Questions tagged [computational-biology]

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25 questions
63 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 ...
30 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 ...
71 views

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 -> ...
76 views

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 ...
729 views

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 ...
265 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 ...
38 views

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 ...
33 views

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 ...
285 views

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 ...
373 views

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 ...
74 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_\...
391 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 ...
254 views

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 ...
78 views

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 ...
398 views

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 ...
188 views

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 ...
522 views

“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 (...
135 views

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-...
253 views

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 ...
112 views

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-...
2k views

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 ...
56 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,...
166 views

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 ...