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Jim Bosley


Last seen: 8 days ago

Clermont, Bosley LLC

44 total contributions since 2017

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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 ...

4 months 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...

5 months ago | 1 answer | 0

1

answer

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...

10 months ago | 1 answer | 0

1

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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...

12 months ago | 1 answer | 0

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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 ...

12 months ago | 0

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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...

12 months ago | 1 answer | 0

1

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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...

1 year 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...

1 year 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(...

1 year 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...

1 year ago | 0 answers | 0

0

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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...

1 year 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...

1 year ago | 2 answers | 0

2

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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...

1 year ago | 3 answers | 0

3

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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...

1 year 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...

1 year 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...

1 year ago | 1 answer | 0

1

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Answered
How To Clear Java Heap Space Memory????
jonathan wrote: "years are passing on this one folks. hello? Mathworks please address this." I'm thinking that maybe eight year...

1 year ago | 0

Answered
How To Clear Java Heap Space Memory????
This error kept me from publishing completed work. That is, Matlab did the analysis, but publish could not complete for the scri...

1 year ago | 0

Question


nlme fitting error for covariate in popPK model
I select a column (WT) in my dataset as a covariate. When I set up the covariate in the nlme fitting page (interactively, not ...

2 years ago | 1 answer | 0

1

answer

Question


Can I create a variant that captures all current parameter, species and compartment values?
So I'd like to be able to do something like this: sbr = sbioroot; % Get the root object lastn = length(sbr.m...

2 years ago | 1 answer | 0

1

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Question


Not finding info on arrays of variant objects
The help page on <https://www.mathworks.com/help/simbio/ref/variantobject.html?searchHighlight=variant%2520array&s_tid=doc_srcht...

2 years ago | 1 answer | 0

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Question


Better understanding of variants sought (also project files)
If I create a model using the dashboard, including variants(suppose 2, 'var1', and 'var2'), and save the model, the variants are...

2 years ago | 1 answer | 0

1

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Question


Could Simbiology simulations have a preload function?
In Simulink, one can write preload scripts that run upon opening a model or upon any number of other actions. In Simbiology...

2 years ago | 1 answer | 0

1

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Question


Dimensional analysis with math functions flags a warning
I'm getting a warning when I run with dimensional analysis. _ *Cannot perform dimensional analysis for rule 'rule_13' becau...

2 years ago | 1 answer | 0

1

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Answered
Shorthand for sbioselect/set
So I decided to write the code and am embarrassed with how simple it is. But a question arose. Here's the code: function ...

2 years ago | 0

Question


Shorthand for sbioselect/set
In running simbiology models using scripts, one often wants to change parameter values. For a single parameter (e.g. "p1") we c...

2 years ago | 2 answers | 0

2

answers

Question


sbioloadproject or sbiosaveproject loses graphical information
If you Google "Why did I become a biologist?" most answers include "I loved science and hated math". One of the key element...

2 years ago | 1 answer | 0

1

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Answered
Variable Stoichiometric Coefficients in SimBiology?
This is an old thread, but I wanted to bounce this off the community. It seems that you can fool the model. If the stoichiomet...

2 years ago | 0

Answered
persistent variable precludes simbiology acceleration, how can I keep an array available in memory
Arthur, Thanks! This is good news. As I wrote above, the "persistent" approach seems to me to be more elegant than "global"...

2 years ago | 0

Answered
persistent variable precludes simbiology acceleration, how can I keep an array available in memory
Arthur, thanks for your note and this information. I'm confused, though, because when I had persistent variables, the error mes...

2 years ago | 0

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