Biology Stack Exchange
Biology Stack Exchange

Questions tagged [modeling]

10 questions
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Success of computer simulations in biology, new discoveries

In an interview with Tim Hunt, Hunt makes the following comment: There are some people nowadays who think you can sort of model everything on a computer. But I'm not one of those. I don't think anyone has actually discovered anything modeling…
ShanZhengYang
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Example of well understood/modeled biological mechanism

I am working on modeling psychiatric disorders, where multivariate time series data - which I think is necessary to do any interesting modeling - is only broadly available recently, due to the availability of surveys via mobile devices. To get into…
jmb
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Interesting examples of models

I am studying the general use of models in biology in terms of methodology, applications, usefulness etc, and I would really appreciate any recommendations of some specific examples of models from any area in biology. Some examples are the logistic…
Floyd
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Why this decay term in Anaerobic Digestion Model?

I am reading about the AM2 model, which appears to be a simplified version of the ADM1 model for modeling anaerobic processes. The author of this doctoral thesis extended the simpler AM2 model by introducing hydrolysis. Given a substrate state…
Theodor Johnson
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Is it possible to mathematically model the growth of plants?

Are there mathematical equations that represent/model the growth of plants? For example, if I have a Bellis perennis and I want to know how it develops in a given environment (Sun is shining, defined amount of water etc). How can one say if it grows…
jackon
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Why Differential equation is not a good way to model chemical reaction networks

I'm a computer scientist and mostly code and have worked with Boolean models of cell level molecule transfer. Now i'm reading about the Biological pathways and modelling chemical reaction networks / Actions / Post translation modification and have…
Pushpa
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What allows diverse ecology to thrive despite forces reducing species diversity?

Ecology and business are a useful model for understanding one another. One species fills a niche until it is outcompeted by another just as one business fills a niche until it is outcompeted by another. Businesses adopt successful strategies and…
Tal
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Can GENESIS simulation software be adapted to other types of tissues?

GENESIS simulation software http://genesis-sim.org/ is designed for neurobiological systems and it is able to inculude in the simulation the different resolution levels - starting from the molecular interaction and ending with neuronal interaction.…
TomR
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Identity and similarity for Multiple Sequence Alignment (MSA) of proteins

I have to do homology modeling for a transmembrane protein (sodium channel) and right now I am in the process of aligning the sequences of the template with the homologous proteins I have found. I am using T-Coffee to do the alignment. I would like…
wrong_path
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Predicting protein folding with Alphafold

I’m trying to figure out how to use Alphafold, which is a biological analysis software for predicting the folding of amino acid sequences. I’ve been trying to follow the directions on the creators’ website for downloading it and using it but there’s…
Aaron
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