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Rate law dependent synthesis #328

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kaizu opened this issue Feb 15, 2019 · 2 comments
Open

Rate law dependent synthesis #328

kaizu opened this issue Feb 15, 2019 · 2 comments
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kaizu commented Feb 15, 2019

Enable the following model:

with reaction_rules():
    ~X > X | (k * X / (K + X))

run_simulation(t, solver='gillespie')

Except for ode, no solver supports rate law dependent reactions. This proposal suggests accepting the rate law for synthetic reactions (zero-th order).
@kaizu kaizu self-assigned this Feb 15, 2019
kaizu added a commit to kaizu/ecell4_base that referenced this issue Feb 21, 2019
@kaizu
ecell#328 Support ReactionRuleDescriptor in gillespie
db727d8
kaizu added a commit to kaizu/ecell4_base that referenced this issue Feb 21, 2019
@kaizu
ecell#328 Support ReactionRuleDescriptor in meso
c5edc22
kaizu added a commit to kaizu/ecell4_base that referenced this issue Feb 21, 2019
@kaizu
ecell#328 Use stoichiometry in a descriptor
db54e8c
kaizu added a commit to kaizu/ecell4_base that referenced this issue Feb 21, 2019
@kaizu
ecell#328 Check the validity of a descriptor
ad4b794
kaizu added a commit to kaizu/ecell4_base that referenced this issue Feb 25, 2019
@kaizu
ecell#328 Fix a silly mistake
4249a04
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kaizu commented Mar 3, 2019

gillespie and meso support it now.

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kaizu commented Jun 13, 2019 •
edited

  • gillespie
  • meso
  • spatiocyte
  • bd
  • egfrd

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