Stack Exchange Network

Stack Exchange network consists of 175 Q&A communities including Stack Overflow, the largest, most trusted online community for developers to learn, share their knowledge, and build their careers.

Visit 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.

0
votes
0answers
18 views

Is there a consensus on the best Machine Learning model for Antimicrobial Resistance (AMR) prediction?

Prediction of bacterial resistance/susceptibility to antimicrobials (from genotypic data) using Machine Learning methods is a problem that has started receiving interest in recent years. The ...
4
votes
0answers
26 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 ...
0
votes
0answers
25 views

How did Smith et al 2004 deal with missing HI [Hemagglutination Inhibition assay] values and HI values <10?

In the scientific paper "Mapping the Antigenic and Genetic Evolution of Influenza Virus's" Supporting Material, Smith et al write about determining antigenic distance Dij. However, I don't understand ...
1
vote
0answers
25 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 ...
0
votes
0answers
10 views

Primer design: Calculating free energy for secondary structure

I'm attempting to automate primer design (specifically, primers for RPA, which requires longer primers [~30-35 nc] than PCR), and need to figure out how to calculate the free energy of a primer pair ...
1
vote
1answer
36 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 ...
3
votes
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 ...
0
votes
1answer
56 views

Homology modelling of protein with two identical subunits in its quaternary structure

I am using homology modelling to assign the 3D structure of Torpedo acetylcholine receptor (Unwin 2004, 2bg9 in RCSB) to human muscle nAChR. The problem is, both Torpedo receptor, and human receptor ...
5
votes
0answers
67 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 ...
0
votes
1answer
42 views

How does collaboration on reconstructing metabolic networks work?

I am a researcher in psychology and I am trying to come up with a framework/platform in which psychological phenomena can be studied from a dynamical systems / computational perspective in ...
0
votes
0answers
17 views

Looking for references on protein activity prediction

My colleagues have measured Kcat for 29 mutants of a certain enzyme and they've studied the possible impact of those mutations on the protein's physicochemical properties through computational models. ...
3
votes
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 ...
1
vote
0answers
178 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 ...
2
votes
1answer
61 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 (...
1
vote
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 / ...
2
votes
1answer
94 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
vote
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, ...
0
votes
2answers
80 views

How do you derive steady-state conditions from the open-state differential equation of ion channels?

My books describes this differential equation for the open state of an ion channel: Where $k$ are the rate constants, $k_1$ denotes a forward reaction $k_{-1}$ denotes a reverse reaction in the ...
3
votes
1answer
98 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 ...
5
votes
1answer
84 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 ...
5
votes
1answer
94 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 ...
0
votes
1answer
72 views

What is neuronal computation? [closed]

Can someone give me a good explanation of what is neuronal computation and some examples of its use in neuroscience investigation?
5
votes
1answer
216 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 ...
1
vote
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 ...
1
vote
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 ...
1
vote
1answer
154 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 ...
6
votes
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 ...
4
votes
1answer
48 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 ...
11
votes
5answers
585 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 ...
7
votes
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 ...
1
vote
0answers
93 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 ...
1
vote
1answer
411 views

Examples of biological turing machines [closed]

Are there any examples of biological Turing machines? And what can they do?
1
vote
0answers
96 views

Where to go next with clustered C elegans neuronal time series

I'm doing some independent research with the C Elegans nervous system (with the OpenWorm project) and was looking for some guidance as to where I should go next. Right now, I'm dealing with calcium ...
4
votes
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 ...
1
vote
0answers
40 views

Need to solve a “pseudo-metabolic” network for rates

following problem: I have data on a certain complex association network (from monomers 1 ... 8 to complexes of all combinations, such as, 12 ... 13 ... 18 and so on until 12345678, so that I know ...
4
votes
2answers
462 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 ...
5
votes
1answer
76 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 ...
1
vote
1answer
116 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 ...
4
votes
1answer
225 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 ...
9
votes
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 ...
1
vote
0answers
67 views

Values of Miu_max and Ks from parameter estimation?

Background I have this simple biomass growth model: $$ \mu = \mu_{max}\cdot \left(\frac{S}{K_S+S}\right) \cdot \left(\frac{1}{1+S/K_{iS}}\right) \cdot \left(\frac{K_{iP}}{K_{iP}+P}\right) \\ \frac{...
2
votes
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....
1
vote
2answers
148 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/...
0
votes
1answer
57 views

Bioinformatics - DNA binding, sequence-specific protein data

I am a computer scientist and we are working on protein function prediction algorithms. Right now, we would like to examine protein-DNA binding properties computationaly. For this, we would make use ...
2
votes
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 ...
3
votes
1answer
130 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 ...
4
votes
1answer
423 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 ...
2
votes
1answer
176 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 ...
23
votes
3answers
2k views

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 ...
16
votes
2answers
393 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 ...