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Local function support #412

merged 12 commits into from Sep 25, 2019


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alubbock commented Feb 4, 2019

Local functions are defined are mathematical rate law expressions which are evaluated separately for every molecular instance. This can greatly reduce the number of expressions required in a model.

See Sneddon et al. for further details and a motivating example.

The PR adds a new core construct, pysb.core.Tag and operator @ for adding tags. Here is an example model automatically converted from BioNetGen's localfunc.bngl example:

from pysb import Model, Monomer, Parameter, Expression, Compartment, Rule, Observable, Initial, MatchOnce, Annotation, Tag, ANY, WILD


Monomer('A', ['b', 'b', 'b'])
Monomer('B', ['a'])

Parameter('kp', 0.5)
Parameter('km', 0.1)
Parameter('k_synthC', 0.5)
Parameter('k_degrC', 0.5)
Parameter('Ab_b_b_0', 1.0)
Parameter('Ba_0', 3.0)
Parameter('C_0', 0.0)
Parameter('_Trash_0', 0.0)

Observable('Atot', A())
Observable('Btot', B())
Observable('Ctot', C())
Observable('AB0', A(b=MultiState(None, None, None)), match='species')
Observable('AB1', A(b=MultiState(1, None, None)) % B(a=1), match='species')
Observable('AB2', A(b=MultiState(1, 2, None)) % B(a=1) % B(a=2), match='species')
Observable('AB3', A(b=MultiState(1, 2, 3)) % B(a=1) % B(a=2) % B(a=3), match='species')
Observable('AB_motif', A(b=1) % B(a=1))


Expression('f_synth', k_synthC*AB_motif(x)**2)
Expression('_rateLaw1', f_synth(x))

Rule('_R1', A() @ x >> A() @ x + C(), _rateLaw1)
Rule('_R2', A(b=None) + B(a=None) | A(b=1) % B(a=1), kp, km)
Rule('_R3', C() >> Trash(), k_degrC)

Initial(A(b=MultiState(None, None, None)), Ab_b_b_0)
Initial(B(a=None), Ba_0)
Initial(C(), C_0)
Initial(Trash(), _Trash_0, fixed=True)

Note that x has been defined as a tag, and the expression f_synth and rule _R1 are dependent on that tag.


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coveralls commented Feb 4, 2019

Coverage Status

Coverage increased (+0.9%) to 79.52% when pulling 3753cdf on alubbock:localfxns into 4f9f4a1 on pysb:master.

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jmuhlich left a comment

Sorry for the delay in getting to this. Incidentally, the energy-BNG framework introduces derived expressions as well, but I think you handled it better here than I did in my energy branch. Looking forward to getting this merged.

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codecov-io commented Sep 23, 2019

Codecov Report

Merging #412 into master will increase coverage by 0.21%.
The diff coverage is 89.72%.

Impacted file tree graph

@@            Coverage Diff             @@
##           master     #412      +/-   ##
+ Coverage   79.44%   79.65%   +0.21%     
  Files          96       96              
  Lines        9677     9901     +224     
+ Hits         7688     7887     +199     
- Misses       1989     2014      +25
Impacted Files Coverage Δ
pysb/ 76.92% <ø> (ø) ⬆️
pysb/generator/ 96.77% <100%> (+0.14%) ⬆️
pysb/tests/ 100% <100%> (ø) ⬆️
pysb/ 88% <100%> (+1.04%) ⬆️
pysb/tests/ 97.19% <100%> (+0.72%) ⬆️
pysb/export/ 92.1% <100%> (+0.21%) ⬆️
pysb/simulator/ 91.07% <100%> (ø) ⬆️
pysb/tests/ 95.45% <100%> (+0.26%) ⬆️
pysb/simulator/ 89.41% <57.14%> (-0.79%) ⬇️
pysb/ 91.94% <80%> (-1.27%) ⬇️
... and 3 more

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jmuhlich commented Sep 25, 2019


@alubbock alubbock merged commit 9a552c8 into pysb:master Sep 25, 2019
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@alubbock alubbock deleted the alubbock:localfxns branch Sep 25, 2019
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