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2
votes
1answer
61 views

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

Im 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, which I ...
5
votes
2answers
1k 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
16 views

Membrane-partitioning free energy [closed]

What is membrane-partitioning free energy? Can we look for difference in free energy upon partitioning in GROMACS? What are the methods I would need to use to determine the free energy of ...
1
vote
0answers
29 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) \\ ...
2
votes
1answer
24 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 ...
1
vote
2answers
52 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 ...
0
votes
1answer
33 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
49 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
69 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
85 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
89 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 ...
20
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 ...
12
votes
2answers
156 views

How can we verify predictions of protein folding in silico?

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 ...
8
votes
2answers
581 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 ...
3
votes
0answers
70 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 ...
4
votes
1answer
54 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". ...
2
votes
2answers
112 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
votes
2answers
108 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 ...
0
votes
0answers
18 views

How to get chemical structures in PDB format?

I am about to embark on the final step of a research project that involves molecular docking. Specifically, I am planning on docking an alpha(2,6)-linked sialic acid glycan to the influenza ...
-1
votes
1answer
37 views

What is some computer science technology that can help the development of biology? [closed]

What is some computer science technology that can help the development of biology(eg. artificial intelligence, resolution technology) and briefly talks about their potentials?
0
votes
1answer
58 views

Supercomputer and undergraduates [closed]

Is it common for an undergraduate to run their thesis (evolutionary genomics) in a supercomputer? In my country, few supercomputers exist, but I'm not sure how it is for bachelors in the US or Europe. ...
-1
votes
1answer
60 views

Why the name coined for MARKUP LANGUAGE for SBML? [closed]

I'm get the confusion about SYSTEM BIOLOGY filed. SBML is refer to as SYSTEM BIOLOGY MARKUP LANGUAGE why we should called as ...
2
votes
2answers
64 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?
4
votes
1answer
205 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 ...
3
votes
0answers
141 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. ...
2
votes
1answer
40 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 ...
0
votes
1answer
77 views

Hidden Markov Model

I read about the hidden markov model in bioinformatics. I amn't able to understand what it is. Can anyone explain me in brief and in very very simple words what it is ? I have NO background in ...
6
votes
1answer
245 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 ...
3
votes
0answers
65 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 ...
3
votes
1answer
276 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 ...