SBML converters¶
sbmlutils provides functionality for converting formats to SBML and SBML to some formats.
XPP to SBML¶
In this example a given xpp model is converted to SBML.
[1]:
from sbmlutils.converters import xpp
# convert to SBML
xpp.xpp2sbml(xpp_file="./xpp/SkM_AP_KCa.ode", sbml_file="./xpp/SkM_AP_KCa.xml");
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xpp2sbml: ./xpp/SkM_AP_KCa.ode -> ./xpp/SkM_AP_KCa.xml
--------------------------------------------------------------------------------
WARNING 'sboTerm' should be set on '<Parameter Vm|Vm = -75>' factory.py:461
WARNING 'sboTerm' should be set on '<Parameter m|m = 0.0>' factory.py:461
WARNING 'sboTerm' should be set on '<Parameter h|h = 1.0>' factory.py:461
WARNING 'sboTerm' should be set on '<Parameter n|n = 0.0>' factory.py:461
WARNING 'sboTerm' should be set on '<Parameter Vt|Vt = -70>' factory.py:461
WARNING 'sboTerm' should be set on '<Parameter c|c = 0.15>' factory.py:461
WARNING 'sboTerm' should be set on '<Parameter o|o = 0.15>' factory.py:461
WARNING 'sboTerm' should be set on '<Parameter cer|cer = 200>' factory.py:461
WARNING 'sboTerm' should be set on '<Parameter gNa_max|gNa_max = 0.9>' factory.py:461
WARNING 'sboTerm' should be set on '<Parameter gcabar|gcabar = 0.05>' factory.py:461
WARNING 'sboTerm' should be set on '<Parameter gK_max|gK_max = 0.415>' factory.py:461
WARNING 'sboTerm' should be set on '<Parameter gL_max|gL_max = 0.0024>' factory.py:461
WARNING 'sboTerm' should be set on '<Parameter gkca|gkca = 0.5>' factory.py:461
WARNING 'sboTerm' should be set on '<Parameter ENa|ENa = 50.0>' factory.py:461
WARNING 'sboTerm' should be set on '<Parameter EK|EK = -70.0>' factory.py:461
WARNING 'sboTerm' should be set on '<Parameter EL|EL = -75.0>' factory.py:461
WARNING 'sboTerm' should be set on '<Parameter ECa|ECa = 50>' factory.py:461
WARNING 'sboTerm' should be set on '<Parameter En|En = -40.0>' factory.py:461
WARNING 'sboTerm' should be set on '<Parameter Em|Em = -42.0>' factory.py:461
WARNING 'sboTerm' should be set on '<Parameter Eh|Eh = -41.0>' factory.py:461
WARNING 'sboTerm' should be set on '<Parameter Ct|Ct = 0.04>' factory.py:461
WARNING 'sboTerm' should be set on '<Parameter Cm|Cm = 0.0090>' factory.py:461
WARNING 'sboTerm' should be set on '<Parameter Rs|Rs = 15.0>' factory.py:461
WARNING 'sboTerm' should be set on '<Parameter Am|Am = 200.0>' factory.py:461
WARNING 'sboTerm' should be set on '<Parameter alpha_n_max|alpha_n_max = factory.py:461 0.0229>'
WARNING 'sboTerm' should be set on '<Parameter beta_n_max|beta_n_max = factory.py:461 0.09616>'
WARNING 'sboTerm' should be set on '<Parameter v_alpha_m|v_alpha_m = 10.0>' factory.py:461
WARNING 'sboTerm' should be set on '<Parameter v_alpha_n|v_alpha_n = 7.0>' factory.py:461
WARNING 'sboTerm' should be set on '<Parameter v_alpha_h|v_alpha_h = 14.7>' factory.py:461
WARNING 'sboTerm' should be set on '<Parameter alpha_m_max|alpha_m_max = factory.py:461 0.208>'
WARNING 'sboTerm' should be set on '<Parameter beta_m_max|beta_m_max = factory.py:461 2.081>'
WARNING 'sboTerm' should be set on '<Parameter v_beta_n|v_beta_n = 40.0>' factory.py:461
WARNING 'sboTerm' should be set on '<Parameter v_beta_m|v_beta_m = 18.0>' factory.py:461
WARNING 'sboTerm' should be set on '<Parameter v_beta_h|v_beta_h = 7.6>' factory.py:461
WARNING 'sboTerm' should be set on '<Parameter alpha_h_max|alpha_h_max = factory.py:461 0.0156>'
WARNING 'sboTerm' should be set on '<Parameter beta_h_max|beta_h_max = factory.py:461 3.382>'
WARNING 'sboTerm' should be set on '<Parameter kd|kd = 0.18>' factory.py:461
WARNING 'sboTerm' should be set on '<Parameter alpha|alpha = 4.5e-6>' factory.py:461
WARNING 'sboTerm' should be set on '<Parameter kpmca|kpmca = 0.2>' factory.py:461
WARNING 'sboTerm' should be set on '<Parameter pleak|pleak = 0.0005>' factory.py:461
WARNING 'sboTerm' should be set on '<Parameter kserca|kserca = 0.4>' factory.py:461
WARNING 'sboTerm' should be set on '<Parameter d1|d1 = 0.84>' factory.py:461
WARNING 'sboTerm' should be set on '<Parameter d2|d2 = 1.0>' factory.py:461
WARNING 'sboTerm' should be set on '<Parameter k1|k1 = 0.18>' factory.py:461
WARNING 'sboTerm' should be set on '<Parameter k2|k2 = 0.011>' factory.py:461
WARNING 'sboTerm' should be set on '<Parameter bbar|bbar = 0.28>' factory.py:461
WARNING 'sboTerm' should be set on '<Parameter abar|abar = 0.48>' factory.py:461
WARNING 'sboTerm' should be set on '<Parameter fer|fer = 0.01>' factory.py:461
WARNING 'sboTerm' should be set on '<Parameter vcytver|vcytver = 5>' factory.py:461
WARNING 'sboTerm' should be set on '<Parameter fcyt|fcyt = 0.01>' factory.py:461
WARNING 'sboTerm' should be set on '<Parameter period|period = 50>' factory.py:461
WARNING 'sboTerm' should be set on '<Parameter iStim_mag|iStim_mag = 2>' factory.py:461
WARNING 'sboTerm' should be set on '<Parameter iStim_beg|iStim_beg = 5>' factory.py:461
WARNING 'sboTerm' should be set on '<Parameter iStim_dur|iStim_dur = 1>' factory.py:461
WARNING 'sboTerm' should be set on '<Function max|minimum>' factory.py:461
WARNING 'sboTerm' should be set on '<Function min|maximum>' factory.py:461
WARNING 'sboTerm' should be set on '<Function heav|heavyside>' factory.py:461
WARNING 'sboTerm' should be set on '<Function mod|modulo>' factory.py:461
WARNING 'name' should be set on '<Function alp>' factory.py:436
WARNING 'sboTerm' should be set on '<Function alp>' factory.py:461
WARNING 'name' should be set on '<Function beta>' factory.py:436
WARNING 'sboTerm' should be set on '<Function beta>' factory.py:461
WARNING 'name' should be set on '<Function tau>' factory.py:436
WARNING 'sboTerm' should be set on '<Function tau>' factory.py:461
WARNING 'name' should be set on '<Function ooinf>' factory.py:436
WARNING 'sboTerm' should be set on '<Function ooinf>' factory.py:461
WARNING 'name' should be set on '<RateRule Vm>' factory.py:436
WARNING 'name' should be set on '<RateRule m>' factory.py:436
WARNING 'name' should be set on '<RateRule h>' factory.py:436
WARNING 'name' should be set on '<RateRule n>' factory.py:436
WARNING 'name' should be set on '<RateRule Vt>' factory.py:436
WARNING 'name' should be set on '<Parameter d>' factory.py:436
WARNING 'sboTerm' should be set on '<Parameter d>' factory.py:461
WARNING 'name' should be set on '<RateRule d>' factory.py:436
WARNING 'name' should be set on '<RateRule o>' factory.py:436
WARNING 'name' should be set on '<RateRule c>' factory.py:436
WARNING 'name' should be set on '<RateRule cer>' factory.py:436
WARNING 'name' should be set on '<Parameter iStim>' factory.py:436
WARNING 'sboTerm' should be set on '<Parameter iStim>' factory.py:461
WARNING 'name' should be set on '<Parameter beta_n>' factory.py:436
WARNING 'sboTerm' should be set on '<Parameter beta_n>' factory.py:461
WARNING 'name' should be set on '<Parameter beta_m>' factory.py:436
WARNING 'sboTerm' should be set on '<Parameter beta_m>' factory.py:461
WARNING 'name' should be set on '<Parameter beta_h>' factory.py:436
WARNING 'sboTerm' should be set on '<Parameter beta_h>' factory.py:461
WARNING 'name' should be set on '<Parameter alpha_n>' factory.py:436
WARNING 'sboTerm' should be set on '<Parameter alpha_n>' factory.py:461
WARNING 'name' should be set on '<Parameter alpha_m>' factory.py:436
WARNING 'sboTerm' should be set on '<Parameter alpha_m>' factory.py:461
WARNING 'name' should be set on '<Parameter alpha_h>' factory.py:436
WARNING 'sboTerm' should be set on '<Parameter alpha_h>' factory.py:461
WARNING 'name' should be set on '<Parameter dinf>' factory.py:436
WARNING 'sboTerm' should be set on '<Parameter dinf>' factory.py:461
WARNING 'name' should be set on '<Parameter taud>' factory.py:436
WARNING 'sboTerm' should be set on '<Parameter taud>' factory.py:461
WARNING 'name' should be set on '<Parameter alphad>' factory.py:436
WARNING 'sboTerm' should be set on '<Parameter alphad>' factory.py:461
WARNING 'name' should be set on '<Parameter betad>' factory.py:436
WARNING 'sboTerm' should be set on '<Parameter betad>' factory.py:461
WARNING 'name' should be set on '<Parameter gca>' factory.py:436
WARNING 'sboTerm' should be set on '<Parameter gca>' factory.py:461
WARNING 'name' should be set on '<Parameter w>' factory.py:436
WARNING 'sboTerm' should be set on '<Parameter w>' factory.py:461
WARNING 'name' should be set on '<Parameter jmem>' factory.py:436
WARNING 'sboTerm' should be set on '<Parameter jmem>' factory.py:461
WARNING 'name' should be set on '<Parameter jleak>' factory.py:436
WARNING 'sboTerm' should be set on '<Parameter jleak>' factory.py:461
WARNING 'name' should be set on '<Parameter jserca>' factory.py:436
WARNING 'sboTerm' should be set on '<Parameter jserca>' factory.py:461
WARNING 'name' should be set on '<Parameter jer>' factory.py:436
WARNING 'sboTerm' should be set on '<Parameter jer>' factory.py:461
WARNING 'name' should be set on '<Parameter INa>' factory.py:436
WARNING 'sboTerm' should be set on '<Parameter INa>' factory.py:461
WARNING 'name' should be set on '<Parameter IT>' factory.py:436
WARNING 'sboTerm' should be set on '<Parameter IT>' factory.py:461
WARNING 'name' should be set on '<Parameter IKCa>' factory.py:436
WARNING 'sboTerm' should be set on '<Parameter IKCa>' factory.py:461
WARNING 'name' should be set on '<Parameter ICa>' factory.py:436
WARNING 'sboTerm' should be set on '<Parameter ICa>' factory.py:461
WARNING 'name' should be set on '<Parameter IL>' factory.py:436
WARNING 'sboTerm' should be set on '<Parameter IL>' factory.py:461
WARNING 'name' should be set on '<Parameter IK>' factory.py:436
WARNING 'sboTerm' should be set on '<Parameter IK>' factory.py:461
WARNING 'name' should be set on '<Parameter i_na>' factory.py:436
WARNING 'sboTerm' should be set on '<Parameter i_na>' factory.py:461
WARNING 'name' should be set on '<Parameter i_kca>' factory.py:436
WARNING 'sboTerm' should be set on '<Parameter i_kca>' factory.py:461
WARNING 'sboTerm' should be set on '<Parameter t|model time>' factory.py:461
ERROR All SBML paths should be of type 'Path', but '<class 'str'>' found for: sbml.py:45 ./xpp/SkM_AP_KCa.xml
─────────────────────────────────────── Validate SBML ───────────────────────────────────────
./xpp/SkM_AP_KCa.xml valid : TRUE check time (s) : 0.009
─────────────────────────────────────────────────────────────────────────────────────────────
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