# 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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### How to calculate torsion angles (phi and psi) from ResidueCoordinates of protein?

I am trying to compute the torsion angles (phi, psi) from coordinates of protein (using pdb file in Mathematica). I am following the approach explained here. The output values are in the range of -180 ...
113 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, ...
57 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, ...
4k 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 ...
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. ...
147 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 ...
120 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: ...
117 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 ...
50 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 ...
446 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! ...