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): '''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