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Culture Primitive: Include Orbital radius? #142

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photocyte opened this issue Apr 27, 2022 · 1 comment
Open

Culture Primitive: Include Orbital radius? #142

photocyte opened this issue Apr 27, 2022 · 1 comment

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@photocyte
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Hi there, for the Culture primitive under the culturing library , the orbital_radius is not defined.

What do people think about adding it with an optional parameter? (The default could be 19 mm which is the de facto standard orbital radius for benchtop orbital shakers)

paml.show_libraries()
library: culturing

Primitive: https://bioprotocols.org/paml/primitives/culturing/Culture
Input Parameters:
	volume: http://www.ontology-of-units-of-measure.org/resource/om-2/Measure (Optional) 
	inoculum: http://sbols.org/v3#Component 
	container: http://bioprotocols.org/paml#SampleArray 
	growth_medium: http://sbols.org/v3#Component 
	replicates: http://bioprotocols.org/uml#ValueSpecification (Optional) 
	orbital_shake_speed: http://www.ontology-of-units-of-measure.org/resource/om-2/Measure (Optional) 
	duration: http://www.ontology-of-units-of-measure.org/resource/om-2/Measure 
	temperature: http://www.ontology-of-units-of-measure.org/resource/om-2/Measure (Optional) 

Is this the right file to look at trying to add a orbital_radius input parameter? The syntax / mechanism of how to add that, is not very obvious.
https://github.com/Bioprotocols/paml/blob/main/paml/lib/culturing.ttl

Also, wouldn't it be better for Culture to be some sort of subclass / combination of a (unclear if they already exist)Incubate & Shake Primitives?

Also, what about things like, photosynthetic organisms, that need light in their culturing & would have their own parameters (light intensity, light duration/light cycle)?

@photocyte
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Hi @bbartley , was suggested to add you to this thread. It is not time sensitive.

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