Biology Stack Exchange
Biology Stack Exchange

Questions tagged [computational-model]

A computational model is a mathematical model in computational science that requires extensive computational resources to study the behavior of a complex system by computer simulation.

Computational models can be used to study various biologic processes which are extremely complex like the way the brain functions.

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120-year-old gene regulation problem independently solved by a computer. How?

My Background: I'm a mathematics graduate student with a physics background. I have a very little biology knowledge and a little knowledge of machine learning and statistics. Topic: I recently found out about the following computational biology…
Christian Bueno
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How can computer predictions of protein folding be verified computationally?

Currently, there is a lot of research focused on solving the folding patterns of proteins using computers (Folding@Home, https://fold.it/portal/, etc.). The question that I have is: How do you know when you get it right? Is there some way of…
Stack Tracer
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What is the difference between a mechanistic and a statistical predictive model?

The simplest description of the difference between these two approaches that I have found are on this site who summarise the difference as: Mechanistic model: a hypothesized relationship between the variables in the data set where the nature of the…
PaulBarr
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What was the first piece of work in computational biology?

What was the first piece of work in computational biology? I'm ideally looking for a paper. I am not interested in works that involve data management or data analysis but work that model biological processes through numerical simulations or…
RNs_Ghost
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What are we missing about the real workings of the evolutionary process?

As a scientist (and a computer scientist at that) my view is that if we cannot simulate a process we have not understood it properly. I have been following the interesting field of Artificial Life for quite some time and the results are sobering -…
vonjd
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Start studying mathematical biology from basics

I am really passionate about theoretical and quantitative biology and I would like to build my future career around this topic. I've just got my bachelor's degree in biology (ecology) but scince I've had only one math class through the years, my…
Sielu
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Scoring matrices (BLOSUM & PAM) in BLAST and other sequence-comparison programs

The Wikipedia page on BLAST states that: The scores are created by comparing the word in the list in step 2* with all the 3-letter words. By using the scoring matrix (substitution matrix) to score the comparison of each residue pair, there are 203…
Vandana Nain
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Definitions and examples of some math-releated ecology branches

I would like to have an example of application and a brief description/definition (two or three lines) of the following fields. I would like to understand the exact differences between them. Other related informations are also extremely appreciated…
Aurelius
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Do free computer programs exist that can simulate drug permeability in bacterial membranes?

I am currently trying to make derivatives of a molecule in hopes of making it more permeable to bacterial membranes. I wanted to know whether there are any bacterial membrane simulating programs where I can dock my molecule and see its predicted…
helpantibioticswinagain
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What's a reasonable time constant for a mathematical model of a neuron?

Background I've been studying various mathematical models of neurons. So far I've covered the classic Hodgkin-Huxley model (to describe the potential difference of a single neuron) and the integrate and fire model for two neurons (to describe the…
Derek Fulton
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Can cognitive functioning of the human brain change the physical state of the brain?

Can cognitive functioning of the human brain change the physical state of the brain? E.g. does self-awareness, self-reflection change the number of neurons or synapses among neurons? I.e. I am trying to develop self-modifying neural networks as…
TomR
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white blood cells and cancer cells transport through lymphatic vessels

It is a well-known fact that both of these cells can reach the lymphatic vessels from interstitial space. How does it do so physically? Are there any mathematical models describing this process? It seems like there are endothelial cells along the…
TanMath
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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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Are neurons roughly a magnetic dipole?

I would like to make a simulation (concerning genetic evolution) and I want to use a very simplistic model of neurons. I don't really care there are different kinds of neurons, I don't care much that the extracellular field is different at…
Yann
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How many residues can a reliable ab initio structural model contain?

A recent question on ab initio that I answered involved touching on the limitations of ab initio modelling. A review from 2009 put forward that typically only in the order of 100-110 residues could be reliably modelled. 7 years after that paper: I…
James
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