def test_sauro2004_fig3 ():
network = SteadyFluxAnalyzer('''\
v1:S1=>S2
v2:ES=>S1+E
E+S2=>ES
''')
#print network
fluxes, indep_fluxes, kernel = network.get_kernel_GJE ()
variables = fluxes[network.rank:]
print network.label_matrix (kernel, ['%s='%f for f in fluxes], variables)
print network.source_data
def test_sauro2004_fig3():
network = SteadyFluxAnalyzer('''\
v1:S1=>S2
v2:ES=>S1+E
E+S2=>ES
''')
#print network
fluxes, indep_fluxes, kernel = network.get_kernel_GJE()
variables = fluxes[network.rank:]
print network.label_matrix(kernel, ['%s=' % f for f in fluxes], variables)
print network.source_data
def test_wiki_SteadyFluxAnalyzer():
from sympycore.physics.sysbio import SteadyFluxAnalyzer
print
example_network = '''
A => B
B => C
B <=> D
C => D
C => E
D => E
A <=
C =>
D =>
E =>
'''
print example_network
ex = SteadyFluxAnalyzer (example_network, split_bidirectional_fluxes = True)
print ex
print 'reactions:'
print ex.reactions
print 'fluxes:'
print ex.species
ex.compute_kernel_GJE ()
fluxes, indep_fluxes, kernel = ex.get_kernel_GJE ()
print 'fluxes:'
print fluxes
print 'rank:'
print ex.rank
print 'kernel:'
print kernel
print ex.label_matrix (kernel, fluxes, indep_fluxes)
dependent_candidates=[r for r in ex.reactions if r.count ('_')>1]
#dependent_candidates = ['R_A_B', 'R_B_C', 'R_B_D','R_C_E', 'R_A']
print 'dependent_candidates:'
print dependent_candidates
ex.compute_kernel_GJE(dependent_candidates=dependent_candidates)
fluxes, indep_fluxes, kernel = ex.get_kernel_GJE()
print 'fluxes:'
print fluxes
print 'indep_fluxes:'
print ex.label_matrix (kernel, fluxes, indep_fluxes)
dep_fluxes = fluxes[:ex.rank]
indep_symbols = map(Symbol,indep_fluxes)
for i in range(ex.rank): print dep_fluxes[i],'=',[indep_symbols] * kernel[i].T
fluxes, indep_fluxes, kernel = ex.get_kernel_GJE(ex.reactions)
print 'ex.stoichiometry * kernel:'
print ex.stoichiometry * kernel
print ex.label_matrix (kernel, fluxes, indep_fluxes)
ex.compute_kernel_SVD()
fluxes, kernel = ex.get_kernel_SVD()
alpha = ['a%s'%i for i in range(kernel.shape[1])]
print fluxes
print kernel.round(decimals=3)
print ex.label_matrix (Matrix(kernel.round(decimals=3)), fluxes, alpha)
import numpy
print numpy.dot(kernel.T, kernel).round(decimals=3)
print 'statistics:'
ex.show_statistics ()
return
print 'large system:'
ex = SteadyFluxAnalyzer ('http://www.biomedcentral.com/content/supplementary/1752-0509-4-160-s2.xml',
add_boundary_fluxes = True)
ex.compute_kernel_GJE()
ex.compute_kernel_SVD()
ex.show_statistics ()
print ex.get_relation_SVD_error ()
def test_wiki_SteadyFluxAnalyzer():
from sympycore.physics.sysbio import SteadyFluxAnalyzer
print
example_network = '''
A => B
B => C
B <=> D
C => D
C => E
D => E
A <=
C =>
D =>
E =>
'''
print example_network
ex = SteadyFluxAnalyzer(example_network, split_bidirectional_fluxes=True)
print ex
print 'reactions:'
print ex.reactions
print 'fluxes:'
print ex.species
ex.compute_kernel_GJE()
fluxes, indep_fluxes, kernel = ex.get_kernel_GJE()
print 'fluxes:'
print fluxes
print 'rank:'
print ex.rank
print 'kernel:'
print kernel
print ex.label_matrix(kernel, fluxes, indep_fluxes)
dependent_candidates = [r for r in ex.reactions if r.count('_') > 1]
#dependent_candidates = ['R_A_B', 'R_B_C', 'R_B_D','R_C_E', 'R_A']
print 'dependent_candidates:'
print dependent_candidates
ex.compute_kernel_GJE(dependent_candidates=dependent_candidates)
fluxes, indep_fluxes, kernel = ex.get_kernel_GJE()
print 'fluxes:'
print fluxes
print 'indep_fluxes:'
print ex.label_matrix(kernel, fluxes, indep_fluxes)
dep_fluxes = fluxes[:ex.rank]
indep_symbols = map(Symbol, indep_fluxes)
for i in range(ex.rank):
print dep_fluxes[i], '=', [indep_symbols] * kernel[i].T
fluxes, indep_fluxes, kernel = ex.get_kernel_GJE(ex.reactions)
print 'ex.stoichiometry * kernel:'
print ex.stoichiometry * kernel
print ex.label_matrix(kernel, fluxes, indep_fluxes)
ex.compute_kernel_SVD()
fluxes, kernel = ex.get_kernel_SVD()
alpha = ['a%s' % i for i in range(kernel.shape[1])]
print fluxes
print kernel.round(decimals=3)
print ex.label_matrix(Matrix(kernel.round(decimals=3)), fluxes, alpha)
import numpy
print numpy.dot(kernel.T, kernel).round(decimals=3)
print 'statistics:'
ex.show_statistics()
return
print 'large system:'
ex = SteadyFluxAnalyzer(
'http://www.biomedcentral.com/content/supplementary/1752-0509-4-160-s2.xml',
add_boundary_fluxes=True)
ex.compute_kernel_GJE()
ex.compute_kernel_SVD()
ex.show_statistics()
print ex.get_relation_SVD_error()