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Minor Updates to case studies #2

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1 change: 1 addition & 0 deletions case_studies/Fig10_Groves2016/Groves2016_AND_ordered-complex.kinda
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36 changes: 19 additions & 17 deletions case_studies/Fig10_Groves2016/fig10_simulate_AND.py
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Original file line number Diff line number Diff line change
Expand Up @@ -60,23 +60,25 @@ def simulate(sim_mode):

return sstats, list(zip(rxns, rxn_times))

if MODE == 'demo':
params = {
'relative_error': 0.5,
'init_batch_size': 50,
'max_batch_size': 5000,
'max_sims': 5000,
if __name__ == "__main__":

if MODE == 'demo':
params = {
'relative_error': 0.5,
'init_batch_size': 50,
'max_batch_size': 5000,
'max_sims': 5000,
}
elif MODE == 'publication':
params = {
'relative_error': 0.025,
'init_batch_size': 500,
'max_batch_size': 10000,
'max_sims': 500000,
'sims_per_worker': 5
elif MODE == 'publication':
params = {
'relative_error': 0.025,
'init_batch_size': 500,
'max_batch_size': 10000,
'max_sims': 500000,
'sims_per_worker': 5
}

## Run simulations at each mode
sstats_disassoc = simulate('ordered-complex')
sstats_cbc = simulate('count-by-complex')
sstats_cbd = simulate('count-by-domain')
## Run simulations at each mode
sstats_disassoc = simulate('ordered-complex')
sstats_cbc = simulate('count-by-complex')
sstats_cbd = simulate('count-by-domain')
43 changes: 22 additions & 21 deletions case_studies/Fig10_Groves2016/fig10_simulate_OR.py
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Original file line number Diff line number Diff line change
Expand Up @@ -63,24 +63,25 @@ def simulate(sim_mode, **params):

return sstats, list(zip(rxns, rxn_times))

## Set up parameters dict
if MODE == 'demo':
params = {
'relative_error': 0.5,
'init_batch_size': 50,
'max_batch_size': 5000,
'max_sims': 5000,
}
elif MODE == 'publication':
params = {
'relative_error': 0.025,
'init_batch_size': 1000,
'max_batch_size': 25000,
'max_sims': 500000,
'sims_per_worker': 25
}

## Run simulations at each mode
sstats_disassoc, rxn_times_disassoc = simulate('ordered-complex', **params)
sstats_cbc, rxn_times_cbc = simulate('count-by-complex', **params)
sstats_cbd, rxn_times_cbd = simulate('count-by-domain', **params)
if __name__ == "__main__":
## Set up parameters dict
if MODE == 'demo':
params = {
'relative_error': 0.5,
'init_batch_size': 50,
'max_batch_size': 5000,
'max_sims': 5000,
}
elif MODE == 'publication':
params = {
'relative_error': 0.025,
'init_batch_size': 1000,
'max_batch_size': 25000,
'max_sims': 500000,
'sims_per_worker': 25
}

## Run simulations at each mode
sstats_disassoc, rxn_times_disassoc = simulate('ordered-complex', **params)
sstats_cbc, rxn_times_cbc = simulate('count-by-complex', **params)
sstats_cbd, rxn_times_cbd = simulate('count-by-domain', **params)
4 changes: 2 additions & 2 deletions case_studies/Fig10_Groves2016/fig10d.py
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Original file line number Diff line number Diff line change
Expand Up @@ -29,8 +29,8 @@ def plot_reaction_data(rxns_reactants, datasets, dataset_labels, dataset_colors,
k2_err[:, i] = [rxn_stats.get_k2_error(max_sims=0) for rxn_stats in rxns_stats]

left = np.arange(num_rxns)*(num_datasets+1) + i
axes_k1.bar(left = left, height = k1[:,i], width=1, yerr = k1_err[:,i], capsize = 5, color = dataset_colors[i], edgecolor = '0.0')
axes_k2.bar(left = left, height = k2[:,i], width=1, yerr = k2_err[:,i], capsize = 5, color = dataset_colors[i], edgecolor = '0.0')
axes_k1.bar(x = left, height = k1[:,i], width=1, yerr = k1_err[:,i], capsize = 5, color = dataset_colors[i], edgecolor = '0.0')
axes_k2.bar(x = left, height = k2[:,i], width=1, yerr = k2_err[:,i], capsize = 5, color = dataset_colors[i], edgecolor = '0.0')

xticks = np.arange(num_rxns)*(num_datasets+1) + (num_datasets-1)/2.
xlabels = [' + '.join(r) for r in rxns_reactants]
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