mwatts15 / PyOpenWorm

Unified data access library for data about the c. elegans anatomy and model for the OpenWorm project
MIT License
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API documentation #4

Open mwatts15 opened 10 years ago

mwatts15 commented 10 years ago
mwatts15 commented 10 years ago

A flavor of the developing API: http://my-openworm-docs.readthedocs.org/en/latest/api.html

slarson commented 10 years ago

Looking nice!

DickGordonCan commented 10 years ago

Dear Mark, In:


Example:

v = Quantity("600","um") c = Cell(lineageName="AB plapaaaap") c.divisionVolume(v)


"um" should be "(µm)^3". Thanks. Yours, -Dick Gordon

VahidGh commented 10 years ago

Looking good... Assuming we will need to support more biological networks (beside neural networks) in order to complete locomotion dynamics, we need to add muscle cell class (or other cell types). so, we could have a more general connection class like this: Connection(pre: Cell, post:Cell,...) and inherit other type of connections from this class.

mwatts15 commented 10 years ago

We could generalize the signaling relationship to:

On Mon, Jun 2, 2014 at 5:27 AM, Vahid Ghayoomi notifications@github.com wrote:

Looking good... Assuming we will need to support more biological networks (beside neural networks) in order to complete locomotion dynamics, we need to add muscle cell class (or other cell types). so, we could have a more general connection class like this: Connection(pre: Cell, post:Cell,...) and inherit other type of connections from this class.

— Reply to this email directly or view it on GitHub https://github.com/mwatts15/PyOpenWorm/issues/4#issuecomment-44822131.

Cheers, Mark Watts Department of Computer Science University of Texas at Austin

slarson commented 10 years ago

Based on some comments from today's discussion:

slarson commented 10 years ago

More comments from today's discussion

For now let's hold off on the Signaling class but we should save this and come back to it if we have time at the end:

Signaling(sender : Population, receiver : Population, messengerSpecies : Object )


Signaling.sender() : Population
++++++++++++++++++++++++++++++++

Signaling.receiver() : Population
++++++++++++++++++++++++++++++++++

Signaling.messengerSpecies() : Object
+++++++++++++++++++++++++++++++++++++

Signaling(p1,p2,"Glutamate") <-- behind the scenes Connection relationships get created and that means having a way to define if connections are all - to - all or random or some other connection pattern

Let's also leave the Simulation class out for now until we have time perhaps at the end.
mwatts15 commented 10 years ago

I've started written some tests (af5c7aee5be2330da83cbb211d02d2a0d9fd390d) based on this one: Ability to add a DOI / PMID / WormBaseID to Evidence is important

mwatts15 commented 10 years ago

@slarson I have checked off items which I've addressed in the draft API (9fd57fa). I'll be adding missing stubs and transferring the documentation to code.

slarson commented 10 years ago

@mwatts15 looking good!