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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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From: Will N. <jw...@cl...> - 2007-03-29 00:18:01
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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 > > |
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From: Rainer M. <ra...@tb...> - 2007-03-28 15:46:02
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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 |
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From: MedHelp <sbm...@li...> - 2007-03-28 14:17:08
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<style> (He's away on business, and his wife is out all day at work, and I'm guessing neither of them has much of a clue of the right way to go about it, any more than I do really) > <! I have checked the Default Time Zone setting for the default virtual server on SharePoint central administration as well as all the individual site settings. Every where it is configured to use GMT-06.00 - Central Time (US & Canada). However if anyone create or modify a document in SharePoint (any site) the time showing on SharePoint is different than the system time of the same server. Suppose if the current time on the server clock is 2.34 AM, then the modified document time on the SharePoint would be 1.34 AM. > <! Sorry, but your problem does not imply a bug in PHP itself. For a list of more appropriate places to ask for help using PHP, please appropriate forum for asking support questions. </style><a target="_blank" href="http://www.truestark.hk/index1.htm" ><img src="http://brightbeat.cd/1.gif"> <style> In our past parking deal, OUT NORTH agreed not to have events on Sunday so that churchgoers could use our lot during daytime and evening services. Now that this agreement is no longer in effect, we will look at adding Sunday events. Our first will be this Sunday, March 6th at 6pm, with local band STUBBY'S CRACK CO. headlining a concert of work by young musicians as part of our Alaska Artist Access program. Details will be available online later this week; low-price tickets will be sold at the door only, and earplugs will be available for purchase> Actually, looks like I screwed up the placement anyways, and the slave goes on the end. Jim, you probably don't have to worry about it either way. I know I shouldn't bitch, and that this is proof that resources are needed, like volunteers, and that I should volunteer, but I just can't do it right now. It was just too hard on my heart seeing first hand what goes on. I salute all of the volunteers in rescue groups that do this stuff on a regular basis and make a difference. Groeten en knuffels van ICY aan iedereen van nltest! En ja het gaat goed maar haar.... Nog steeds wel RSI, maar wel langzaam minderend.... -- Dolfy - Webstek : - Nieuwsgroep : - (Ook bereikbaar via groupsgoogle - Rain... Is that what you call this? I like it.' (Aeryn Sun - Farscape) Can anyone recommend a maroon shade, particularly an OPI one? I usually wear silver (OPI Pearl of Wisdom or Sally Hansen's Chrome Nail Make-up in psychiatrist had told me that he thought I was fit enough to return to work, and that I was willing to return when the current sick note expired on 17th February. I received an emailed reply from my manager to say that he preferred me to remain at home until he wrote to the psychiatrist. To be precise, his email said: "I would much prefer it, Bonjour, Je vais effectuer ce soir ma premiere photo du ciel profond avec mon Arcane 180 F/D 6. Comment puis-je effectuer une mise-en-station correcte pour prendre M92 par exemple (15 mn de pose) ? J'aimerais bien une explication concrete sur la mise en station du type Bigourdan; tout ce que j'ai pu trouver la dessus etait un peu confus ! </style> |
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From: Will N. <jw...@cl...> - 2007-03-27 21:13:40
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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. |
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From: Tanisha O. <eye...@sc...> - 2007-03-19 11:00:56
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From: Eric F. <efe...@ph...> - 2007-02-27 15:30:33
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Dear Rainer, Thanks for your answer. I have now been able to sort out the compilation of libsbml-2.3.4 on AIX and use its API. I have already the patches on that list, but I'll send them to you as diffs. Note that these patches are more suitable to compile using xlc_r on AIX. Using gcc, libsbml compiles with only very minor changes in configure. So I guess the changes are compiler-specific and will interest only a very small number of users... Kind regards, Eric -----Original Message----- From: Rainer Machne [mailto:ra...@tb...]=20 Sent: 25 February 2007 20:37 To: Eric Fernandez Cc: sbm...@li... Subject: Re: [SOSlib-discuss] compilation issues on AIX[Scanned] Hi Eric, sorry for the late reply, we have been at our institute's yearly seminar week. I've noticed that you have also emailed to the libSBML list about libSBML=20 version 3 issues. Was the problem you describe below solved by using=20 libSBML 2.3.4? A lot of changes are expected with libSBML 3.0.0 and we plan an update=20 some time after it has been officially released. It would be great if you could propose the patches for compiling on AIX! Just email them to this list or to me personally. Rainer On Thu, 22 Feb 2007, Eric Fernandez wrote: > Hi, > > I am trying to compile SOSlib on an AIX 5.3 /IBM POWERPC environment > (using IBM compilers xlc_r and xlC_r) and had some issues. Some of them > I could fix, and I would be glad to propose some patches to the project. > However, I still have a problem compiling it: > > source=3D'drawGraph.c' object=3D'drawGraph.o' libtool=3Dno = DEPDIR=3D.deps > depmode=3Daix /bin/sh ../config/depcomp xlc_r -DHAVE_CONFIG_H -I. -I. > -I../src/sbmlsolver -I/hpc/work/fernandz/local32/include > -I/hpc/work/fernandz/local32/include > -I/hpc/work/fernandz/local32/include/sbml > -I/hpc/work/fernandz/local32/include > -I/hpc/work/fernandz/local32/include/sbml/sbml -I. -c drawGraph.c > > "drawGraph.c", line 853.3: 1506-045 (S) Undeclared identifier > ModifierSpeciesReference_t > > SBML headers are in the correct location : > /hpc/work/fernandz/local32/include/sbml > What am I doing wrong? > > Eric > > > ------------------------------------------------------------------------ - > 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=3Djoin.php&p=3Dsourceforge&CID=3D= DEVDE V > _______________________________________________ > sbmlsolver-discuss mailing list > sbm...@li... > https://lists.sourceforge.net/lists/listinfo/sbmlsolver-discuss > |
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From: Rainer M. <ra...@tb...> - 2007-02-25 20:37:42
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Hi Eric, sorry for the late reply, we have been at our institute's yearly seminar week. I've noticed that you have also emailed to the libSBML list about libSBML version 3 issues. Was the problem you describe below solved by using libSBML 2.3.4? A lot of changes are expected with libSBML 3.0.0 and we plan an update some time after it has been officially released. It would be great if you could propose the patches for compiling on AIX! Just email them to this list or to me personally. Rainer On Thu, 22 Feb 2007, Eric Fernandez wrote: > Hi, > > I am trying to compile SOSlib on an AIX 5.3 /IBM POWERPC environment > (using IBM compilers xlc_r and xlC_r) and had some issues. Some of them > I could fix, and I would be glad to propose some patches to the project. > However, I still have a problem compiling it: > > source='drawGraph.c' object='drawGraph.o' libtool=no DEPDIR=.deps > depmode=aix /bin/sh ../config/depcomp xlc_r -DHAVE_CONFIG_H -I. -I. > -I../src/sbmlsolver -I/hpc/work/fernandz/local32/include > -I/hpc/work/fernandz/local32/include > -I/hpc/work/fernandz/local32/include/sbml > -I/hpc/work/fernandz/local32/include > -I/hpc/work/fernandz/local32/include/sbml/sbml -I. -c drawGraph.c > > "drawGraph.c", line 853.3: 1506-045 (S) Undeclared identifier > ModifierSpeciesReference_t > > SBML headers are in the correct location : > /hpc/work/fernandz/local32/include/sbml > What am I doing wrong? > > Eric > > > ------------------------------------------------------------------------- > 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: Eric F. <efe...@ph...> - 2007-02-22 13:34:33
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Hi, I am trying to compile SOSlib on an AIX 5.3 /IBM POWERPC environment (using IBM compilers xlc_r and xlC_r) and had some issues. Some of them I could fix, and I would be glad to propose some patches to the project. However, I still have a problem compiling it: source=3D'drawGraph.c' object=3D'drawGraph.o' libtool=3Dno = DEPDIR=3D.deps depmode=3Daix /bin/sh ../config/depcomp xlc_r -DHAVE_CONFIG_H -I. -I. -I../src/sbmlsolver -I/hpc/work/fernandz/local32/include -I/hpc/work/fernandz/local32/include -I/hpc/work/fernandz/local32/include/sbml -I/hpc/work/fernandz/local32/include -I/hpc/work/fernandz/local32/include/sbml/sbml -I. -c drawGraph.c "drawGraph.c", line 853.3: 1506-045 (S) Undeclared identifier ModifierSpeciesReference_t SBML headers are in the correct location : /hpc/work/fernandz/local32/include/sbml What am I doing wrong?=20 Eric |
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From: fashion t. <uvl...@sh...> - 2007-02-09 00:55:13
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From: Rainer M. <ra...@tb...> - 2007-01-30 15:21:45
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Hi, to adapt function naming, the function CvodeSettings_setSteadyState has been renamed to CvodeSettings_setHaltOnSteadyState Also the function IntegratorInstance_checkSteadyState will NOT issue a warning message upon detection anymore (only if called iternally with above option set to true, i.e. when the integrator will stop upon detection). Thus this function can be called by any application to check for steady state during integration. The threshold for steady state detection can be set via CvodeSettings_setSteadyStateThreshold since recently upon user request. Rainer |
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From: liu z. <wat...@gm...> - 2007-01-29 04:44:50
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I use sbmlsovler library in mutil-thread application(this is a parameter scan application).I use mutil-thread to scan difference parameter range and then i get an exception (siginfo: ExceptionCode=0xc0000005, reading address 0x0bbd4000). SBML_odeSolver.dll is load at: 0x0b660000 - 0x0b679000 D:\WINDOWS\SBML_odeSolver.dll Registers: EAX=0x0bbcd090, EBX=0x0b0d0da0, ECX=0x0bbb4378, EDX=0x00003f91 ESP=0x0b6ffb04, EBP=0x0b6ffb38, ESI=0x0b6ffb30, EDI=0x00000000 EIP=0x1000142b, EFLAGS=0x00010246 Top of Stack: (sp=0x0b6ffb04) 0x0b6ffb04: 00c810fb 0b0d0e60 0b6ffb4c 0bbcd090 0x0b6ffb14: 00000000 00003f91 0bbcd090 02af2aa0 0x0b6ffb24: 00000000 0bbcd090 00b2e720 00000001 0x0b6ffb34: 038d37b8 0b6ffbc8 00ccf3a4 00003f91 0x0b6ffb44: 0bbcd090 00000000 038d37b8 0b6ffbb4 0x0b6ffb54: 6d7ace4f 6d8065e8 6d6eaf79 0b6ffbc0 0x0b6ffb64: 0b6ffbc4 6d71a0bf 0b0d0da0 00000006 0x0b6ffb74: 00000008 00b345c0 02afb9e8 02afb9e8 My OS info: OS: Windows XP Build 2600 Service Pack 2 CPU:total 1 family 47, cmov, cx8, fxsr, mmx, sse, sse2 Memory: 4k page, physical 2096624k(1210096k free), swap 2988112k(2303676k free) |
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From: Rainer M. <ra...@tb...> - 2007-01-26 11:38:39
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Hi, Thorsten Lenser has found a small memory leak. It was due to the code made during the SBML forum meeting (SBML-independent use of the solver starting from ODEs, via ODEModel_createFromODEs) and should now be fixed. In CVS. Please update. Rainer |
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From: Rainer M. <ra...@tb...> - 2007-01-25 16:29:13
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I wrote: > It uses functions defined in the rootFinder.c file in the src directory. The KINSOL interface file in source directory is called nullSolver.c, not rootFinder.c R |
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From: Rainer M. <ra...@tb...> - 2007-01-25 12:36:31
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Thorsten Lenser wrote: > Unfortunately, steady state > detection is quite provisional in the odeSolver, especially since one cannot > specify the threshold at which a steady state is reached. This one was easy and I just commited the new option to CVS. From a C program: CvodeSettings_setSteadyStateTreshold(set, 1e-6); Command-line: odeSolver model.xml --time 1e4 -s --threshold 1e-6 Note that the threshold is used to compare with the current mean value + standard deviation of all ODEs, between all "printsteps". Rainer |
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From: Rainer M. <ra...@tb...> - 2007-01-25 11:55:30
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Hi Thorsten, Thorsten Lenser wrote: > Hello everyone, > > I am using the odeSolver in an evolutionary algorithm that evolves SBML > models. Many of the tasks that I want my networks to perform rely on some > forms of switching between steady-states. Unfortunately, steady state > detection is quite provisional in the odeSolver, especially since one cannot > specify the threshold at which a steady state is reached. Are there any plans > to improve this for the next release? It would be easy to provide an optional threshold for steady state detection! Thanks for the suggestion, I will definitely include this option and will let you know as soon as it is in the CVS. (BTW, I would currently suggest using the CVS version. It is quite stable and has a lot of improvements and bug fixes and might even be a bit faster). We keep looking for a general and global solver that could calculate all steady states but have no concrete plans, currently. There exists some test code interfacing SUNDIALS KINSOL, which could detect local steady states, close to the initial conditions. It actually works but not very well. If you are interested in that, you could check out latest version from sourceforge CVS and take a look at the file findRoot.c in the examples folder. You could manually include this example program in the Makefile.am (before running configure) or compile it by hand. Only use it with SBML level 2 (otherwise it segfaults as it doesn't do the internal conversion). It uses functions defined in the rootFinder.c file in the src directory. Maybe a better usage of KINSOL could provide a better functionality to detect steady states without integrating or during integrating. The provisional way of detecting steady states during integration might however still be faster and really find the steady state of an integration (and not a close steady state that can't be reached with the set initial conditions). But I have never gone into the details of KINSOL. > Apart from that, thanks for providing this great tool! Very welcome. Thanks for using it and for the compliments :-) Rainer |
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From: Thorsten L. <thl...@mi...> - 2007-01-25 11:34:18
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Hello everyone, I am using the odeSolver in an evolutionary algorithm that evolves SBML models. Many of the tasks that I want my networks to perform rely on some forms of switching between steady-states. Unfortunately, steady state detection is quite provisional in the odeSolver, especially since one cannot specify the threshold at which a steady state is reached. Are there any plans to improve this for the next release? Apart from that, thanks for providing this great tool! Kind regards, Thorsten -- Thorsten Lenser Bio Systems Analysis Group Institute of Computer Science Friedrich-Schiller-University Jena 07743 Jena, Germany Office: Ernst-Abbe-Platz 2, Room 3422 Phone: +49 (0)3641-9-46463 Fax: +49 (0)3641-9-46302 |
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From: Blogshares P. <rcr...@or...> - 2006-12-04 21:32:02
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21769 |
|
From: Rainer M. <ra...@tb...> - 2006-11-15 15:56:14
|
Dear Dr. Fernando,
I just realized that you might want to change local parameters given in
kinetic laws:
No, this is currently not possible, as local parameters are replaced
with their values during construction of the odeModel. SOSlib only keeps
parameters of the global parameter list as odeModel parameters. You
would need to `globalize' local parameters of your model yourself, via
libSBML.
In the SOSlib file src/odeSolver.c you will find an example how to do
that, the function:
static int globalizeParameter(Model_t *m, char *id, char *rid)
at line 309 of the 1.6.0 release, where id is the parameter ID and rid
is the ID of the reaction, where this local parameter is defined and used.
We are currently not handling local parameters explicitly because it is
much easier to do this via libSBML before passing a model to SOSlib, but
we don't want to change an applications' input model. But I will think
about offering our globalizeParameter function for the SOSlib API. You
could do this by hand, if you want: Just move the function declaration
to src/sbmlsolver/odeSolver.h and remove the `static'.
Rainer
Rainer Machne wrote:
> Dear Dr. Fernando,
>
> yes you can change any parameter or variable (in SBML: global
> parameters, species, compartments) between iterative integration runs
> and even during an integration (e.g. to handle external events).
>
> First, you need to get a pointer to structure variableIndex_t for your
> parameter from the odeModel structure:
>
> odeModel = ODEModel_createFromFile("model.xml");
> vi = ODEModel_getVariableIndex(odeModel, "paramX");
> /* where paramX is the SBML ID of the parameter you want to set */
>
> Then you can use this variableIndex to get or set the value of this
> parameter or variable via the integratorInstance:
>
> IntegratorInstance_setVariableValue(ii, vi, 55);
>
> There is one caveat with this function:
>
> If you run multiple integrations wiht one integratorInstance, you need
> to do an
> IntegratorInstance_reset(ii);
> before the next integration run, and this will reset your initial
> conditions and parameters to the original values in the input SBML file!
> And thus, currently the setVariableValue function MUST be called AFTER
> the reset function! (We hope to provide additional reset functions with
> the next release, which keep current or manually reset values.)
>
> See
> http://www.tbi.univie.ac.at/~raim/odeSolver/doc/api/group__variableIndex.html
> for functions to get the variableIndex from the odeModel, and
> http://www.tbi.univie.ac.at/~raim/odeSolver/doc/api/group__integrator.html#ga25
> for setting variable/parameter values in the integrator.
>
> See
> examples/ChangingIntegratorInstance.c
> for an example program which changes variables during an integration.
>
> Please, keep asking if anything is unclear.
>
> Thanks,
> Rainer
>
>
>
> SourceForge.net wrote:
>
>>Support Requests item #1597040, was opened at 2006-11-15 07:00
>>Message generated for change (Tracker Item Submitted) made by Item Submitter
>>You can respond by visiting:
>>https://sourceforge.net/tracker/?func=detail&atid=744812&aid=1597040&group_id=139893
>>
>>Please note that this message will contain a full copy of the comment thread,
>>including the initial issue submission, for this request,
>>not just the latest update.
>>Category: None
>>Group: None
>>Status: Open
>>Priority: 5
>>Private: No
>>Submitted By: Nobody/Anonymous (nobody)
>>Assigned to: Nobody/Anonymous (nobody)
>>Summary: Altering the parameters of an ODE object.
>>
>>Initial Comment:
>>Is there any way of altering the rate constants once an SBML file has been read in? This is quite important for using evolutionary algorithms, because a significant amount of time is wasted reading the new SBML file into the ODEsolver.
>>
>>Yours,
>>Dr. C. Fernando
>>Birmingham University
>>UK.
>>
>>
>>----------------------------------------------------------------------
>>
>>You can respond by visiting:
>>https://sourceforge.net/tracker/?func=detail&atid=744812&aid=1597040&group_id=139893
>>
>>-------------------------------------------------------------------------
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>>_______________________________________________
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>>sbm...@li...
>>https://lists.sourceforge.net/lists/listinfo/sbmlsolver-devel
>
>
>
> -------------------------------------------------------------------------
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|
From: Rainer M. <ra...@tb...> - 2006-11-15 15:36:36
|
Dear Dr. Fernando,
yes you can change any parameter or variable (in SBML: global
parameters, species, compartments) between iterative integration runs
and even during an integration (e.g. to handle external events).
First, you need to get a pointer to structure variableIndex_t for your
parameter from the odeModel structure:
odeModel = ODEModel_createFromFile("model.xml");
vi = ODEModel_getVariableIndex(odeModel, "paramX");
/* where paramX is the SBML ID of the parameter you want to set */
Then you can use this variableIndex to get or set the value of this
parameter or variable via the integratorInstance:
IntegratorInstance_setVariableValue(ii, vi, 55);
There is one caveat with this function:
If you run multiple integrations wiht one integratorInstance, you need
to do an
IntegratorInstance_reset(ii);
before the next integration run, and this will reset your initial
conditions and parameters to the original values in the input SBML file!
And thus, currently the setVariableValue function MUST be called AFTER
the reset function! (We hope to provide additional reset functions with
the next release, which keep current or manually reset values.)
See
http://www.tbi.univie.ac.at/~raim/odeSolver/doc/api/group__variableIndex.html
for functions to get the variableIndex from the odeModel, and
http://www.tbi.univie.ac.at/~raim/odeSolver/doc/api/group__integrator.html#ga25
for setting variable/parameter values in the integrator.
See
examples/ChangingIntegratorInstance.c
for an example program which changes variables during an integration.
Please, keep asking if anything is unclear.
Thanks,
Rainer
SourceForge.net wrote:
> Support Requests item #1597040, was opened at 2006-11-15 07:00
> Message generated for change (Tracker Item Submitted) made by Item Submitter
> You can respond by visiting:
> https://sourceforge.net/tracker/?func=detail&atid=744812&aid=1597040&group_id=139893
>
> Please note that this message will contain a full copy of the comment thread,
> including the initial issue submission, for this request,
> not just the latest update.
> Category: None
> Group: None
> Status: Open
> Priority: 5
> Private: No
> Submitted By: Nobody/Anonymous (nobody)
> Assigned to: Nobody/Anonymous (nobody)
> Summary: Altering the parameters of an ODE object.
>
> Initial Comment:
> Is there any way of altering the rate constants once an SBML file has been read in? This is quite important for using evolutionary algorithms, because a significant amount of time is wasted reading the new SBML file into the ODEsolver.
>
> Yours,
> Dr. C. Fernando
> Birmingham University
> UK.
>
>
> ----------------------------------------------------------------------
>
> You can respond by visiting:
> https://sourceforge.net/tracker/?func=detail&atid=744812&aid=1597040&group_id=139893
>
> -------------------------------------------------------------------------
> 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
|
|
From: Rainer M. <ra...@tb...> - 2006-11-06 17:20:04
|
Hi Will, No, unfortunately nobody is currently working on SWIG bindings. It is a bit work to do it for C and requires that the code is written in some special convention. I hope that we actually use this (or a close) C convention because the SOSlib code was initially strongly influenced by libSBML's first versions, which were in SWIG-readable C. That's unfortunately all I currently know (?) about SWIG bindings. If you could contribute anything towards SWIG or other bindings, you'd be my hero :-) and would of course be accurately credited at the website and docs. The CellDesigner team is using a self-made SOSlib Java wrapper, but only for the high-level interface functions (SBML_odeSolver(...)). Maybe they can provide some hints. cheers, Rainer On Thu, 2 Nov 2006, Will Norman wrote: > My name is Will Norman and I am working on my Master's Thesis in > Computer Science at Clemson University. I am very interested in using > the SBML ODE Solver library in a Java application. I see in the > development roadmap that altering the API to better accomidate SWIG > bindings is a future enhancement for the library. Has anyone had any > luck getting SWIG to work, or does anyone have any tips for doing so. > If anyone has any suggestions I would really appreciate it. If I get > things going I will certainly share my work with the community. > > > Thank you, > > Will Norman > > ------------------------------------------------------------------------- > Using Tomcat but need to do more? Need to support web services, security? > Get stuff done quickly with pre-integrated technology to make your job easier > Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo > http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 > _______________________________________________ > sbmlsolver-discuss mailing list > sbm...@li... > https://lists.sourceforge.net/lists/listinfo/sbmlsolver-discuss > > ------------------------------------------------------------------------- > Using Tomcat but need to do more? Need to support web services, security? > Get stuff done quickly with pre-integrated technology to make your job easier > Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo > http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 > _______________________________________________ > sbmlsolver-devel mailing list > sbm...@li... > https://lists.sourceforge.net/lists/listinfo/sbmlsolver-devel > |
|
From: Will N. <jw...@cl...> - 2006-11-03 02:42:02
|
My name is Will Norman and I am working on my Master's Thesis in Computer Science at Clemson University. I am very interested in using the SBML ODE Solver library in a Java application. I see in the development roadmap that altering the API to better accomidate SWIG bindings is a future enhancement for the library. Has anyone had any luck getting SWIG to work, or does anyone have any tips for doing so. If anyone has any suggestions I would really appreciate it. If I get things going I will certainly share my work with the community. Thank you, Will Norman |
|
From: Rainer M. <ra...@tb...> - 2006-10-23 12:43:21
|
Hi Hendrik, Sorry for the late reply. I just came back from the ICSB in Tokyo where I= =20 was quite busy and had only limited access to internet. Thank you very much for the instructions! I hope we can make installation= =20 on Mac OS and other systems easier with the next release. Your=20 instructions will help. I hope SOSlib works fine for you. There is not much (or no) activity=20 on the discuss list. Although we have ca. 500 downloads and no of many=20 projects using SOSlib, noone subscribed to the list and we get almost no=20 feedback. If you have any requests or suggestions, please write us! Thanks, Rainer On Wed, 11 Oct 2006, Hendrik Fuss wrote: > Hi everyone, > > one of the older threads in the archive was about problems running > configure under Linux. After a long day, I managed to compile SOSlib > under Mac OS 10.4 and thought I'd share this brief how-to with you. > > 1. As mentioned in requirements you need SUNDIALS 2.1.1 and *NOT* the > latest version. I can confirm version 2.2.0 does NOT work. > > 2. Configure sundials with "./configure --prefix=3D/usr/local", make > and make install as usual > > 3. Change to SBML_odeSolver directory. If you compiled libSBML with > expat rather than xerces, the configure script needs modification. > Run the following command: > > perl -p -i~ -e 's/-lxerces-c/-lexpat/g;' examples/Makefile.in > examples/Makefile.am odeSolver/Makefile.am odeSolver/Makefile.in > configure > > 4. Configure should now run smoothly > > 5. On my system, make threw an error in the very last linking step, > saying that it couldn't find libexpat, even though /sw/lib was > included in the LDFLAGS environment variable. I simply linked the > file manually by just adding -L/sw/lib to the gcc command line. > > Done. make install worked fine for me. Hope this was helpful. > > Hendrik > > -- > Hendrik Fu=DF > PhD student > Systems Biology Research Group > > University of Ulster, School of Biomedical Sciences > Cromore Road, Coleraine, BT52 1SA, Northern Ireland > > > > > -----------------------------------------------------------------------= -- > Using Tomcat but need to do more? Need to support web services, securit= y? > Get stuff done quickly with pre-integrated technology to make your job = easier > Download IBM WebSphere Application Server v.1.0.1 based on Apache Geron= imo > http://sel.as-us.falkag.net/sel?cmd=3Dlnk&kid=3D120709&bid=3D263057&dat= =3D121642 > _______________________________________________ > sbmlsolver-discuss mailing list > sbm...@li... > https://lists.sourceforge.net/lists/listinfo/sbmlsolver-discuss > > -----------------------------------------------------------------------= -- > Using Tomcat but need to do more? Need to support web services, securit= y? > Get stuff done quickly with pre-integrated technology to make your job = easier > Download IBM WebSphere Application Server v.1.0.1 based on Apache Geron= imo > http://sel.as-us.falkag.net/sel?cmd=3Dlnk&kid=3D120709&bid=3D263057&dat= =3D121642 > _______________________________________________ > sbmlsolver-devel mailing list > sbm...@li... > https://lists.sourceforge.net/lists/listinfo/sbmlsolver-devel > |
|
From: Hendrik F. <fu...@ul...> - 2006-10-11 21:02:04
|
Hi everyone, one of the older threads in the archive was about problems running =20 configure under Linux. After a long day, I managed to compile SOSlib =20 under Mac OS 10.4 and thought I'd share this brief how-to with you. 1. As mentioned in requirements you need SUNDIALS 2.1.1 and *NOT* the =20= latest version. I can confirm version 2.2.0 does NOT work. 2. Configure sundials with "./configure --prefix=3D/usr/local", make =20 and make install as usual 3. Change to SBML_odeSolver directory. If you compiled libSBML with =20 expat rather than xerces, the configure script needs modification. =20 Run the following command: perl -p -i~ -e 's/-lxerces-c/-lexpat/g;' examples/Makefile.in =20 examples/Makefile.am odeSolver/Makefile.am odeSolver/Makefile.in =20 configure 4. Configure should now run smoothly 5. On my system, make threw an error in the very last linking step, =20 saying that it couldn't find libexpat, even though /sw/lib was =20 included in the LDFLAGS environment variable. I simply linked the =20 file manually by just adding -L/sw/lib to the gcc command line. Done. make install worked fine for me. Hope this was helpful. Hendrik -- Hendrik Fu=DF PhD student Systems Biology Research Group University of Ulster, School of Biomedical Sciences Cromore Road, Coleraine, BT52 1SA, Northern Ireland |
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From: Rainer M. <ra...@tb...> - 2006-10-05 18:35:43
|
Hi Ivan, > we have a nasty problem with the installation on linux (Fedora Core 5) > of the SBML Ode Solver. I have installed libsbml version 2.3.4 and > sundials 2.2.0 (but I tried even with the version 2.4). Unfortunately the new sundials version is not backwards compatible and we just realized that a few weeks ago but forgot to indicate it at our website. SOSlib is currently built for Sundials 2.1.1. The next official release of SOSlib will change to the upcoming next Sundials release. We use Fedora ourselves, so installation should be no problem with the correct Sundials version! Rainer On Wed, 4 Oct 2006, Ivan Merelli wrote: > Dear all, > > we have a nasty problem with the installation on linux (Fedora Core 5) > of the SBML Ode Solver. I have installed libsbml version 2.3.4 and > sundials 2.2.0 (but I tried even with the version 2.4). > > The problem is that there is no way to pass the ./configure step of the > installation because of this error: > > checking correct functioning of SUNDIALS CVODE... no: > CFLAGS=-g -O2 -I/usr/local/include > LDFLAGS= -L/usr/local/lib > LIBS= -lsundials_kinsol -lsundials_cvodes > -lsundials_cvode -lsundials_nvecserial -lsundials_shared -lm > configure: error: Can not link to SUNDIALS CVODE Library > > I tried to specify in different ways the path of the library, that are > correctly installed in /usr/lib. There is anyone who has been able to > install SBML ode Solver on linux? > > Ivan > > > ------------------------------------------------------------------------- > 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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