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Frequently Asked Questions
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  • What do I need to use GenSSI Toolbok?

    You need MATLAB and:

    • the Symbolic Math Toolbox for MATLAB versions up to R2007b+;
    • the MAPLE Toolbox for MATLAB versions R2007b+ and later.

    This is due to the change of the symbolic engine as explained in http://www.mathworks.com/help/toolbox/symbolic/rn/f0-60374.html

    If you have the Symbolic Math Toolbox for MATLAB and you do not want to purchase the MAPLE Toolbox, please note that you can install a previous version of MATLAB (we suggest R2007b) and then use GenSSI without problems.

  • Does it run under Windows, Linux, etc.?

    This version runs under Windows, the Linux version will be available soon. The toolboxes described above are needed.

  • What is Nder and how can I choose it?

    Nder represents the number of derivatives and it should be chosen such as the rank of the identifiability tableau is equal to the number of the parameters. At least Nobs*(1+Noc)^Nder Lie derivative components are needed to achieve the maximum rank. But it is possible that extra derivatives are needed if zero or dependent Lie derivatives components are generated, that is why after each iteration the expected rank value is given if an extra derivative is to be considered. Different structural identifiability results may appear because the rank condition is not fulfilled. Section has been added to refer to the way the number of derivatives should be chosen (Section 1.7).

  • Is it possible to obtain different structural identifiability analysis results for different values of Nder?

    The number of derivatives should be chosen such as the rank of the identifiability tableau is equal to the number of the parameters. At least Nobs*(1+Noc)^Nder Lie derivative components are needed to achieve the maximum rank. But it is possible that extra derivatives are needed if zero or dependent Lie derivatives components are generated, that is why after each iteration the expected rank value is given if an extra derivative is to be considered. Different structural identifiability results may appear because the rank condition is not fulfilled. Section has been added to refer to the way the number of derivatives should be chosen (Section 1.7).

  • What this error means?

    ??? Error using ==> sym.cat>checkDimensions at 76
    CAT arguments dimensions are not consistent.

    Error in ==> sym.cat>catMany at 39
    [resz, ranges] = checkDimensions(sz,dim);

    Error in ==> sym.cat at 29
    y = catMany(dim, strs);

    Error in ==> sym.horzcat at 25
    y = cat(2,args{:});

    Error in ==> sym.subs>tryFunctionHandle at 213
    Y = [Y(:).' usym(:).'];

    Error in ==> sym.subs>mupadsubs at 140
    [G,worked] = tryFunctionHandle(F,X,Y);

    Error in ==> sym.subs at 127
    G = mupadsubs(F,X,Y);


    This error appears when the MAPLE Toolbox for MATLAB is not found. See also the answer from the first question.

  • How can I solve this error?

    ??? Error using ==> maple at 129
    Error, numeric exception: division by zero

    Error in ==> sym.subs>dosubs at 206
    G = sym(maple(['subs(' pat ',' expr ');']));

    Error in ==> sym.subs at 188
    G = dosubs(expr, pat);

    Error in ==> GenSSI_computes_LieDerivatives at 63
    Jacs=subs(Jac,X,IC);

    Error in ==> GenSSI_generating_series at 37
    GenSSI_computes_LieDerivatives

    Error in ==> ToyModel at 186
    GenSSI_generating_series(F,G,Noc,Neq,Nder,Nobs,H,X,IC,Par,result_folder);


    Please check the zero initial conditions and also revise the equations of the model.

  • How is defined the vector of observables?

    If a state variable is observable, then the corresponding component in H is equal to this state variable, otherwise the component of H is zero.

  • For the observables represented as sums of several variables, can this toolbox be applied?

  • Yes, the toolbox was tested also for models characterized by such measurements, such as NF-kB model.



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