CellDesigner Help

Naming Convention of Species

As CellDesigner is compliant to SBML, all names of components in a model must be conforming to the SBML convention. CellDesigner 4.0 is now compliant to SBML Level 2 Version 1, any character that can be mapped to UTF-8 encoding can be used for the component names. If you want the special characters, such as + plus, line break, superscript and subscript, you should follow the special rules to input such characters.

See also: Details of the Naming Conventions are described in [Help] - [Name Expression] menu.

Caution: 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 precedent and followup '_'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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