https://github.com/dilawar/singhandbhalla_camkii_subunitexchange_2018

Subunit exchange enhances information retention by CaMKII in dendritic spines
https://github.com/dilawar/singhandbhalla_camkii_subunitexchange_2018

biological-memory biorxiv camkii python research-paper research-project simulation subunit-exchange tex

Last synced: about 15 hours ago
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Subunit exchange enhances information retention by CaMKII in dendritic spines

• Host: GitHub
• URL: https://github.com/dilawar/singhandbhalla_camkii_subunitexchange_2018
• Owner: dilawar
• License: mit
• Created: 2018-07-30T06:47:56.000Z (over 6 years ago)
• Default Branch: master
• Last Pushed: 2018-12-08T03:55:39.000Z (about 6 years ago)
• Last Synced: 2024-11-09T12:49:33.580Z (about 2 months ago)
• Topics: biological-memory, biorxiv, camkii, python, research-paper, research-project, simulation, subunit-exchange, tex
• Language: TeX
• Homepage: https://elifesciences.org/articles/41412
• Size: 55.8 MB
• Stars: 0
• Watchers: 1
• Forks: 2
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
# Subunit exchange enhances information retention by CaMKII in dendritic spines

This repository contains model file, instructions to generate data, and some small 

data-set used in the following paper:

[__Subunit exchange enhances information retention by CaMKII in dendritic spines__](https://elifesciences.org/articles/41412) 

published in eLife (https://elifesciences.org/articles/41412).

# The model

The model is in `Python` which requires [https://moose.ncbs.res.in](pymoose) and

other python libraries: numpy, scipy, pandas, networkx. Except of `pymoose` and

`numpy` others library are optional but they are recommended especially for

analyzing and plotting data.

The model script is available in `./model` directory. See

[./model/README.md](model/README.md) for detailed instructions before you

continue. And for a sample output run with default parameters.

# Figures in the paper

Figures in the paper are generated by using `Tex/PGF` + `gnuplot`. I don't

recommend that you try to generate figures unless you are very comfortable

with TeX. However, raw experiments generates plots using `matplotlib`; some of

them are included in each folder for verification.

## Regenerating figures

Install `gnuplot` along with `texlive-2017`. If you are lucky, following will regenerate

the figure:

    $ cd ./PaperFigures

    $ make

    

All figures will be generated in `pdf` format.

# Generating raw data used in figures

Data used in paper is stored in folders which starts with `exp_`.

See `README.md` file in each of these folders for details. In most folders, we

do not include data when it is very large. For small data-set, however, I have

included the data along with the scripts.

# Development repository

This repository is skimmed version of

https://bitbucket.org/dilawar/camkii-pp1-system where model development took

place. This repository has full history of work but very unorganized. It not a recommended

source of this model. 

![Cover page art by eLife](./41412-cover-a4.png)