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2
votes
0answers
24 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 ...
3
votes
1answer
67 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 -> ...
-1
votes
1answer
71 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 ...
1
vote
0answers
532 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 ...
1
vote
0answers
169 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 ...
1
vote
0answers
35 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 ...
1
vote
1answer
32 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 ...
11
votes
4answers
266 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 ...
-1
votes
1answer
339 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 ...
1
vote
0answers
69 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_\...
5
votes
0answers
308 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 ...
1
vote
1answer
228 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 ...
3
votes
1answer
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 ...
1
vote
1answer
345 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 ...
0
votes
1answer
185 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 ...
1
vote
1answer
446 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 (...
1
vote
1answer
132 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-...
8
votes
4answers
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 ...
1
vote
0answers
54 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,...
3
votes
1answer
161 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 ...
3
votes
1answer
159 views

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?
17
votes
8answers
2k views

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 ...