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0answers
21 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
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1answer
23 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 ...
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4answers
150 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 ...
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0answers
25 views

Meta-analysis of public 16S data - help!

I am trying to start a meta-analysis for which I want to extract some 16S-based information from public databases. Moreover, I want to relate this information with any metadata found in the associated ...
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votes
1answer
239 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
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0answers
50 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} - ...
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0answers
92 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 ...
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0answers
69 views

Could anyone help me with dde23 function

I have been trying to graph these equations using dde23 but keep having a error. This is very important for my presentation so I would really appreciate any help ...
1
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1answer
120 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
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1answer
76 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 ...
0
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1answer
165 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 pqr, with topol.top taken from pdb2gmx and use it to produce pdb file, then use pdb2pqr. Which one is ...
0
votes
1answer
115 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
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1answer
94 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
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1answer
123 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 ...
7
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
52 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 ...
3
votes
1answer
155 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
154 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?
16
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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 ...