SBML Level 3 Package Proposal: Stochastic Differential Equations (SDE)

[Lucian Smith]

Hey, everyone!  We've been talking about this at COMBINE and HARMONY meetings, but finally, following the Level 3 Package Development process, T.J. Sego, Rahuman Sheriff, and I would like to formally propose that the SBML community accept the idea:  "We should develop a L3 package for stochastic differential equations."

Here is the full proposal:

https://docs.google.com/document/d/1od1ZWv6apH4XPqcXbBR_Al_uwiOA1jmCuq2uIzJ29jk/edit?tab=t.0#heading=h.i11tldx2xa35

Note that this is a *proposal*, not a *draft specification*.  While we would love to have everyone's comments on the draft spec, what we need to start the official process is a vote by the community that just says, "Yes, we should have a package that covers this."

So!  This begins a formal 2-week 'call for feedback' time.  Feel free to comment here or on the document itself with any comments, complaints, or suggestions you might have.

In two weeks, we'll vote, and if the result is 'accept', we'll formally invite people to a package working group and work on the specification itself will continue.

Full details of the package development process can be found:

https://sbml.org/documents/process/level-3-process/

Thank you all!

-Lucian Smith

[Lucian Smith]

Thanks to everyone who's been commenting on the proposal and draft specification for SDE.  Most of the comments thus far have been about the specification itself, instead of on the 'proposal' side of things.  We welcome more contributions to the discussion, at:

https://docs.google.com/document/d/1g_lVAZGEW4VQg_h1yOOHJvMR_Hphp77Ss3_O7HaomF8/

My own interpretation of the current points of contention are that they concern the scope and implementation details of the proposed package, not whether the package as a whole should be worked on.  As such, I would like to go ahead and call for votes on the *proposal* on Monday.  But if people disagree, let me know!  

-Lucian Smith

[Hoops, Stefan (sh9cq)]

Hello Lucian,

It might seem that this is a minor point but I would suggest that we
remove the implementation SDE of the simulation from the proposal
title. I prefer to use some thing: 
Intrinsic Noise Specification. 

Thus the scope will be broader as it is not limited to SDEs though
those will probalby the main use case. Additionally the new title names
the additional model component described.

Thanks,
Stefan

--
Stefan Hoops, Ph.D.
Research Associate Professor
Biocomplexity Institute & Initiative
University of Virginia
995 Research Park Boulevard
Charlottesville, VA 22911

Phone: +1 540 570 1301
Email: sho...@virginia.edu

[Lucian Smith]

I am certainly not opposed to expanding the scope of the package, but I would want to know exactly how it was going to be expanded, and what kind of modeling would additionally be covered.  Currently, the only concrete proposed change to the draft specification I've seen has been to *limit* the scope of the package from 'SDEs using a variety of integrals' to 'SDEs using the Ito integral alone'.

What other forms of 'intrinsic noise' are being proposed?  What kind of modeling would they allow that the current proposal/spec does not?

If it's currently unclear what the answers to those questions are, I think it would be OK to defer that to the package working group to work on in the coming months.  But if people have a clear idea now, that'd be great.

-Lucian

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