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The title is resonably non-descript, but I can explain it easily:
Say I have an initial Emax model:
v = emax1*[G]^n1/(ec501^n1+[G]^n1)
And I want to place v inside of a second Emax model:
y = emax2*v^n2/(ex502^n2+v^n2)
Currently, I have the full function of v inside y, twice, it's very long and whilst I only need to get it correct once, for readability in the future I'd rather have it in form #2. I've played around with non-constant parameters but I need the steady state to be v, not the rate rule, and I haven't worked out how to make a parameter shift to a form like v, as an observation might.
Are there any recommended solutions or do I simply need to keep with having v fully expressed in y?
Thank you,
Dan
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Hi All,
I'm currently attempting to implement a Hodgkin-Huxley-type model of membrane potential, ideally I would like a species that represents the membrane potential as its own distinct entity, so as the reference elsewhere. I've currently established a molarity-based work around but it would be great if I could set the units for the species as millivolt, but that throws an error.
Is there an established way to do this? I imagine I'm not the first person to be trying to model a voltage-gated ion channel!
Thank you for your help.
Hello,
I've looked around and I haven't found anything obvious about this, but is it possible to link to species/reactions, graphically, in a non-mass transfer sense? I have areas in my model where it would conceptually make sense to be able to see that species or reactions are linked, but if I link them in the standard way it demands that it be involved in the stoichiometry.
Perhaps some kind of dotted line, or similar?
Thank you, best regards,
Dan
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Adam and Heather will be discussing new features in R2023b and answering your questions in a few hours - visit the link below to check out the preview and sign up for notification.
Hello all,
I've been trying to shift my workflow more towards simbiology, it has a lot of very interesting features and it makes sense to try and do everything in one place if it works well..! Part of my hesitancy into this was some bad experiences handling units in the past, though this was almost certainly all out of my own ignorance, relatedly:
Getting onto my question.
In this model I have a species traveling around the body via blow flow, think a basic PBPK model. My species are picomolarities, if everything is already in concentrations, why is it necessary to initially divide by the compartment volume? i.e. 1/Pancreas below.
If my model dealt in molar quantities this would make a lot of sense, the division would represent the transition to concentrations. This, however, now necessitates my parameters be in units of liter/minute, which is actually correct, but I'd like clarification on why it's correct, ha!
Perhaps this is more of a modelling question than a simbiology question, but if there are answers I'd love to hear them. Thanks!
Adam Danz just launched a new blog about MATLAB Graphics and App Building.
As you know, He has been a prolific contributor to MATLAB Answers and one of his answers recently won the Editor's Choice Award.
If there are any topics or questions you are interested in, please share with Adam, and I am sure he will get those into his blog.
4 months ago, the new API was published to access content on the MATLAB Central community. I shared my MATLAB code to access the API at that time, but the team just released the official SDK.
MATLAB toolbox on File Exchange: https://www.mathworks.com/matlabcentral/fileexchange/135567-matlab-central-interface-for-matlab
Houman and Rameez will talk about how you can model wireless networks (5G, WLAN, Bluetooth, 802.11ax WLAN mesh, etc.) in MATLAB in the upcoming livestream. They will start with the basics such as nodes, links, topology and metrics. Then they will introduce a new free add-on library that lets you model such networks, and show you how to use it.
- Date: Thu, Oct 5, 2023
- Time: 11 am EDT (or your local time)
Bookmark this link:
Congratulations, @Adam Danz for winning the Editor's Pick badge awarded for MATLAB Answers, in recognition of your awesome solution in overlapping images in grid layout.
Thank you for going to great lengths to help a user in this thread by suggesting alternative approach to representing stack of playing cards in MATLAB, highlighting very interesting features like hggroup.
This badge recognizes awesome answers people contribute and yours was picked for providing a very detailed and helpful answer.
Thank you so much for setting a high standard for MATLAB Answers and for your ongoing contribution to the community.
MATLAB Central Team
You had a meteoric rise to in our community since you started answering questions in June 2020.
You provided 3218 answers and 926 votes. You are ranked #23 in the community. Thank you for your contribution to the community and please keep up the good track record!
MATLAB Central Team
Hi All,
I'm attempting to put a set of simbiology global sensitivity analysis plots into my thesis and I'm running into some issues with the GSA plots. Firstly, the figures are very large, it would be quite beneficial to grab a set of the plots and arrange them myself, is there any documentation on how to mess around with the '1x1 Sobol' produced by sbiosobol? Or just GSA plots in general.
The second problem is that the results appear to be relative to the most sensitive parameter in that run. Is it recommended to have a resonably sensitive 'baseline' parameter in each run? I find it difficult to compare plots when a not so sensitive parameter is being recorded as near '1' for the whole run because it's being stacked against a set of very insensitive parameters. I.e. if i have multiple sets of GSAs due to a large model, how can I easily compare results? If I could do some single run through with every parameter that would be the ideal, I imagine, but then the default plot would be half a mile off the bottom of my screen, haha! Perhaps there is a solution to the first question that might help there?
Thank you for your help,
Dan
MATLAB Onramp is a free online tutorial and it has been very popular with new MATLAB users to learn how to use it, and MathWorks have been adding more and more modules. The lastest one just dropped https://matlabacademy.mathworks.com/details/power-systems-simulation-onramp/orps
It shows you the basics of power system simulation by modeling a simple microgrid. You will learn how to simulate and measure three-phase circuits, and how to evaluate algorithms like droop control and maximum power point tracking.
Here's a screenshot from 22 years ago. Thanks for building one of the best engineering and science communities together.
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Hi all,
I've translated a model from another piece of software (monolix) into simbio programmatically to make use of your very easy global sensitivity analysis system.
It looks a little something like this, for a 'single' line example:
r1 = addreaction(model,'InsI -> InsP');
r1.ReactionRate = 'InsI*kip/vi'; %- is + panc
k1 = addkineticlaw(r1, 'Unknown');
Multiplied about 20 fold, as you can see I have included my volumes within the reaction rates myself (vi). The model functions perfectly and I have corrected the outputs at the end:
[time, x, names] = sbiosimulate(model,csObj,dObj1);
x(:,1) = x(:,1)/vi;
So that they are in concentration, as needed. However, when it comes to sensitivity analysis because I have corrected them post-model it is technically incorrect, it is analysing the absolute quantities. This is quite noticible in the sensitivity to the volumes.
Is there an easy fix to this, I've had to fight dimensionality with units in the past using simbio and I'd be great if there was some way of dividing a compartment output by a volume, for example. It is a functionality that exists in monolix, so I was hopeful it might here!
Thank you for your time.
EDIT:
I think I've worked it out, I had to refactor my model to operate in concentrations, just refitting it now. Now I should just be able to use unitless compartments.
Hello, an intern working at MathWorks is finishing up his program soon and he would like to interview some MATLAB users. He is looking for people who can give their perspective on the question:
"What makes MATLAB and Simulink special in comparison to other languages?"
Ultimately he plans to condense the answers into 15-second videos or sound bites.
If people are willing to participate but want more time to talk about their experience with MATLAB, he doesn't have time left for in-depth interviews but he can find someone else to take over the project.
Please send me an email via my profle if you are interested.
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