CellDesigner Help

Naming Convention of Species

As CellDesigner is compliant to SBML, all names of Components in a model must conform to the SBML convention. CellDesigner 4.2 is compliant to SBML Level 2 Version 4 and any character that can be mapped to UTF-8 encoding can be used for the Component names. If you want to use special characters, such as "+ (plus)", line break, superscript and subscript, you should follow the special rules to input such characters.

Details of the Naming Conventions are described in Help - Name Expression menu.

CellDesigner uses the "name" attributes as information to distinguish Species. Therefore, even if the rendered names look the same, the different "name" attributes, for example, "Gáloch" and "G_alpha_", mean different Species.

Examples

A special character is expressed by a sequence of characters with preceding and following '_'s. Here are some examples:

  1. Ca2+ ("Ca" with "2+" superscript)
    • Ca_super_2_plus__endsuper_
    • Ca_super_2+_endsuper_
  2. G alpha beta gamma ("G" with Greek "áâãloch" subscripts)
    • G_sub__alpha__beta__gamma__endsub_
    • G_sub_áâãloch_endsub_
  3. Complex of Cdc2 and CyclinB ("Cdc2" followed by "+CyclinB" in the new line).
    • Cdc2_br__plus_CyclinB
    • Cdc2_br_+CyclinB

Quick Reference

   
BREAK (LINE FEED) _br_   
START OF SUPERSCRIPT _super_
END OF SUPERSCRIPT _endsuper_   
START OF SUBSCRIPT _sub_
END OF SUBSCRIPT _endsub_
PLUS + _plus_
MINUS - _minus_
SLASH / _slash_
UNDERSCORE _ _underscore_
SPACE _space_
 
CAPITAL
SMALL
GREEK LETTER ALPHA _Alpha_ _alpha_
GREEK LETTER BETA _Beta_ _beta_
GREEK LETTER GAMMA _Gamma_ _gamma_
GREEK LETTER DELTA _Delta_ _delta_
GREEK LETTER EPSILON _Epsilon_ _epsilon_
GREEK LETTER ZETA _Zeta_ _zeta_
GREEK LETTER ETA _Eta_ _eta_
GREEK LETTER THETA _Theta_ _theta_
GREEK LETTER IOTA _Iota_ _iota_
GREEK LETTER KAPPA _Kappa_ _kappa_
GREEK LETTER LAMBDA _Lambda_ _lambda_
GREEK LETTER MU _Mu_ _mu_
GREEK LETTER NU _Nu_ _nu_
GREEK LETTER XI _Xi_ _xi_
GREEK LETTER OMICRON _Omicron_ _omicron_
GREEK LETTER PI _Pi_ _pi_
GREEK LETTER RHO _Rho_ _rho_
GREEK LETTER SIGMA _Sigma_ _sigma_
GREEK LETTER TAU _Tau_ _tau_
GREEK LETTER UPSILON _Upsilon_ _upsilon_
GREEK LETTER PHI _Phi_ _phi_
GREEK LETTER CHI _Chi_ _chi_
GREEK LETTER PSI _Psi_ _psi_
GREEK LETTER OMEGA _Omega_ _omega_
     

 

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