pySBOL3 communication with SynBioHub

[GONZALO VIDAL PENA]

Hi everyone,

I'm one of the developers of Flapjack  and I'm making its integration with SBOL. Because the Flapjack backend is based on Python the idea was to use pySBOL3 to do the SBOL integration. The problem is that I could not find how to get SBOL objects from SynBioHub, that in previous implementations of pySBOL were sbol.PartShop.pull(). I search in pySBOL3 documentations and could not find something similar, maybe one of you knows how to do it.

The basic idea is to use SBOL components on SynBioHub to create implementations, use that implementations as subcomponents, add experimental data and upload the a SBOL Experiment to SynBioHub.

The questions are: can I download and upload (or pull and push) SBOL objects to SynBioHub using pySBOL3? Or is there another way to use the SBOL URIs for this purpose? 

Kind regards,

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Gonzalo Vidal

Synthetic Biologist

Gonza10V

Biological and Medical Engineering PhD student

Institute for Biological and Medical Engineering

IIBMer

[Chris Myers]

Hi Gonzalo, 

SynBioHub does not yet support SBOL3.  Therefore, pySBOL3 does not yet support SynBioHub.  I can think of a few possible solutions:

1) Use pySBOL2 and SBOL2

2) Use pySBOL2 to fetch the designs in SBOL2, then convert them using the SBOL2 to SBOL3 converter:

http://convert.sboltools.org

Not sure though if this has an API yet, but you could do it with sbolgraph locally.

Best wishes,

Chris

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