Questions tagged [systems-biology]
Questions about accessing biological data, built-in functionalities directly applicable to biological modeling, or about creating such tools etc.
11
questions
5
votes
1answer
109 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, ...
0
votes
0answers
55 views
Numerical Investigation of two Component Reaction-Diffusion System with Perturbative Advection
I am given two coupled differential equations and try to analyze them numerically because as far as I know, there is no analytical solution known(only the steady-state on an infinite domain is known, ...
7
votes
1answer
260 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. ...
0
votes
0answers
144 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
1answer
117 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:
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25
votes
2answers
3k 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 ...
0
votes
2answers
114 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 ...
0
votes
0answers
48 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 ...
2
votes
1answer
445 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!
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2
votes
1answer
292 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, ...
27
votes
1answer
3k 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 ...
