Questions tagged [visualization]

Questions relating to representations of biological data.

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1answer
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CRISPR/Cas9 edited E.coli on AFM?

I am doing CRISPR/Cas9 experiment on E. coli. I am introducing recombinant plasmid BPK764 (which carries Cas9 + sgRNA designed and added later in that plasmid) into compentent E.coli cells which ...
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17 views

History of plasmid maps

To create a small history of visual representations in biology, I am seeking the earliest published papers or books that have used plasmid maps as figures ; or strategies to effectively search for ...
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77 views

Automating figure-making with PyMOL

What I want to do I have a list of almost 200 PDB entries that I need to visually inspect. Luckily, the thumbnail image displayed on the PDB website (examples with RCSB or PDBe for a well-known ...
4
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1answer
62 views

Can you extract specific data from EEG

First of all, sorry if this is the wrong place to ask this question, please redirect me if it is so. I have a project in mind involving and EEG, which is the following : Using a "consumer-grade" EEG ...
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1answer
104 views

More informative phylogenetic trees

In the presentation of phylogenetic trees, the geometric shape of the trees often seems somehow arbitrary and is more driven by aesthetics than by informative reasons. But wouldn't it make sense to ...
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1answer
973 views

How to determine the height/bits in a sequence logo?

I am trying to create a sequence logo, and I am completely confused by how to determine the height/bits for each column. So, for example I understand how to create the flat sequence logo: (add up all ...
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0answers
48 views

Cytoscape export network

I'm using Cytoscape to visualise a ppi network having 2000 proteins ... I m trying to export it but the supported format are only cytoscype formats not a usable ones and for the table format the ...
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1answer
459 views

Asymmetric volcano plot

Nearly all volcano plot I've seen tend to be roughly symmetric around the y-axis, with a fairly equal number of up- and down-regulated genes. What are the potential reasons for a volcano plot that is ...
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4answers
126 views

How do I effectively visualize data showing change in a lot of samples over two time periods? [closed]

I've tallied the number of glands in a plant this year and last year. My full data set has about 20 plants in it (I've reproduced the data from 10 of the plants here). I want to show that the plants ...
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0answers
35 views

Resources for similarity between embryos

Is there a scientific paper/reputable image resource out there which I can use that the embryos of different organisms (vertebrata) are similar in their early developmental stages(without falling into ...
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1answer
105 views

Reconstruction of wildlife distribution based on poorly-sampled data [closed]

cross-posted to Signal Processing, Cross Validated, and World Building Stack Exchange Hi, I thought I'd also put this here in case there are any field biologists with ideas on the matter. Problem: ...
34
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1answer
19k views

What do you see when your eyes are closed?

If you are in pitch black and you close your eyes, you sometimes can see strange shapes of various colors. A lot of the time these shapes and colors change as you observe them. This phenomenon still ...
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3answers
667 views

Plotting metabolic networks?

I need to draw a map of the core metabolism of E.coli. Associated with each reaction in the map I have a number that indicates the flux through this reaction. I want the map to reflect these fluxes ...
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1answer
4k views

How do I read a sequence logo?

I'm looking at a paper that uses several sequence logos to illustrate the consensus sequence of certain sites. Here is the most important of the sequence logos I'm interested in: The explanations I ...
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3answers
2k views

How should I put a large phylogeny into a scientific paper?

I've been trying to put a phylogeny tree into a scientific paper. This tree includes ~220 species, which is too too large for one page for journal articles (Letter or A4 size). But in my paper it is ...
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1answer
131 views

Superposing DNA

I have a series of protein models with DNA docked. I now want to superpose the DNA on a reference DNA molecule and extract the translational distance applied and the rotation angle used. I can ...
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1answer
2k views

How do I view the simulated protein structure along with ligand in VMD?

I did a simulation of a protein-ligand complex, and it has stabilized after 5 ns. I have got the respective pdb files for every ns, but when I try to view in VMD (Visual Molecular Dynamics), I cannot ...
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3answers
4k views

3D models of adult male brain in the Blender software? Any open-sourced version for research?

I am trying to find 3D model of brains. I am particularly interested in adult-male -brains in Blender-model. I could find such 3D models of brains for sale here but because I am researching I would ...
6
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4answers
696 views

Compressing structural information in PDB files

There seems to be a lot of redundancy in PDB files. These files can of course be compressed with general-purpose compression programs like gzip, but I can't help but imagine that these tools are ...
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2answers
219 views

How to typeset gene regulatory networks

I have a relatively simply gene regulatory network I would like to visualize, complete with the common arrow and bar symbols used to show, respectively, which genes enhance or repress with other genes....