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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.

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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 ...
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2answers
394 views

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 ...
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5answers
590 views

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 ...
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1answer
13k views

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 ...
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2answers
2k views

What are we missing about the real workings of the evolutionary process? [closed]

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 ...
8
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1answer
363 views

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 ...
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2answers
5k views

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 ...
7
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1answer
377 views

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 ...
6
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1answer
114 views

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 ...
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1answer
50 views

Olympic's epidemiological impact on Zika?

I've seen a lot of fear mongering, misinformation and overall general panic concerning the zika virus surrounding the Rio Olympics. However, little has been said about the actual epidemiological ...
5
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1answer
220 views

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 ...
5
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1answer
77 views

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 ...
5
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1answer
90 views

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 ...
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0answers
74 views

Can cognitive functioning of the human brain change the physical state of the brain? [closed]

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 ...
5
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1answer
95 views

Success of computer simulations in biology, new discoveries [closed]

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 ...
4
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2answers
482 views

Is it possible to create a restriction map using python? [closed]

I have some fragments of DNA from single and double digests using three different restriction enzymes. I'm trying to construct a restriction map of a linear fragment of DNA. The map needs indicate the ...
4
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1answer
186 views

A good software for agent based modelling?

Hello i'm gonna start my master degree in systems biology and i'm thinking of working with agent based modelling, but i really don´t know which platform can be the best to simulate interactions ...
4
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1answer
230 views

What are some useful (starter) metrics to use on phylogenetic trees?

I'm doing a computational biology project in which I simulate evolution under different inheritance rulesets and I am generating phylogenetic trees (beautifully visualised in Python with ete3). My ...
4
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1answer
67 views

Multistability in the lactose ultization network

Reading the paper here, I'm confused about the production of figure 4d. The method of production is detailed in the supplementary information under the heading "Theoretical phase diagram". ...
4
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1answer
432 views

Forward versus backward numerical simulations in population genetics

My question is closely related to this post. There are a number of existing platforms to perform numerical individual-based simulation in populations genetics. An almost exhaustive list of such ...
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0answers
28 views

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 ...
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2answers
72 views

Simulating Drug Entry in Protein and binding?

Is there any simulation protocol or paper which can simulate the dynamics of drug entry and interaction with the target protein?
3
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2answers
47 views

Interesting examples of models [closed]

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 ...
3
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2answers
80 views

Using evolutionary algorithms in molecular biology? [closed]

I am currently an MSc student studying molecular biology (on paper I'm a chemist) and soon I have to talk to my supervisor about my future, PhD research topic. Besides molecular biology I'm also ...
3
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1answer
131 views

Hodgin-Huxley model for a single neuron

I am viewing (through edX ) an introduction course to computational neuroscience. In the second lecture, the Hodgin-Huxley model is considered. I am going over some of the questions and have ...
3
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1answer
520 views

Ventral stream pathway and architecture proposed by Poggio's group

Please can you give me a very brief explanation about all functions in the ventral stream architecture summarized in this figure: This figure is from Serre et al.'s A quantitative theory of ...
3
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1answer
99 views

Spatiotemporal patterns in neural networks

It turns out that my work in nonlinear dynamics directly maps to a close variant of the Integrate and Fire model. My model produces spatiotemporal patterns that resemble foam. I have to stress that ...
3
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1answer
171 views

Neural coupling between Pinsky-Rinzel (reduced Traub) neuron with a Wang-Buzsaki neuron?

I have read two papers related to modeling neurons. The first one is the paper by Pinsky and Rinzel and the second one by Wang and Buzsaki. The first mentioned neuron model is a excitatory neuron ...
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0answers
200 views

Human female chest model or data representation?

I am looking for professionally used representation of female chest (I know how it sounds ;). Generally - a model comprehensive enough to effectively represent human chest, with focus on breasts. ...
3
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0answers
79 views

The Operation of tuning in the S1 layer of ventral model

According to my previous question in ventral Stream pathway and architecture, I want now to get a brief example about how the S1 layer is constructed. In other words, how all the simple units are ...
2
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2answers
186 views

Can all biological processes be understood as computations and studied as such? [closed]

Can we understand a cell as an organic computational device? In that case the whole organism can be considered an ensemble of a large number of interacting computational devices? If this is the case,...
2
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2answers
140 views

Core Biological concepts explained to a Computer Scientist?

I am a computer scientist delving into Bioinformatics and I need to gain insight in biological phenomena. How would you explain three core concepts as: Evolution, Selection and Variation, to a ...
2
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1answer
62 views

Calcium concentration in activated dendritic spines?

What are the typical calcium levels reached in single postsynaptic spines following activation of NMDA receptors by an EPSP or backpropagating spike? Everyone seems to refer to that one Neuron paper (...
2
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1answer
103 views

how to solve gap reactions in genome scale metabolic reconstruction [closed]

I'm making a project about modeling of nannochloropsis metabolism. My model is in the refinement stage. However, it is not running in the FBA test. Then i found there are 87 reactions that did not run....
2
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1answer
68 views

Hodgin-Huxley model for a single neuron - continuation

As continuation to This question I have posted. Another set of questions is given for the same model : This time it is also given that for $t<0$ the membrane potential is $u_0$, and at $t=0$ it ...
2
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1answer
178 views

Has anyone modelled calcium oscillations using Matlab software? [closed]

I have been trying to model calcium oscillations using MatLab, but I cannot obtain the oscillation. I created a function where I put all the equations and used ode15s to call the function. I have ...
2
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1answer
60 views

Protein Conformation Modeling

I'm interested in learning about computational modeling in biophysics. I have heard some amount about people modeling proteins as a network of ideal springs to examine things like conformation ...
2
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1answer
97 views

Effect and functional role of voltage-gated channels on dendrites [closed]

I'd like to understand better the effect and functional role of voltage-gated channels on dendrites. What I believe to have understood: It is important that a more distal post-synaptical potential (...
1
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1answer
427 views

Examples of biological turing machines [closed]

Are there any examples of biological Turing machines? And what can they do?
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2answers
151 views

Problems in optimisation with applications to biology? [closed]

I will soon have around 8 weeks to do a research project of my choosing as I am finishing my undergrad in computer science. My experience is mostly in optimisation algorithms (mostly combinatorial/...
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1answer
117 views

Can exhaustive algorithms produce MSAs that are suitable for 3D structure modelling?

While predicting 3D structure of a protein through homology modelling, the most important step is Multiple Sequence Alignment of template sequences with the target protein whose 3D model is to be ...
1
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1answer
68 views

Number of Bacteria

I am creating a mathematical model for the growth of Synechocystis. sp PCC 6803 and Methanosarcina barkeri Fusaro in photobioreactors and anaerobic membrane bioreactors respectively. I have a couple ...
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2answers
97 views

Can two arms-racing species be stabilized?

I am trying to build an evolution simulator in which there is group A and group B, each group has 9 members each generation. Each generation, each member of group A will enter a competition (in the ...
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1answer
156 views

Phylogenetic algorithms: How to interpret multiple ML trees from the same dataset?

There's still something that confuses me about how many of these algorithms work, and how results are presented in the literature. Let's consider a Maximum Likelihood based algorithm like MrBayes or ...
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0answers
26 views

Projects in DNA Computing [closed]

I am physicist and have recently heard about DNA computing. I want to work in this area. I want your ideas on a "feasible but new project" (maximum time I can put on the project: 6 Months ), I can ...
1
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1answer
41 views

Dynamic of the number of cells over time as the embryo grows

I would like to investigate the dynamic of the number of cells over time as the embryo grows. I am interested in any multicellular animal species for which we can have some data. How does the number ...
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0answers
186 views

How to correlate survival probability to gene expression profile?

I am reading up survival analysis of cancer patients and correlating them to gene expression. I came across this tutorial. Its mostly code. So what I still have not been able to understand is how ...
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0answers
69 views

Why Differential equation is not a good way to model chemical reaction networks [closed]

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 / ...
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0answers
42 views

3D Object Modelling in the Brain

Could somebody point out the neuroscience literature dedicated to the modelling of 3D objects in the human mind? I'm interested in the brain regions, and particularly the details of the circuitry, ...
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0answers
94 views

How can I perform a 1:1 sequence-structure alignment for a pdb template dimer and homologous dimer sequence?

I have: 1. A PDB dimer protein structure template of a real solved protein. 2. An unsolved, but highly homologous dimer protein (>90% sequence identity.) How can I use MODELLER to make a theoretical ...