barcelona-2016-slides

Tellurium: A Python-based Integrated Modeling Environment

J Kyle Medley, University of Washington

Tellurium

BioModels Example

import tellurium as te
r = te.loada('''
    //Created by libAntimony v2.7.0
    model *BIOMD0000000012()
      // Compartments and Species:
      ...
    end
''')

r.simulate(0,50,1000)
r.plot()

See https://gist.github.com/0u812/06c379ff7083c779440f for source

BioModels Example

Antimony Conversion

import antimony as sb

sb.loadSBMLFile('input.xml')

print(sb.getModuleNames())
sbstr = sb.getAntimonyString(sb.getModuleNames()[-1])

with open('output.sb', 'w') as f:
  f.write(sbstr)

Antimony

//Created by libAntimony v2.7.0
model *BIOMD0000000012()

  // Compartments and Species:
  compartment cell;
  species PX in cell, PY in cell, PZ in cell, X in cell, Y in cell, Z in cell;

  // Assignment Rules:
  beta := tau_mRNA/tau_prot;
  alpha0 := (a0_tr*eff*tau_prot)/(ln(2)*KM);
  a0_tr := ps_0*60;
  alpha := (a_tr*eff*tau_prot)/(ln(2)*KM);
  a_tr := (ps_a - ps_0)*60;
  t_ave := tau_mRNA/ln(2);
  kd_mRNA := ln(2)/tau_mRNA;
  kd_prot := ln(2)/tau_prot;
  k_tl := eff/t_ave;

  // Reactions:
  Reaction1: X => ; kd_mRNA*X;
  Reaction2: Y => ; kd_mRNA*Y;
  Reaction3: Z => ; kd_mRNA*Z;
  Reaction4:  => PX; k_tl*X;
  Reaction5:  => PY; k_tl*Y;
  Reaction6:  => PZ; k_tl*Z;
  Reaction7: PX => ; kd_prot*PX;
  Reaction8: PY => ; kd_prot*PY;
  Reaction9: PZ => ; kd_prot*PZ;
  Reaction10:  => X; a0_tr + (a_tr*KM^n)/(KM^n + PZ^n);
  Reaction11:  => Y; a0_tr + (a_tr*KM^n)/(KM^n + PX^n);
  Reaction12:  => Z; a0_tr + (a_tr*KM^n)/(KM^n + PY^n);

  // Species initializations:
  PX = 0;
  PY = 0;
  PZ = 0;
  X = 0;
  Y = 20/cell;
  Z = 0;

  // Compartment initializations:
  cell = 1;

  // Variable initializations:
  tau_mRNA = 2;
  tau_prot = 10;
  eff = 20;
  KM = 40;
  n = 2;
  ps_a = 0.5;
  ps_0 = 0.0005;

  // Other declarations:
  var beta, alpha0, a0_tr, alpha, a_tr, t_ave, kd_mRNA, kd_prot, k_tl;
  const cell, tau_mRNA, tau_prot, eff, KM, n, ps_a, ps_0;

  // Unit definitions:
  unit volume = 1e-15 litre;
  unit substance = item;
  unit time_unit = 60 second;

  // Display Names:
  volume is "cubic microns";
  substance is "item";
  time_unit is "minute";
  PX is "LacI protein";
  PY is "TetR protein";
  PZ is "cI protein";
  X is "LacI mRNA";
  Y is "TetR mRNA";
  Z is "cI mRNA";
  tau_mRNA is "mRNA half life";
  tau_prot is "protein half life";
  eff is "translation efficiency";
  t_ave is "average mRNA life time";
  ps_a is "tps_active";
  ps_0 is "tps_repr";
  Reaction1 is "degradation of LacI transcripts";
  Reaction2 is "degradation of TetR transcripts";
  Reaction3 is "degradation of CI transcripts";
  Reaction4 is "translation of LacI";
  Reaction5 is "translation of TetR";
  Reaction6 is "translation of CI";
  Reaction7 is "degradation of LacI";
  Reaction8 is "degradation of TetR";
  Reaction9 is "degradation of CI";
  Reaction10 is "transcription of LacI";
  Reaction11 is "transcription of TetR";
  Reaction12 is "transcription of CI";
end