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.
41 questions
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Modeling Homeostatic Regulation with Python: How to Simulate Dynamic Systems
Hello Computational Science community,
I am working on modeling a dynamic system that involves homeostatic regulation in Python and I could use some guidance on how to implement it. Here's a brief ...
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how to overcome division by zero in the Hodgkin Huxley neuron model
I've implemented the Hodgkin Huxley model, which worked fine in my visualization, I got the spiking etc.
Then I've build a network with a few thousand neurons and experienced random NAN (not a number) ...
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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 ...
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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 ...
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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, ...
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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.
...
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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 ...
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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 ...
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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, ...
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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 ...
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SIRS Model doesn't depend on initial conditions?
So i have been working (as an undergrad, by working i mean "Redoing a few things my professor does") in a SIRS model for epidemies. SIRS stands here for:
Susceptible -> Infected -> Recovered -> ...
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Is it possible to simulate life? [closed]
Has anybody ever managed to simulate even the simplest form of life by merely simulating the interactions of the molecules of the organisms body?
What would be the theoretical minimum number of ...
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How to compute $\Delta f/ f$ in computational neuroscience? [closed]
I want to compute $\Delta f/f$ (as explained in this link, reference 1), but I am not able to do integration as I have distinct values and no function to generate the continuous time based values.
I ...
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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 ...
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How come the use of delay differential equations in model parameter estimation better than ordinary differential equations? [closed]
in systems biology why is the use of delay differential equations better than ordinary differential equations i.e. compartment models in delay modelling? is there a data independence angle in models ...
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Help with some starter metrics 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 ...
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How to make a good mesh in a biologically accurate model with very small domains
I have been trying to make a biologically accurate 2D spatial model of tissue layers, where different physiological processes happen. This includes mainly chemical reactions, diffusion and fluxes over ...
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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/...
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How to initiate spirals in this model?
I am trying to reproduce Tang & Othmer paper which is related to excitations and oscillations in G-protein model in Dictyostelium discoideum, an amoeba species. The mathematical model in the paper ...
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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_\...
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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 ...
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How can I plot the Ramachandran regions in MatLab?
I have a scatter plot where I need to shade the Ramachandran allowed regions for aminoacids. I know there is a function that plots them for you, but it is not helpful for my case since I need the ...
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Is there any numerical application whose performance heavily depends on the division operation?
I am an undergraduate student majoring in computer science.
Recently, I am interested in the division operation, which is not directly supported by some architectures. While some architectures ...
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Is it necessary to use Poisson - Boltzmann equation if I only need to build electrostatic potential from a PQR file?
A PQR file of a protein describes the positions in $x$, $y$ and $z$ and the charges of every atom in it. If you have them, you can construct the charge density $\rho(x)$ of the protein, then use it to ...
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PQR files make from pdb2pqr are different to GROMACS
I have a pdb file and I would like to make a pqr one. In GROMACS, I use editconf -mead to produce the pqr file, with topol.top taken from pdb2gmx and use it to ...
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What are the areas a student must focus before entering the computational biology research?
I am not a biologist. But highly motivated by the recent advancements and problems in modern biology. I have been shortlisted for a PhD(computational biology programme at IMSc, Madras) interview in ...
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"boundary" vs "interface"?
I am working with biofilm and there are many documents talking about boudary conditions while others talks about interface or both of boundary and interface. So, boundary and interface are the same (...
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Finding the correct Molecular Dynamics library
I just started working on some Biophysics research, and I was looking around for a good MD library to use. There is one right now at the university set up in C, with openMC parallelization, but the ...
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Calculating AIC (in R or any other statistical software)
I am trying to fit the log-log plot of the cumulative distribution of a network to one of three models: Exponential (EXP) ($P(k)\sim e^{-ak}$), Exponentially truncated power law (TRU) ($P(k)\sim k^{a-...
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Side chain rotamers sampling in protein
What is the best tool to sample rotamers in side chain amino acids in a protein? More exactly, I want to sample the different rotamers only for lysine residues while keeping backbone rigid. I've tried ...
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Are there any QM macromolecule simulation methods that can use an electron density map as input?
I am not an xray crystallographer, but from what I've heard there's often a good deal of guess work and intuition involved in the process of fitting a ball-and-stick molecular model to a crystal-...
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Symbolic solution of a system of 7 nonlinear equations
I've got a system of ordinary differential equations - 7 equations, and ~30 parameters governing their behavior as part of a mathematical model of disease transmission. I'd like to find the steady ...
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What are all of the different methods for parameterizing an amino acid (or other small molecule)?
What are all of the different ways to derive the partial charges, van der Waals interactions, bond lengths, etc. of an amino acid (in other words, all of the parameters that could be used in a ...
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Are open-source codes available to study protein folding?
I would like to test the influence of solvation parameters in implicit solvation models and wonder which codes are freely available as standalone programs for protein folding of small proteins, and ...
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Can quantum methods be applied to the protein-ligand docking problem?
In the problem of protein-ligand docking, most of the time people are happy if they can just predict the final conformation the ligand adopts into the protein's binding pocket. Most of the time one ...
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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,...
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Global optimal sequence alignment algorithms
As far as global optimal sequence alignment goes, is the Needleman-Wunsch and Hirschberg's algorithm still state of the art? Or have there been any improvements to these algorithms since they were ...
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Best practices for describing agent-based models
I work fairly heavily in mathematical biology/epidemiology, where most of the modeling/computational science work is still dominated by sets of ODEs, admittedly sometimes fairly elaborate sets of them....
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Artificial RNA 3D folding
I have a 50-base, artificially created RNA sequence and I would like to obtain its 3D structure.
What software should I use for this purpose?
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Alternative to Bron-Kerbosch algorithm for enumerating maximal cliques in inverse interval graphs
I often use inverse interval graphs to represent biologically relevant features along a genomic sequence. For example, given a (relatively) small genomic region, the graph would contain a node for ...
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Parsing protein structure data in C
My background is in genomics, but I have recently been working with problems related to protein structure. I wrote a few relevant programs in C, building my own PDB file parser from scratch in the ...
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