33
votes
Accepted
Turing patterns
I developed a reaction-diffusion-advection model of pattern formation in semi-arid vegetation (tiger bush) 20 years ago, which shows a type of Turing instability. Plants ($n$) consume water ($w$) and ...
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22
votes
Turing patterns
I did some work with the Brusselator some time ago. This is the reaction-diffusion equations which generate Turing patterns. There are some things you need to know:
(1) The non-linear PDEs have ...
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12
votes
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Solving ODEs vs VoronoiMesh
The following example makes use of my package, IGraph/M.
Needs["IGraphM`"]
First we generate some random points to use as Voronoi centres. We apply a few steps ...
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9
votes
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How to use Manipulate for protein sequence alignment?
I'm using as examples the mouse and human sequences for Rhodopsin (the protein in retinal rod cells that detects photons).
...
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6
votes
Performing maximum likelihood estimation for SIR Model
ParametricNDSolve and NonlinearModelFit work for this cases.
...
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6
votes
6
votes
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4
votes
Accepted
Avoiding Concave Polygons
The logic might need some tweaking depending on the order of the points, but for these examples, it works. Essentially, replace the computation of the two new endpoints ...
- 34.4k
4
votes
Accepted
Modeling Infection Spread among Different Age Groups with Contact Matrix
I really enjoy your epidemic series :-) It is always better to decouple the weedy details of a specific model from the key question. Key question should be purified to bare minimum. Perhaps helpful, --...
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3
votes
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3
votes
Implementing Izhikevich's spiking neuron model
We can use input data from the page. Tonic Spiking model can be implemented as follows
...
- 48.8k
3
votes
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Plotting several curves of the same variable for different values of a parameter
ParametricNDSolve is the tool for the job, combined with Table:
...
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3
votes
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3
votes
Accepted
3
votes
Bioinformatics: RNA-seq and Gene Set Analysis Pipelines
Gene List Pre-Processing
ABOUT:
In this example we have two gene lists, both from mice. One gene list contains columns of features, the other has condition replicates.
GOAL:
The goal is to
Convert ...
- 5,442
2
votes
Difficulties in compiling the steady state of a biological model
Comment
Maple gives multiple solutions,
...
- 12k
2
votes
Accepted
Birth Death Process with Delay
I figure it out how to simulate birth-death process with one species. Black curve is DDE (delayed DE).
...
- 10.9k
2
votes
Accepted
SIR Parameter Estimation in Mathematica
It looks like we try to estimate parameter $\beta$ with known $\gamma, \mu$ using one point only reportedData = n*0.08. In this case we can compute $\beta$ as ...
- 48.8k
2
votes
Accepted
1
vote
Accepted
1
vote
Non Linear System of Diferential Equations with periodic function
Your main problem was not to define all paramters.
A good way to look whether you got all variables is
Variables[Level[eqs, -1]]
Two posibilities of solution:
a) ...
- 17.4k
1
vote
Insert two random time points to data
Perhaps you can make use of StepFunction from my answer to question How can the behavior of InterpolationOrder->0 be controlled?:
...
- 132k
1
vote
Accepted
1
vote
Difficulties in compiling the steady state of a biological model
Here's how I would do it:
...
- 20.4k
Only top scored, non community-wiki answers of a minimum length are eligible