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From: Will N. <jw...@cl...> - 2007-03-27 21:22:42
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I am building a web-app that uses the SBML Solver library, and was wondering what the acceptable parameters are for the two modes of sensitivity analysis. Here is what I am thinking, is this correct? For Parameter: Takes in a single parameter (either variable or constant) and one or more variable Species, Parameters or Compartments For Variable: Takes in a single variable Species, Parameter, or Compartment and one or more variable or constant Parameters Thanks for the clarification. ------------------------------------------------------------------------- Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT & business topics through brief surveys-and earn cash http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV _______________________________________________ sbmlsolver-discuss mailing list sbm...@li... https://lists.sourceforge.net/lists/listinfo/sbmlsolver-discuss |
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From: Rainer M. <ra...@tb...> - 2007-03-28 15:46:09
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Dear Will, I guess, you referring to program Sense (Sense.exe in Windows) in the example folder. In that case: yes, you are right. In the "p" mode you can choose one parameter and will get sensitivities to this parameter for one or more chosen variables. In the "v" mode you can choose one variable (as above) and will get sensitivities of this variable to one ore more chosen parameter.s Variables are * species, if their concentration is defined by reactions or SBML rate rules (and not if set set constant or defined by an assignment rule), or * parameters if defined by a rate rule (and not if constant or defined by an assigment rule). Please note that currently variable compartments are not handled correctly!! Thus I left them out in above description. Ok? Also note, that it would be very easy to just create your own little C program, specific to your requirements. Using the current CVS version will also improve sensitivity analysis significantly! In 1.6.0 sensitivities are calculated w.r.t. all constants of the model, while in current CVS version sensitivities are calculated only for the chosen constants. However, I haven't adapted the example/Sense program to that improvement yet. Furthermore current CVS version allows to calculate sensitivities w.r.t. to initial conditions of variables. regards, Rainer Will Norman wrote: > I am building a web-app that uses the SBML Solver library, and was > wondering what the acceptable parameters are for the two modes of > sensitivity analysis. > > Here is what I am thinking, is this correct? > > For Parameter: > > Takes in a single parameter (either variable or constant) > > and one or more variable Species, Parameters or Compartments > > For Variable: > > Takes in a single variable Species, Parameter, or Compartment > > and one or more variable or constant Parameters > > Thanks for the clarification. > > > > > ------------------------------------------------------------------------- > Take Surveys. Earn Cash. Influence the Future of IT > Join SourceForge.net's Techsay panel and you'll get the chance to share your > opinions on IT & business topics through brief surveys-and earn cash > http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV > _______________________________________________ > sbmlsolver-discuss mailing list > sbm...@li... > https://lists.sourceforge.net/lists/listinfo/sbmlsolver-discuss > > ------------------------------------------------------------------------- > Take Surveys. Earn Cash. Influence the Future of IT > Join SourceForge.net's Techsay panel and you'll get the chance to share your > opinions on IT & business topics through brief surveys-and earn cash > http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV > _______________________________________________ > sbmlsolver-devel mailing list > sbm...@li... > https://lists.sourceforge.net/lists/listinfo/sbmlsolver-devel ------------------------------------------------------------------------- Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT & business topics through brief surveys-and earn cash http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV _______________________________________________ sbmlsolver-discuss mailing list sbm...@li... https://lists.sourceforge.net/lists/listinfo/sbmlsolver-discuss |
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From: Will N. <jw...@cl...> - 2007-03-29 00:18:04
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Rainer Machne wrote: > Dear Will, > > I guess, you referring to program Sense (Sense.exe in Windows) in the > example folder. > > In that case: yes, you are right. > > In the "p" mode you can choose one parameter and will get > sensitivities to this parameter for one or more chosen variables. > In the "v" mode you can choose one variable (as above) and will get > sensitivities of this variable to one ore more chosen parameter.s Just to clarify when you say parameter here do you mean the SBML type Parameter, or in an abstract sense where parameter is just what is passed to the program (and could be an SBML Parameter or Species). Thanks once again for the help! > > Variables are > > * species, if their concentration is defined by reactions or SBML rate > rules (and not if set set constant or defined by an assignment rule), or > > * parameters if defined by a rate rule (and not if constant or defined > by an assigment rule). > > Please note that currently variable compartments are not handled > correctly!! Thus I left them out in above description. > > Ok? > > Also note, that it would be very easy to just create your own little C > program, specific to your requirements. > > Using the current CVS version will also improve sensitivity analysis > significantly! In 1.6.0 sensitivities are calculated w.r.t. all > constants of the model, while in current CVS version sensitivities are > calculated only for the chosen constants. However, I haven't adapted > the example/Sense program to that improvement yet. > Furthermore current CVS version allows to calculate sensitivities > w.r.t. to initial conditions of variables. > > regards, > Rainer > > > > > > > > > Will Norman wrote: >> I am building a web-app that uses the SBML Solver library, and was >> wondering what the acceptable parameters are for the two modes of >> sensitivity analysis. >> >> Here is what I am thinking, is this correct? >> >> For Parameter: >> >> Takes in a single parameter (either variable or constant) >> >> and one or more variable Species, Parameters or Compartments >> >> For Variable: >> >> Takes in a single variable Species, Parameter, or Compartment >> >> and one or more variable or constant Parameters >> >> Thanks for the clarification. >> >> >> >> >> ------------------------------------------------------------------------- >> >> Take Surveys. Earn Cash. Influence the Future of IT >> Join SourceForge.net's Techsay panel and you'll get the chance to >> share your >> opinions on IT & business topics through brief surveys-and earn cash >> http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV >> >> _______________________________________________ >> sbmlsolver-discuss mailing list >> sbm...@li... >> https://lists.sourceforge.net/lists/listinfo/sbmlsolver-discuss >> >> ------------------------------------------------------------------------- >> >> Take Surveys. Earn Cash. Influence the Future of IT >> Join SourceForge.net's Techsay panel and you'll get the chance to >> share your >> opinions on IT & business topics through brief surveys-and earn cash >> http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV >> >> _______________________________________________ >> sbmlsolver-devel mailing list >> sbm...@li... >> https://lists.sourceforge.net/lists/listinfo/sbmlsolver-devel > > ------------------------------------------------------------------------- Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT & business topics through brief surveys-and earn cash http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV _______________________________________________ sbmlsolver-discuss mailing list sbm...@li... https://lists.sourceforge.net/lists/listinfo/sbmlsolver-discuss |
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From: Rainer M. <ra...@tb...> - 2007-03-29 10:08:20
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Will Norman wrote: > Rainer Machne wrote: >> Dear Will, >> >> I guess, you referring to program Sense (Sense.exe in Windows) in the >> example folder. >> >> In that case: yes, you are right. >> >> In the "p" mode you can choose one parameter and will get >> sensitivities to this parameter for one or more chosen variables. >> In the "v" mode you can choose one variable (as above) and will get >> sensitivities of this variable to one ore more chosen parameter.s > > Just to clarify when you say parameter here do you mean the SBML type > Parameter, or in an abstract sense where parameter is just what is > passed to the program (and could be an SBML Parameter or Species). I mean the latter, parameters, or constants, of the derived ODE system, which can be SBML Parameters or Species or Compartments. This is always confusing and it's good that you ask. Maybe we should start to speak of "constants" rather then "parameters" in our tutorials and programs to avoid this confusion: SBML Species, Parameters, Compartments <-> ODE Variables, Constants. Rainer > Thanks once again for the help! > > >> Variables are >> >> * species, if their concentration is defined by reactions or SBML rate >> rules (and not if set set constant or defined by an assignment rule), or >> >> * parameters if defined by a rate rule (and not if constant or defined >> by an assigment rule). >> >> Please note that currently variable compartments are not handled >> correctly!! Thus I left them out in above description. >> >> Ok? >> >> Also note, that it would be very easy to just create your own little C >> program, specific to your requirements. >> >> Using the current CVS version will also improve sensitivity analysis >> significantly! In 1.6.0 sensitivities are calculated w.r.t. all >> constants of the model, while in current CVS version sensitivities are >> calculated only for the chosen constants. However, I haven't adapted >> the example/Sense program to that improvement yet. >> Furthermore current CVS version allows to calculate sensitivities >> w.r.t. to initial conditions of variables. >> >> regards, >> Rainer >> >> >> >> >> >> >> >> >> Will Norman wrote: >>> I am building a web-app that uses the SBML Solver library, and was >>> wondering what the acceptable parameters are for the two modes of >>> sensitivity analysis. >>> >>> Here is what I am thinking, is this correct? >>> >>> For Parameter: >>> >>> Takes in a single parameter (either variable or constant) >>> >>> and one or more variable Species, Parameters or Compartments >>> >>> For Variable: >>> >>> Takes in a single variable Species, Parameter, or Compartment >>> >>> and one or more variable or constant Parameters >>> >>> Thanks for the clarification. >>> >>> >>> >>> >>> ------------------------------------------------------------------------- >>> >>> Take Surveys. Earn Cash. Influence the Future of IT >>> Join SourceForge.net's Techsay panel and you'll get the chance to >>> share your >>> opinions on IT & business topics through brief surveys-and earn cash >>> http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV >>> >>> _______________________________________________ >>> sbmlsolver-discuss mailing list >>> sbm...@li... >>> https://lists.sourceforge.net/lists/listinfo/sbmlsolver-discuss >>> >>> ------------------------------------------------------------------------- >>> >>> Take Surveys. Earn Cash. Influence the Future of IT >>> Join SourceForge.net's Techsay panel and you'll get the chance to >>> share your >>> opinions on IT & business topics through brief surveys-and earn cash >>> http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV >>> >>> _______________________________________________ >>> sbmlsolver-devel mailing list >>> sbm...@li... >>> https://lists.sourceforge.net/lists/listinfo/sbmlsolver-devel >> > > > ------------------------------------------------------------------------- > Take Surveys. Earn Cash. Influence the Future of IT > Join SourceForge.net's Techsay panel and you'll get the chance to share your > opinions on IT & business topics through brief surveys-and earn cash > http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV > _______________________________________________ > sbmlsolver-discuss mailing list > sbm...@li... > https://lists.sourceforge.net/lists/listinfo/sbmlsolver-discuss > > ------------------------------------------------------------------------- > Take Surveys. Earn Cash. Influence the Future of IT > Join SourceForge.net's Techsay panel and you'll get the chance to share your > opinions on IT & business topics through brief surveys-and earn cash > http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV > _______________________________________________ > sbmlsolver-devel mailing list > sbm...@li... > https://lists.sourceforge.net/lists/listinfo/sbmlsolver-devel |
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