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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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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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2answers
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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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0answers
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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 ...
1
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1answer
197 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
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1answer
218 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; ...
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1answer
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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 ...