well.set_properties({'area' : well_area})
# Set concentrations of well components
if row == 'A':
well.set_properties({'concentrations' : {receptor_name : Pstated, ligand_name : Lstated[column]} })
well.set_properties({'concentration_uncertainties' : {receptor_name : 0.10 * Pstated, ligand_name : 0.08 * Lstated[column]} })
elif row == 'B':
well.set_properties({'concentrations' : {ligand_name : Lstated[column]} })
well.set_properties({'concentration_uncertainties' : {ligand_name : 0.08 * Lstated[column]} })
# Attach plate reader data
for wavelength in ['280', '350', '480']:
well.set_properties({' absorbance_' + wavelength + 'nm' : data['Abs_' + wavelength]['well_data'][well_name] })
emission_wavelength = '480'
for excitation_wavelength in ['280', '350']:
well.set_properties({'fluorescence_top_ex' + excitation_wavelength + 'nm_em' + emission_wavelength + 'nm' : data[excitation_wavelength + '_TopRead']['well_data'][well_name]})
well.set_properties({'fluorescence_bottom_ex' + excitation_wavelength + 'nm_em' + emission_wavelength + 'nm' : data[excitation_wavelength + '_BottomRead']['well_data'][well_name]})
# Add to well group
well_group.append(well)
# TODO: Analyze the well group.
# This is just a non-working stub for now.
# Create a model
from assaytools.analysis import CompetitiveBindingAnalysis
model = CompetitiveBindingAnalysis(wells=well_group, receptor=receptor_name, ligands=[ligand_name])
# fit the maximum a posteriori (MAP) estimate
map = model.map_fit()
# run some MCMC sampling and return the MCMC object
mcmc = model.run_mcmc()
' absorbance_' + wavelength + 'nm':
data['Abs_' + wavelength]['well_data'][well_name]
})
emission_wavelength = '480'
for excitation_wavelength in ['280', '350']:
well.set_properties({
'fluorescence_top_ex' + excitation_wavelength + 'nm_em' + emission_wavelength + 'nm':
data[excitation_wavelength +
'_TopRead']['well_data'][well_name]
})
well.set_properties({
'fluorescence_bottom_ex' + excitation_wavelength + 'nm_em' + emission_wavelength + 'nm':
data[excitation_wavelength +
'_BottomRead']['well_data'][well_name]
})
# Add to well group
well_group.append(well)
# TODO: Analyze the well group.
# This is just a non-working stub for now.
# Create a model
from assaytools.analysis import CompetitiveBindingAnalysis
model = CompetitiveBindingAnalysis(wells=well_group,
receptor=receptor_name,
ligands=[ligand_name])
# fit the maximum a posteriori (MAP) estimate
map = model.map_fit()
# run some MCMC sampling and return the MCMC object
mcmc = model.run_mcmc()
