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Questions tagged [computational-biology]

For questions about modeling biological problems computationally. This could include population dynamics, protein folding, compartmental models of disease spread, or other equations that arise from a biological setting.

13 questions with no upvoted or accepted answers
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7 votes
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Is a complete bacteria simulation with an exascale supercomputer possible?

Will it be possible to simulate a complete (at least simple) bacteria atom by atom on an exascale supercomputer? or is it possible already today with the largest systems? Here, I've read that ...
Open Food Broker's user avatar
6 votes
0 answers
733 views

Implementing a Hill-Type Muscle Model

I'm interested in implementing the muscle model used in Geijtenbeek and Wang et al's work. Both papers link to the paper by Geyer and Herr, which describes this model: However, the paper on this ...
Phylliida's user avatar
  • 323
2 votes
0 answers
36 views

Detecting structures (blood vessels) in MR images

What I have are 3D grayscale images of brains where dark pixels indicate blood vessels (see below, red arrows mark blood vessels). The objective is to obtain some descriptive statistics about them, ...
Felix's user avatar
  • 21
2 votes
0 answers
32 views

Identifying the time window at which a meteorological factor influences tree growth the most

This is a problem I am encountering in a research project. I have thought of a naive approach to solve it which relies on many assumptions, is not guaranteed to work, and would be tedious and ...
Lance's user avatar
  • 121
1 vote
0 answers
43 views

Advice for a topic in a seminar

I am a master student in Mathematics, and I have to prepare a seminar for a course in mathematical methods for applied sciences. I have a good background in numerical analysis for ODEs, PDEs and hence ...
andereBen's user avatar
  • 153
1 vote
0 answers
34 views

Why is scoring a separate problem even after docking is done?

With regards to protein-ligand interactions, we talk about two concepts, docking and scoring. I understand that docking means to find the best orientation of a ligand at the active site of a protein, ...
Mahathi Vempati's user avatar
1 vote
0 answers
29 views

Effective fitness formula in the Moran process on a game

I was recently reading some literature about evolutionary game theory and I got particularly interested in Moran process linked to prisoner's dilemma as a model of evolution of two sub-populations. ...
maciek's user avatar
  • 111
1 vote
0 answers
88 views

Implementing boundary condition

I'm studying the transport of species A in the blood vessels, $$\frac{\partial C}{\partial t} = D\frac{\partial ^2 C}{\partial x^2}-v\frac{\partial C}{\partial x}$$ At x=0, I want to use the ...
Natasha's user avatar
  • 421
1 vote
0 answers
463 views

Simulating a Hill-Type muscle model

I'm trying to do biologically based locomotion animation. I have a Hill-Type Muscle Model (see reference 1) that I've implemented in code. I can find the initial lengths of the tendons, then do a step ...
Phylliida's user avatar
  • 323
1 vote
0 answers
64 views

Assembled human ESTs for annotation

I am annotating protein-coding genes in a region of the human genome and am looking for a set of assembled ESTs I can use as evidence for constructing gene models. A quick search of NCBI's SRA shows 4,...
Daniel Standage's user avatar
0 votes
0 answers
43 views

Reference request: Textbook similar in structure to "Computational Materials Science: An Introduction" by June Lee for Computational Biology

In the Computational Materials Science: An Introduction by June Lee, he discusses molecular dynamics and density functional theory with examples from LAMMPS and QuantumEspresso, and explains LAMMPS ...
Josh's user avatar
  • 1
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0 answers
44 views

What is the most complete open and linked dataset to use for taxonomy?

I want to ask questions like 'what family is this species in, and which other species are in this family?'. I am aware of Wikispecies/Wikidata but are there any other good open and linked databases/...
Abbie's user avatar
  • 109
0 votes
0 answers
82 views

Nonlinear 2D modeling of Neural Electromagnetic field in Matlab

I am trying to replicate the MATLAB simulation presented in this paper. More specifically, I have to code the solution to this equation $$\frac{a}{2R_i}\frac{\partial^2 V_m}{\partial x^2} - \left[g_\...
Priyanka's user avatar