Bioprotocols / labop

Laboratory Open Protocol (LabOP) Language
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Culture Primitive: Include Orbital radius? #142

Open photocyte opened 2 years ago

photocyte commented 2 years ago

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 commented 2 years ago

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