely my notes on the presentation. I may have made mistakes: these notes are not guaranteed to be correct. Unless explicitly stated, they represent neither my opinions nor the opinions of my employers. Any errors you can assume to be mine and not the speaker’s. I’m happy to correct any errors you may spot – just let me know!

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