def step(env, rxn, inputs=None):
'''Crosslink DNA/proteins
Notes: some things about this protocol could be changed to make it
amenable to automation. It could also be performed as hybrid auto/nonauto.
'''
env.rprotocol.step('crosslink', 'Crosslink DNA/proteins.')
pel, cro, que, fin = rxn.reactions
# Pellet
s = pellet(env, s, pel.pellet)
s = wash(env, s, pel.wash)
s = resuspend_to_od_target(env, s, pel.params.odtarget)
# Perform serial dilution, measure OD, determine dilution for OD600:0.2
# Crosslinking
s = react(env, cro.solution, cro.incubation, inputs)
# Quench
s_1, s_2 = split(env, s)
s_gly = react(env, que.solution, que.incubation, s_1)
s_tris = react(env, que.solution, que.incubation, s_2)
s = wash(env, s, que.wash, reps=2)
# Wash, measure OD600
s, m = measure(env, s, 'OD:600')
m *= 8e8*ureg.cells/ureg.milliliter
# ** Update sample cell concentrations **
# Wash and resuspend to desired concentration
# Split 1ml aliquots into 50ul aliquots?
s = wash(env, s, wsh.wash)
return s
def step(env, rxn, inputs=None):
'''Crosslink DNA/proteins
Notes: some things about this protocol could be changed to make it
amenable to automation. It could also be performed as hybrid auto/nonauto.
'''
env.rprotocol.step('crosslink', 'Crosslink DNA/proteins.')
pel, cro, que, fin = rxn.reactions
# Pellet
s = pellet(env, s, pel.pellet)
s = wash(env, s, pel.wash)
s = resuspend_to_od_target(env, s, pel.params.odtarget)
# Perform serial dilution, measure OD, determine dilution for OD600:0.2
# Crosslinking
s = react(env, cro.solution, cro.incubation, inputs)
# Quench
s_1, s_2 = split(env, s)
s_gly = react(env, que.solution, que.incubation, s_1)
s_tris = react(env, que.solution, que.incubation, s_2)
s = wash(env, s, que.wash, reps=2)
# Wash, measure OD600
s, m = measure(env, s, 'OD:600')
m *= 8e8 * ureg.cells / ureg.milliliter
# ** Update sample cell concentrations **
# Wash and resuspend to desired concentration
# Split 1ml aliquots into 50ul aliquots?
s = wash(env, s, wsh.wash)
return s
def step(env, rxn, inputs=None):
'''Enzymatic cellular lysis.'''
env.rprotocol.step('lysis', 'Enzymatic cellular lysis.')
lys, prp = rxn.reactions
s = react(env, lys.solution, lys.incubation, inputs)
s = react(env, prp.solution, prp.incubation, s)
return s
def step(env, rxn, inputs=None):
'''Reverse chromatin crosslinks'''
env.rprotocol.step('reversal', 'Reverse chromatin crosslinks')
rna, pk = rxn.reactions
s, t = relocate_volume(env, inputs, vol=5 * ureg.microliter)
s = react(env, rna.solution, rna.incubation, t)
s = react(env, pk.solution, pk.incubation, s)
return s
def step(env, rxn, inputs=None):
'''Reverse chromatin crosslinks'''
env.rprotocol.step('reversal', 'Reverse chromatin crosslinks')
rna, pk = rxn.reactions
s, t = relocate_volume(env, inputs, vol=5*ureg.microliter)
s = react(env, rna.solution, rna.incubation, t)
s = react(env, pk.solution, pk.incubation, s)
return s
def test_react(self, run=True):
if run:
from pcompile.operations import react
tc = TestContext()
rxn = tc.env.reactions.get_current()
target = rxn.solution
incubation = []
inactivation = {}
inputs = rxn.inputs
# So want to run this without actually doing the optimization...
react(tc.env, target, incubation, inactivation, inputs)
def step(env, rxn, inputs=None):
'''Digestion of DNA'''
env.rprotocol.step('digestion', 'Digestion of DNA/proteins.')
dig = rxn.reactions[0]
s = react(env, dig.solution, dig.incubation, inputs)
return s
def step(env, rxn, inputs=None):
'''Digestion of DNA'''
env.rprotocol.step('digestion', 'Digestion of DNA/proteins.')
dig = rxn.reactions[0]
s = react(env, dig.solution, dig.incubation, inputs)
return s
def step(env, rxn, inputs=None):
'''Automated polymerase chain reaction.'''
env.rprotocol.step('pcr', 'Automated polymerase chain reaction')
repcr = rxn.reactions[0]
s = react(env, repcr.solution, repcr.incubation, inputs)
#s = seal(env, s)
s = thermocycle(env, s, repcr.params)
#s = unseal(env, s)
return s
def step(env, rxn, inputs=None):
'''Automated polymerase chain reaction.'''
env.rprotocol.step('pcr', 'Automated polymerase chain reaction')
repcr = rxn.reactions[0]
s = react(env, repcr.solution, repcr.incubation, inputs)
#s = seal(env, s)
s = thermocycle(env, s, repcr.params)
#s = unseal(env, s)
return s
def step(env, rxn, inputs=None):
'''DNA Ligation'''
env.rprotocol.step('ligation', 'DNA Ligation.')
lig = rxn.reactions[0]
s, t = relocate_volume(env, inputs, vol=5 * ureg.microliter)
s = react(env, lig.solution, lig.incubation, t)
return s
def step(env, rxn, inputs=None):
'''DNA Ligation'''
env.rprotocol.step('ligation', 'DNA Ligation.')
lig = rxn.reactions[0]
s, t = relocate_volume(env, inputs, vol=5*ureg.microliter)
s = react(env, lig.solution, lig.incubation, t)
return s