Questions tagged [systems-biology]
Questions about accessing biological data, built-in functionalities directly applicable to biological modeling, or about creating such tools etc.
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Plotting Dengue Infection Prevalence Sensitivity to Biting Rate Variations
I want to explore how varying values of the biting rate affect infection prevalence in humans in our modeled dengue outbreak, keeping all other parameters constant.
I provide you the code that I use ...
5
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1
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Modeling Infection Spread among Different Age Groups with Contact Matrix
In this code, we divided the population into children, adults, and old people.
The probability of infection per contact, $b$, is 5 % for people of all ages
The total population size is 1 million, and ...
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1
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75
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Exploring Variability: 100 Stochastic Simulations of Cumulative Incidence
We know $R_0=0.75$ and $\gamma=0.4$. So with the following code I calculate $\beta$
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2
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SIR Parameter Estimation in Mathematica
All infected individuals go through an incubation period, which lasts on average for 4 days. During this time, individuals are not infectious, nor do they have any excess mortality risk.
All infected ...
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2
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217
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Performing maximum likelihood estimation for SIR Model
The code first produces a plot of the dataset, then simulates the SIR model using the parameter values we found in the manual calibration to the full dataset of the total number infected .
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Writing a sum-of-squares function or SIR model fits
I am trying to write a function that calculates and returns the (sum-of-squares) value (SSQ) for the fit of a simple SIR model, parameterized with given values of $\beta$ and $\gamma$, to any dataset.
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2
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1
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72
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Implementing Izhikevich's spiking neuron model
I am trying to implement Izhikevich's simple spiking neuron model which is given by
V'(t) = 0.04 V^2+5V+140-u+I
u'(t) = a(bv-u)
if V=30 mV then V=c, u=u+d
...
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239
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Plotting a 4-dimensional graph with the fourth dimension depicted using a color scheme
I wish to use Mathematica to plot a 4-D graph of R0 (basic reproduction number of a disease) against three given parameters in which the three parameters are represented by the x-, y-, and z- axes and ...
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Plotting several curves of the same variable for different values of a parameter
I am coding an SIR model using Mathematica. I would like to know how to plot multiple curves of I on the same figure for different values of the parameter beta, say for the values of 0.001, 0.002, 0....
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152
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How to plot contour plots of R0 against two parameters?
I am working on an epidemiological model and I would like to know how to plot contour plots of R0 (basic reproduction number) against two given parameters using Mathematica. An example contour plot is ...
- 99
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76
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Non Linear System of Diferential Equations with periodic function
I am programming a system of differential equations consisting of 3 cell populations; Normal cells N, Tumor cells T and chemotherapy treatment Q, when a function q is constant. The system is as ...
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Avoiding Concave Polygons
In a vertex model, vertices in a lattice are modelled by a set of ODEs. A T1 transition is the following: when a certain edge becomes small enough (given a threshold), two cells stop being connected, ...
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Solving ODEs vs VoronoiMesh
I'm using VoronoiMesh to model cells in an epithelium. The concentration of certain proteins within the cells are determined by solving a system of ODEs per cell. ...
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180
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Three variables bifurcation diagram
I'm trying to reproduce a paper. The point is that I have three variables and I will like to do the bifurcation diagram.The paper is this one:"A chaotic model of ...
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137
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How to use Manipulate for protein sequence alignment?
I have the sequence of a protein from Chain A and Chain B and I want to use Manipulate to show what parts of sequence are identical.
This is what I have:
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27
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Turing patterns
I am new in learning Turing patterns. Is there any sample code available to generate such patterns in ecology model (Lotka–Volterra model)?
The above figure is taken from this paper, and is based on ...
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Insert, remove or shift two random time points of data
This is extension of my previous question.
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Insert two random time points to data
I have a data as following. I want to add two random time points, one for birth one for death.
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How to simulate two coupled birth-death-immigration processes?
I am simulating a birth-death-immigration process for two coupled populations that interact by virtue of the birth-rate in one population being equal to the death-rate in the other population. The two ...
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Difficulties in compiling the steady state of a biological model
I am modeling the yellow fever for an EDO system, in which I have to find the stationary states of the system, and I have great difficulty in finding something that can be very simple. I put the ...
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2
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551
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Birth Death Process with Delay
I would like to simulate birth process with time delay. Here is a reference ref on page 3. Note there is two species whereas in my case I have one species. So only equation (1) and (2) should be ...
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Solving an inequality with conditions on the values
I have to know if an equation is always negative for the realistic set of values that I'm looking at. The problem is that the equation is way too big. I know I can do it manually if I spend a couple ...
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How do I plot this system of ODEs using Manipulate to change the b and k variables?
I'm trying to create an SIR model of disease. These are the starting parameters, and i'd lake to be able to manipulate b and k. Thanks!
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Bioinformatics: RNA-seq and Gene Set Analysis Pipelines
Context
The decreasing price of high-throughput genome sequencing has skyrocketed its use.
While Mathematica is a remarkable language, it does lag behind in some regards for various reasons; notably, ...
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Gillespie Stochastic Simulation Algorithm
The Gillespie SSA is a Monte Carlo stochastic simulation algorithm to find the trajectory of a dynamic system described by a reaction (or interaction) network, e.g. chemical reactions or ecological ...
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