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Jim Bosley


Clermont, Bosley LLC

Last seen: 6 dagen ago |  Active since 2017

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Simbiology "Project Save Error"
For some reason I cannot save simbiology projects. When I try (for new files, and files I've loaded) I'm now getting: "Project...

21 dagen ago | 2 answers | 0

2

answers

Answered
"The support package is not compatible with your version of MATLAB or operating system." for installing minGW in R2022a
Thanks for the help, gentlemen. Ok, let me be more clear than I was. From matlab compiler page I understand that all I have to...

3 maanden ago | 0

Question


Simbiology reaction stoichiometry: R + E ==> P + E, or the simpler R ==> P?
tldr; Is there any benefit or disadvantage to writing the stoichiometry reactions of catalyzed by an enzyme as R + E --> P + ...

3 maanden ago | 1 answer | 0

1

answer

Answered
install command on linux doesn't bring up installer - again
My bad, Philip Wesley already answered this. Answer is here. In a terminal: xhost +SI:localuser:root Then sudo ./install

3 maanden ago | 0

| accepted

Question


"The support package is not compatible with your version of MATLAB or operating system." for installing minGW in R2022a
With some help I got matlab installed in ubuntu. Works fine, however, I get the warning (words to the effect): "You should ins...

3 maanden ago | 3 answers | 0

3

answers

Question


install command on linux doesn't bring up installer - again
I'm having the same problem that others have had (same summary) but the solution did not work. I download the zip file. I unzi...

3 maanden ago | 2 answers | 0

2

answers

Answered
simbiology duplicates sbml id tokens when "duplicate" is used
Florian, Thanks! To remind folks of the use case here, if one creates a model in Simbiology and uses copy/paste on the graphica...

5 maanden ago | 0

Question


simbiology duplicates sbml id tokens when "duplicate" is used
Not sure if this is intended, but I believe that it does highlight a bug. Say I create a model in simbiology, with species A an...

5 maanden ago | 2 answers | 0

2

answers

Question


sbml export does not appear to export modifiers
In a description of the SBML standard, namely Hucka et al., The Systems Biology Markup Language (SBML): Language Specification f...

5 maanden ago | 1 answer | 0

1

answer

Question


Any progress on relaxing the constraints on species units?
In SimBiology, there is a limited set of units one case use. Amount, or concentration. This is often inconvenient, as (for ex...

10 maanden ago | 1 answer | 0

1

answer

Answered
Matlab unable to install R2021b: "unable to write to selected folder" in Ubuntu 20.04
A bit more detail - thanks to Philip (see above) for the answer. Apparently in a terminal window you must run xhost +SI:localu...

11 maanden ago | 12

| accepted

Question


Matlab unable to install R2021b: "unable to write to selected folder" in Ubuntu 20.04
Trying to install R2021b on the system drive. Using Ubuntu 20.04. 384 Gb available. I download matlab_R2020b_glnxa64.zip an...

11 maanden ago | 1 answer | 1

1

answer

Question


Is there any way to export a simbiology model diagram in high resolution?
I have a fairly large and complex simbiology model. I'd like to export the graphical model diagram in a presentation quality ti...

11 maanden ago | 1 answer | 0

1

answer

Question


When will sbmlimport support sbml level 3?
Would be useful to know. I believe 2020b only supports level 2, correct? Has anyone else run into having to use an sblm level ...

bijna 2 jaar ago | 1 answer | 0

1

answer

Question


Semicolons in SimBiology species names: just characters, or functionally active?
I was looking at Sven Mesecke's implementation of the Renin Angiotensin Aldosterone System model of Lo et al. 2011. (For those ...

meer dan 2 jaar ago | 1 answer | 0

1

answer

Question


Any simulation speed differences between models loaded with SimBiology() vs sbioloadproject?
The question is in the title. I haven't seen much difference in numerical efficiency between the same model opened in sbioloadpr...

meer dan 2 jaar ago | 1 answer | 0

1

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Question


Namespace and other html / xml information in SimBiology Notes
Simbiology notes allows (requires?) one to use html for nicely formatted notes. For normal documentation use, where there will b...

bijna 3 jaar ago | 1 answer | 0

1

answer

Question


Constant parameter setting throws error, or... if I don't set a parameter to constant, but don't change it, does it stay constant?
In another thread, I asked about using subject- (group- in SimBiology) dependent parameter values to allow fitting of one part o...

ongeveer 3 jaar ago | 1 answer | 0

1

answer

Answered
Icons for pinned SimBiology(R) graphics
Repeating as a partial answer: As to the last point, found this: Simbiology / Preferences / Indicators Show indicator when a ...

ongeveer 3 jaar ago | 0

| accepted

Question


Icons for pinned SimBiology(R) graphics
When building models graphically usign the dashboard, one can pin graphical elements. This prevents inadvertently messing up a c...

ongeveer 3 jaar ago | 1 answer | 0

1

answer

Question


deleting or removing variant using variant array handle gives unexpected results.
If I have a variable that contains a SimBiology parameter object, and I change it, the object reflects that change: par1 = addp...

ongeveer 3 jaar ago | 1 answer | 0

1

answer

Question


Can I force Matlab to wait 'til it finishes one command to run another?
I have a script that loads a SimBiology model using the simbiology() command. Then I try to get a handle for the model simbiol...

ongeveer 3 jaar ago | 1 answer | 0

1

answer

Answered
Is it possible to get the group (that is the subject) number in sbiofit to do a lookup?
One last thing. I tested using the group to set parameters. Works fine. So a repeat assignment rule is just pv = setparvalu(...

meer dan 3 jaar ago | 0

Question


sbiofitmixed/ nlmefit and weighting two dependent variables
I am fitting a trial with two output measurements (for now). These are CONC1 and CONC2. Supposing that they have very differen...

meer dan 3 jaar ago | 0 answers | 0

0

answers

Answered
Is it possible to get the group (that is the subject) number in sbiofit to do a lookup?
Jérémy Glad if the ideas help. I enjoy the interactions with you, Arthur, Pax, and others on your team. I just want to clarif...

meer dan 3 jaar ago | 0

Question


How can I plot only one fitted variable after using sbiofit?
I'm fitting a model to a dataset. I have two variables I'm fitting simultaneously: the therapy, and the quantity of an endogeno...

meer dan 3 jaar ago | 2 answers | 0

2

answers

Question


Is it possible to get the group (that is the subject) number in sbiofit to do a lookup?
If I'm fitting using lsqnonlin, is there a matlab script function that returns the group number? The idea is to allow use of co...

meer dan 3 jaar ago | 3 answers | 0

3

answers

Question


Fitting multiple dependent variables with time less than zero
Suppose I have a therapeutic d that modulates an endogenous substance e. I've a pd model of e (for the sake of argument, a cons...

meer dan 3 jaar ago | 1 answer | 0

1

answer

Question


The order of plotted things vs the order of the legend
I'm using patch to show a confidence interval in a matlab plot as a colored region. Assume vectors of time values, tv, and mean...

meer dan 3 jaar ago | 1 answer | 0

1

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Question


Is there an object associated with simulate task in the simbiology desktop that contains the name of the task?
I use State_Subplots in "Plots to Generate" in simbiology simulation tasks a lot. "Plots to Generate" allows scripts to be used...

bijna 4 jaar ago | 1 answer | 0

1

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