Questions tagged [systems-biology]
Questions about accessing biological data, built-in functionalities directly applicable to biological modeling, or about creating such tools etc.
26 questions
0
votes
0
answers
65
views
1
vote
1
answer
61
views
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 ...
4
votes
1
answer
73
views
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 ...
0
votes
1
answer
80
views
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 $\beta$
...
2
votes
1
answer
160
views
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 ...
2
votes
2
answers
391
views
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 .
...
0
votes
1
answer
93
views
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.
...
2
votes
1
answer
88
views
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
...
- 61
2
votes
1
answer
246
views
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 ...
- 99
2
votes
1
answer
75
views
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....
- 99
1
vote
1
answer
251
views
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
0
votes
1
answer
79
views
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 ...
5
votes
1
answer
169
views
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, ...
- 4,953
7
votes
1
answer
275
views
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. ...
- 4,953
0
votes
0
answers
191
views
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 ...
-2
votes
1
answer
155
views
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:
...
- 827
28
votes
2
answers
6k
views
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 ...
- 383
2
votes
1
answer
64
views
Insert, remove or shift two random time points of data
This is extension of my previous question.
...
- 10.9k
3
votes
2
answers
80
views
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.
...
- 10.9k
1
vote
0
answers
161
views
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 ...
- 115
0
votes
2
answers
121
views
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 ...
- 1
6
votes
2
answers
571
views
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 ...
- 10.9k
0
votes
0
answers
58
views
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 ...
- 89
2
votes
1
answer
464
views
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!
...
- 23
2
votes
1
answer
425
views
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, ...
- 5,442
32
votes
1
answer
4k
views
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 ...
- 47.2k