isaacsas

# Created by BioNetGen 2.7.0
begin parameters
    1 Lig_tot    6000  # Constant
    2 Rec_tot    400  # Constant
    3 Lyn_tot    28  # Constant
    4 Syk_tot    400  # Constant
    5 kp1        1.328452377888242e-6  # Constant
    6 km1        0  # Constant
    7 kp2        2.5e-1  # Constant
    8 km2        0  # Constant

isaacsas

# NEEDS DiffEqBiological master as of 4/20/19
using DiffEqBase, DiffEqBiological, OrdinaryDiffEq, Sundials, LinearAlgebra, SparseArrays
using ReactionNetworkImporters
using TimerOutputs

# parameters
const networkname = "testbcrbng"
const tf = 10000.

# finite difference

isaacsas

using DiffEqBiological, Plots
rn = @reaction_network begin
         k1, 0 --> Y
         k2p, Y --> 0
         k2pp*P, Y --> 0
         mm(1-P,(k3p+k3pp*A),J3), 0 --> P
         mmr(P,k4*m/J4,J4), Y + P --> Y 
end k1 k2p k2pp k3p k3pp A J3 k4 m J4
p = [0.04,0.04,1.,1.,10.0,0.,0.04,35.,.1,.04]

isaacsas

using DiffEqBiological, SteadyStateDiffEq

rn = @reaction_network begin
  k1, 0 --> Y
  k2p, Y --> 0
  k2pp*P, Y --> 0
  mmr(Po,(k3p+k3pp*A)/J3,J3), Po-->P
  mmr(P,k4*m/J4,J4), Y + P --> Y + Po
end k1 k2p k2pp k3p k3pp A J3 k4 m J4
p = [0.04,0.04,1.,1.,10.0,0.,0.04,35.,.1,.04]

isaacsas

This will have an image of the desired bifurcation plot

isaacsas

S1 = 30000
S2 = 30000
S3 = 30000
S4 = 30000
S5 = 30000
S6 = 30000
S7 = 0
S8 = 0
S9 = 0
S10 = 0

isaacsas

# Created by BioNetGen 2.3.1
begin parameters
    1 p1                 3.0e5  # Constant
    2 p2                 10.0  # Constant
    3 p3                 3.0e-4  # Constant
    4 p4                 3.0e-7  # Constant
    5 p5                 30.0  # Constant
    6 p6                 3.0e-5  # Constant
    7 p7                 0.3  # Constant
    8 p8                 0.1  # Constant

isaacsas

using DiffEqBase, DiffEqJump
using Plots; plotlyjs()

tf      = .01
u0      = [200, 100, 150]

# MODEL SETUP

# DiffEqBiological Version:
using DiffEqBiological

isaacsas

mutable struct DirectMAJumpAggregation{T,S,F1,F2,V} <: AbstractSSAJumpAggregator
    next_jump_time::T         # required field for SSAs, stores time of next jump
    next_jump::Int64          # required field for SSAs, stores index of next jump
    end_time::T               # required field for SSAs, stores time to stop simulation
    cur_rates::Vector{T}      # mass action rates followed by constant_jump rates
    sum_rate::T
    ma_jumps::S
    rates::F1
    affects!::F2
    save_positions::Tuple{Bool,Bool} # required field for SSAs, determines saving of output

isaacsas

mutable struct DirectMAJumpAggregation{T,S,F1,F2} <: AbstractJumpAggregator
    next_jump_time::T
    next_jump::Int64
    end_time::T
    cur_rates::Vector{T}      # mass action rates followed by constant_jump rates
    sum_rate::T
    ma_jumps::S
    rates::F1
    affects!::F2
    save_positions::Tuple{Bool,Bool}