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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
I saw this post on Answers.
I was impressed at the capability of the AI, as I have been at other times when I posed a question to it, at least some of the time. So much so that I wondered...
What if the AI were automatically applied to EVERY question on Answers? Would that be a good or bad thing? For example, suppose the AI automatically offers an answer to every question as soon as it gets posted? Of course, users would still be allowed to post their own, possibly better answers. But would it tend to disincentivise individuals from ansering questions?
Perhaps as bad, would it push Answers into the mode of a homework solving forum? Since if every homework question gets a possibly pretty good automatic AI generated solution, then every student will just post all HW questions, and the forum would quickly become overwhelmed.
I suppose one idea could be to set up the AI to post an answer to all un-answered questions that are at least one month old. Then students would not gain by posting their homework.
In just one week, we have about 200 amazing animations! We see many creative and compelling animations and more importantly a lot of FUN!
Now, let the voting begin! Vote on the animations you love. Also, share them with your friends, classmates, or colleagues. Show the world the beauty of mathematics!
Mini Hack Winners - Week 1
You probably can imagine how hard it is to pick the winners, given so many awesome entries there are! We came up with several categories:
Landscape:
Trees:
Illusion:
Cartoon:
MATropolis:
Geometry:
Congratulations to the winners! Each of you won your choice of a T-shirt, a hat, or a coffee mug. We will contact you after the contest ends.
Finally, we encourage all of you to share your experiences, thoughts, and feedback in our new contest discussions channel!
Loving all the animations I'm seeing so far and feeling so inspired and impressed by what y'all are sharing. Thanks for loading me up with new topics to learn about!
The Flipbook contest is currently in full swing! It's been truly inspiring to see the incredible artwork you've all created using MATLAB! Checkout the gallery page if you haven't already.
We have some exciting news for our contestants today! In order to allow for more complex and unique creations, we've increased the MATLAB Evaluation timeout limit from 55 to 235 seconds!! So, don't hold back! Feel free to throw in those extra intricate lines of code without worrying about timeouts.
To all those already participating, we commend your efforts and encourage you to keep pushing your boundaries. And remember, there's always room for more. So, why not invite your friends and fellow MATLAB enthusiasts to join in the fun?
We also encourage everyone to engage in the contest discussions channel. Share your experiences, insights, and feedback about this contest. Your contributions enrich our community and help us improve future contests.
Looking forward to seeing more and more entries in coming weeks!
We reached the 100 animations milestone in less than 3 days! We are thrilled to see so many creative entries and talented members learning from each other.
Note that this contest is not just for experts. People with all skill levels can participate, improve their MATLAB skills, and have fun!
We have created new resources and tips for you to get started.
- Contest introductory video. The 3-minute video provides you with a quick introduction to how the contest works and how to create a simple animation.
- Animations blog post. The post demonstrates some coding techniques that can make your animations easier.
- AI Chat Playground. This is a new community app we just released. You can leverage the Generative AI tool to write initial draft MATLAB code or modify existing one.
- Get ideas from previous Mini Hack contests. There is a large gallery of amazing images, which provide you with ideas and code to start with.
- Remix is highly encouraged. Learning from others is the most effective way to learn. Make some SMALL changes and see what it would look like.
We look forward to seeing more of you joining us and having more fun!
Unlike last year's contest, there are some new technologies this year that might offer some advantages. Namely generative AI's like ChatGPT, Bard, etc. Not to be excluded, MathWorks just launched the AI Chat Playground :)
The MATLAB AI Chat Playground is open to everyone!
Check it out here on the community: https://www.mathworks.com/matlabcentral/playground
Participants across all skill levels are welcome to join! You can participate by creating a new animation or remixing an existing one with up to 2,000 characters of MATLAB code.
Contest Tips:
- Before you start, we highly recommend you check out the two examples - Bouncing and Spinning - to understand how the contest works.
- Share your thoughts, ask questions, or connect with others in our contest discussion channel.
Note that the first week (Nov. 6th, 2023, ~ Nov. 12th, 2023) is for creating entries only. Voting does not begin until the second week.
We look forward to seeing your creative work. Let the contest begin!
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
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!
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
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.
I am trying to simulate model of blood lymphocyte count from a paper using Simbiology. The rate of in or out following circadian rythym is kp(t)=km + kb cos [(t-tpeak)*2pi/24] Where and how do I write the expression ? I dont think I can write in repeated assignment ?
I am currently facing a compatibility issue when attempting to load a SimBiology model created in MATLAB 2021a into MATLAB 2023a. Specifically, the code capture functionality does not seem to be working.
If anyone has encountered a similar situation or has insights on how to capture the code for a SimBiology model created in an older version of MATLAB, I would greatly appreciate your guidance. Are there any alternative methods or specific steps that can be followed to ensure successful code capture?
Thank you in advance for your time and expertise.
4 weeks of contests is fun but intense. Next, we recommend 3 things to do as warm-down exercises.
To make future contests better and more appealing to you, we created a 1-minute survey to understand your experience. Your feedback is critical to us!
Dave Bulkin is a developer on the MATLAB Graphics and Charting Team. In the Blog post, @Dave B not only examines the code behind the leading entries, but also introduces you to some new visualization techniques.
Matt Tearle is from MathWorks Training Services Team. @Matt Tearle created this problem group to celebrate the 10th anniversary of Cody and the 2022 T20 World Cup (which happened to occur at the same time). Note that the problems can be done without the knowledge of cricket.
Thank you in advance and hope to see you in 2023!
Dear community,
I would like to develop a fermentation model with 4 ODEs, one of which contains variable y. A "repeated assignment", e. g. y=5x+5, contains variable x that has been measured each second. These data (columns with time and corresponding value x in each row) are recorded in the Excel file.
Does anyone have any suggestion how to implement this in symbiology?
Thank you very much in advance,
Tetiana
The 2022 community contests have concluded! During the 4 weeks, we hope you had a lot of fun and learned some MATLAB skills. Together, we've achieved amazing milestones:
- 500+ entries and 5,000+ votes created in the Mini Hack 2022 contest.
- 100,000+ solutions submitted in Cody 10th Anniversary contest
- 2,000+ participants in both contests
Now, it's time to announce weekly winners and grand prize winners!
Mini Hack - Pick of the MATLAB Graphics Team
We invited the MATLAB Graphics team, the authors of the MATLAB functions used in every entry, to be our Mini Hack judges. Here are their picks in 3 categories:
- Our Top 3:
Rising Hand by Augusto Mazzei
Object used: fill; Judge comments: Clever code, nice metaphor, kind comments
Above the clouds by Tim
Object used: patch (via VOXview); Judge comments: Very pretty, looks like it could be in a video game
Monocular rivalry by Jenny Bosten
Object used: Image; Judge comments: We spent a too much time trying to figure out what this illusion was doing to our brains
- Clever use of Charts:
Object used: Bar3; Judge comments: Cute! Nice fireworks!
Object used: histogram2; Judge comments: We didn't realize there was a ship in the flow data set
Object used: plot; Judge comments: Nifty and very different from other entries.
Object used: scatter; Judge comments: Overlapping markers make for a very cool tunnel-like effect
- Things we still loved:
Object used: image; Judge comments: Domain Warping FTW
Object used: surface; Judge comments: Clever use of transparency
Congratulations and you should be very proud of yourself! It's a huge achievement that your entry is recognized by the MATLAB Graphics team!
Mini Hack - special category for Week 4
Mini Hack - grand prize winners
After an intensive (and very time-consuming) review of votes on winning entries, we have finalized the list of grand prize winners. Huge congratulations! We appreciate the time and effort you spent and the awesome entries you created. Each of you won an Amazon gift card.
Anton Kogios, Brandon Caasenbrood, KARUPPASAMYPANDIYAN M, Teodo, Jenny Bosten, MvLevi, Abdullah Caliskan, Stewart Thomas, Jonas Schlatter, and Tim Davis
Cody 10th Anniversary - surprise prize for 28-day streak winners
We are thrilled to see that 37 players have built a streak of 28 days! Coming back every day to solve problems is an incredible achievement. We decided to show our appreciation by awarding a surprise prize to those 37 players. Congratulations! Each of you will get a MathWorks T-shirt.
Christian Schröder, Stefan Abendroth, Mohammed, Victoria, Vasileios Pasialis, Gerardo Domínguez Ramírez, HH, Anton Kogios, Lizhi Zhu, Marco Fuscà, Armando Longobardi, Monica, Rithik KRT, Ayman, Teodo, Lincoln Poon, Elijah Keifert, siranjeevi gurumani, kazuyoshi kouno, Ryan Koh, Manuela Kaiser, Mehmet OZC, Dyuman Joshi, KOTHAPALLI SRI BRINDA, Gergely Patay, abyss, Takumi, Keita Abe, Petr Cerny, Shubham Shubham, Meredith, Andrew K, Atsushi Ueno, Peter Orthmann, Armando Longobardi, Chuang Tao, and David Romero
Cody 10th Anniversary winners – Week 4
The top 3 players for solving the most problems in week 4 are Christian Schröder, Gerardo Dominguez Ramirez, and Stefan Abendroth, Congratulations! Each of you won an Amazon gift card.
Week 4 lucky winners are Qingrui Liu and Basant Ale.
Cody 10th Anniversary winners – grand prize winners
We know how hard it is to be a top-10 leader in the contest leaderboard! It requires a huge time commitment and advanced MATLAB skills. Congratulations! Each of you will win an Amazon gift card.
Christian Schröder, Stefan Abendroth, Mohammed, Victoria, Vasileios Pasialis, Gerardo Domínguez Ramírez, HH, Anton Kogios, Lizhi Zhu, and Marco Fuscà
Lucky voters and participants
Thank you for your participation in our 2022 contests. You don’t need to be on the top of the leaderboards to win. As we announced, we would give out 20 MathWorks T-shirts to lucky voters and participants of the 2 contests.
Ismail Bera Altan, Robin Stolz, Michael Mellin, Kellan Smith, Neha Shaah, Siranjeevi gurumani, Paul Villain, Andrew Horchler, Meg Noah, Saurabh Chaudhary, Pakize erdogmus, Godfrey Ojerheghan, Selena Mastrodonato, Damir Rasic, Thomas Kjeldsen, Meredith, John Noah Ramiterre, Patience Oliveira, Panda, and Sujeet Kumar Choudhary
On behalf of the MATLAB Central community team, we thank you for joining our celebration of the MATLAB Central community 2022 contests. We hope you enjoyed these contests and look forward to seeing you in next year’s contests.
