def SSAModel(base, vol, nrep=1, y0_pop=None):
""" nrep repeats the model (uncoupled system) to allow for the
passing of a matrix of initial values. y0_pop should be a matrix of
size (NREP x NEQ) """
if y0_pop is None:
y0_pop = np.tile((vol * base.y0[:-1]), (nrep, 1)).astype(int)
else:
y0_pop = vol * y0_pop
stoch_fn = stk.StochKitModel(name=base.model.getOption('name') +
'_stoch_' + str(nrep))
bd = mb.SSA_builder(mb.SSA_builder.expand_labelarray(base.ylabels, nrep),
mb.SSA_builder.expand_labelarray(base.plabels, nrep),
y0_pop.flatten(order='C'),
np.tile(base.paramset, (nrep, 1)).flatten(order='C'),
stoch_fn, vol)
for index in xrange(nrep):
si = '_' + str(index)
bd.SSA_tyson_x('x prod nonlinear term' + si, 'X' + si, 'Y' + si,
'P' + si)
bd.SSA_MA_deg('x degradation' + si, 'X' + si, '1')
bd.SSA_MA_tln('y creation' + si, 'Y' + si, 'kt' + si, 'X' + si)
bd.SSA_MA_deg('y degradation linear' + si, 'Y' + si, 'kd' + si)
bd.SSA_tyson_y('y nonlinear term' + si, 'Y' + si, 'a0' + si, 'a1' + si,
'a2' + si)
return stoch_fn
def SSAModel(base, vol, nrep=1, y0_pop=None):
""" nrep repeats the model (uncoupled system) to allow for the
passing of a matrix of initial values. y0_pop should be a matrix of
size (NREP x NEQ) """
if y0_pop is None:
y0_pop = np.tile((vol * base.y0[:-1]), (nrep, 1)).astype(int)
else:
y0_pop = vol * y0_pop
stoch_fn = stk.StochKitModel(name=base.model.getOption('name') +
'_stoch_' + str(nrep))
bd = mb.SSA_builder(mb.SSA_builder.expand_labelarray(base.ylabels, nrep),
mb.SSA_builder.expand_labelarray(base.plabels, nrep),
y0_pop.flatten(order='C'),
np.tile(base.paramset, (nrep, 1)).flatten(order='C'),
stoch_fn, vol)
# ADD REACTIONS
# =============
#
for index in xrange(nrep):
si = '_' + str(index)
bd.SSA_MA(name="Y1_production" + si,
reactants={bd.species_array[bd.ydict['Y2' + si]]: 1},
products={bd.species_array[bd.ydict['Y1' + si]]: 1},
rate=bd.param_array[bd.pdict['c1x1' + si]])
bd.SSA_MA(name="Y1_Y2_deg" + si,
reactants={
bd.species_array[bd.ydict['Y1' + si]]: 1,
bd.species_array[bd.ydict['Y2' + si]]: 1
},
rate=bd.param_array[bd.pdict['c2' + si]])
bd.SSA_MA(name="Y1_X2" + si,
reactants={bd.species_array[bd.ydict['Y1' + si]]: 1},
products={
bd.species_array[bd.ydict['Y1' + si]]: 2,
bd.species_array[bd.ydict['Y3' + si]]: 1
},
rate=bd.param_array[bd.pdict['c3x2' + si]])
bd.SSA_MA(name="Y1_deg" + si,
reactants={bd.species_array[bd.ydict['Y1' + si]]: 2},
rate=bd.param_array[bd.pdict['c4' + si]])
bd.SSA_MA(name="Y2_prod" + si,
reactants={bd.species_array[bd.ydict['Y3' + si]]: 1},
products={bd.species_array[bd.ydict['Y2' + si]]: 1},
rate=bd.param_array[bd.pdict['c5x3' + si]])
return stoch_fn
def SSAModel(base, vol, nrep=1, y0_pop=None):
""" nrep repeats the model (uncoupled system) to allow for the
passing of a matrix of initial values. y0_pop should be a matrix of
size (NREP x NEQ) """
if y0_pop is None:
y0_pop = np.tile((vol*base.y0[:-1]), (nrep, 1)).astype(int)
else: y0_pop = vol*y0_pop
stoch_fn = stk.StochKitModel(
name=base.model.getOption('name') + '_stoch_' + str(nrep))
bd = mb.SSA_builder(
mb.SSA_builder.expand_labelarray(base.ylabels, nrep),
mb.SSA_builder.expand_labelarray(base.plabels[1:], nrep),
y0_pop.flatten(order='C'),
np.tile(base.paramset, (nrep, 1)).flatten(order='C'),
stoch_fn, vol)
# ADD REACTIONS
# =============
#
for index in xrange(nrep):
si = '_' + str(index)
bd.SSA_MM_P_Goodwin('X1 Production'+si,
Prod='X1'+si, Rep='X3'+si,
P=int(base.paramset[base.pdict['h']]))
bd.SSA_MA_tln('X2 Production'+si, 'X2'+si, '1', 'X1'+si)
bd.SSA_MA_tln('X3 Production'+si, 'X3'+si, '1', 'X2'+si)
bd.SSA_MA(name="X1 Deg" + si,
reactants={bd.species_array[bd.ydict['X1' + si]]:1},
rate=bd.param_array[bd.pdict['a' + si]])
bd.SSA_MA(name="X2 Deg" + si,
reactants={bd.species_array[bd.ydict['X2' + si]]:1},
rate=bd.param_array[bd.pdict['i' + si]])
bd.SSA_MA(name="X3 Deg" + si,
reactants={bd.species_array[bd.ydict['X3' + si]]:1},
rate=bd.param_array[bd.pdict['r' + si]])
return stoch_fn
def SSAModel(base, vol):
""" Abandoning, as stochkit (at least the python version) does not
want to handle a tri-molecular reaction. Expansion into multiple
events (i.e. oregonator) will be tried next """
y0_pop = (vol * base.y0[:-1]).astype(int)
stoch_fn = stk.StochKitModel(name=base.model.getOption('name') + '_stoch')
bd = mb.SSA_builder(base.ylabels, base.plabels, y0_pop, base.paramset,
stoch_fn, vol)
# ADD REACTIONS
# =============
rxn1 = stk.Reaction(name="Y1_production",
products={bd.species_array[bd.ydict['Y1']]: 1},
massaction=True,
rate=bd.param_array[bd.pdict['c1x1']])
bd.SSAmodel.addReaction(rxn1)
rxn2 = stk.Reaction(name="Y2_from_Y1",
reactants={bd.species_array[bd.ydict['Y1']]: 1},
products={bd.species_array[bd.ydict['Y2']]: 1},
massaction=True,
rate=bd.param_array[bd.pdict['c2x2']])
bd.SSAmodel.addReaction(rxn2)
rxn3 = stk.Reaction(name="trimolecular",
reactants={
bd.species_array[bd.ydict['Y1']]: 2,
bd.species_array[bd.ydict['Y2']]: 1
},
products={bd.species_array[bd.ydict['Y1']]: 3},
massaction=True,
rate=bd.param_array[bd.pdict['c3']])
bd.SSAmodel.addReaction(rxn3)
rxn4 = stk.Reaction(name="Y2_deg",
reactants={bd.species_array[bd.ydict['Y2']]: 1},
massaction=True,
rate=bd.param_array[bd.pdict['c4']])
bd.SSAmodel.addReaction(rxn4)
return stoch_fn
def SSAModel(base, vol, nrep=1, y0_pop=None):
if y0_pop is None:
y0_pop = np.tile((vol * base.y0[:-1]), (nrep, 1)).astype(int)
else:
y0_pop = vol * y0_pop
stoch_fn = stk.StochKitModel(name=base.model.getOption('name') +
'_stoch_' + str(nrep))
bd = mb.SSA_builder(mb.SSA_builder.expand_labelarray(base.ylabels, nrep),
mb.SSA_builder.expand_labelarray(base.plabels, nrep),
y0_pop.flatten(order='C'),
np.tile(base.paramset, (nrep, 1)).flatten(order='C'),
stoch_fn, vol)
# ADD REACTIONS
# =============
for index in xrange(nrep):
si = '_' + str(index)
# Per mRNA
bd.SSA_MM_P('per mRNA repression' + si,
'vtp' + si,
km=['knp' + si],
Prod=['p' + si],
Rep=['C1P' + si, 'C2P' + si],
P=3)
bd.SSA_MM('per mRNA degradation' + si,
'vdp' + si,
km=['kdp' + si],
Rct=['p' + si])
# Cry1 mRNA
bd.SSA_MM_P('c1 mRNA repression' + si,
'vtc1' + si,
km=['knc1' + si],
Prod=['c1' + si],
Rep=['C1P' + si, 'C2P' + si],
P=3)
bd.SSA_MM('c1 mRNA degradation' + si,
'vdc1' + si,
km=['kdc1' + si],
Rct=['c1' + si])
# Cry2 mRNA (shares cry1 km constants)
bd.SSA_MM_P('c2 mRNA repression' + si,
'vtc2' + si,
km=['knc1' + si],
Prod=['c2' + si],
Rep=['C1P' + si, 'C2P' + si],
P=3)
bd.SSA_MM('c2 mRNA degradation' + si,
'vdc2' + si,
km=['kdc1' + si],
Rct=['c2' + si])
# Free protein creation and degradation
bd.SSA_MA_tln('PER translation' + si, 'P' + si, 'ktxnp' + si, 'p' + si)
bd.SSA_MA_tln('CRY1 translation' + si, 'C1' + si, '1', 'c1' + si)
bd.SSA_MA_tln('CRY2 translation' + si, 'C2' + si, '1', 'c2' + si)
bd.SSA_MM('PER degradation' + si,
'vdP' + si,
km=['kdP' + si],
Rct=['P' + si])
bd.SSA_MM('C1 degradation' + si,
'vdC1' + si,
km=['kdC1' + si],
Rct=['C1' + si])
bd.SSA_MM('C2 degradation' + si,
'vdC2' + si,
km=['kdC1' + si],
Rct=['C2' + si])
#CRY1 CRY2 complexing
bd.SSA_MA_complex('CRY1-P complex' + si, 'C1' + si, 'P' + si,
'C1P' + si, 'vaC1P' + si, 'vdC1P' + si)
bd.SSA_MA_complex('CRY2-P complex' + si, 'C2' + si, 'P' + si,
'C2P' + si, 'vaC1P' + si, 'vdC1P' + si)
bd.SSA_MM('C1P degradation' + si,
'vdCn' + si,
km=['kdCn' + si],
Rct=['C1P' + si, 'C2P' + si])
bd.SSA_MM_C2('C2P degradation' + si,
'vdCn' + si,
km=['kdCn' + si],
Rct=['C2P' + si, 'C1P' + si],
M='MC2n' + si)
return stoch_fn
def SSAModel(base, vol):
y0_pop = (vol * base.y0[:-1]).astype(int)
stoch_fn = stk.StochKitModel(name=base.model.getOption('name') + '_stoch')
SSA_builder = mb.SSA_builder(base.ylabels, base.plabels, y0_pop,
base.paramset, stoch_fn, vol)
# ADD REACTIONS
# =============
# Per mRNA
SSA_builder.SSA_MM_P('per mRNA repression',
'vtp',
km=['knp'],
Prod=['p'],
Rep=['C1P', 'C2P'],
P=3)
SSA_builder.SSA_MM('per mRNA degradation', 'vdp', km=['kdp'], Rct=['p'])
# Cry1 mRNA
SSA_builder.SSA_MM_P('c1 mRNA repression',
'vtc1',
km=['knc1'],
Prod=['c1'],
Rep=['C1P', 'C2P'],
P=3)
SSA_builder.SSA_MM('c1 mRNA degradation', 'vdc1', km=['kdc1'], Rct=['c1'])
# Cry2 mRNA (shares cry1 km constants)
SSA_builder.SSA_MM_P('c2 mRNA repression',
'vtc2',
km=['knc1'],
Prod=['c2'],
Rep=['C1P', 'C2P'],
P=3)
SSA_builder.SSA_MM('c2 mRNA degradation', 'vdc2', km=['kdc1'], Rct=['c2'])
# Free protein creation and degradation
SSA_builder.SSA_MA_tln('PER translation', 'P', 'ktxnp', 'p')
SSA_builder.SSA_MA_tln('CRY1 translation', 'C1', '1', 'c1')
SSA_builder.SSA_MA_tln('CRY2 translation', 'C2', '1', 'c2')
SSA_builder.SSA_MM('PER degradation', 'vdP', km=['kdP'], Rct=['P'])
SSA_builder.SSA_MM('C1 degradation', 'vdC1', km=['kdC1'], Rct=['C1'])
SSA_builder.SSA_MM('C2 degradation', 'vdC2', km=['kdC1'], Rct=['C2'])
#CRY1 CRY2 complexing
SSA_builder.SSA_MA_complex('CRY1-P complex', 'C1', 'P', 'C1P', 'vaC1P',
'vdC1P')
SSA_builder.SSA_MA_complex('CRY2-P complex', 'C2', 'P', 'C2P', 'vaC1P',
'vdC1P')
SSA_builder.SSA_MM('C1P degradation',
'vdCn',
km=['kdCn'],
Rct=['C1P', 'C2P'])
SSA_builder.SSA_MM_C2('C2P degradation',
'vdCn',
km=['kdCn'],
Rct=['C2P', 'C1P'],
M='MC2n')
return stoch_fn