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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6
votes
1answer
240 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
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0answers
96 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
95 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: ...
19
votes
2answers
2k 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
90 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
31 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 ...
1
vote
1answer
300 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! ...
2
votes
1answer
243 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; ...
23
votes
1answer
2k 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 ...