https://github.com/jfdev001/plasmacelldiff

Julia implementation of "Quantitative modeling of the terminal differentiation of B cells and mechanisms of lymphomagenesis" by Martinez2012 (https://doi.org/10.1073/pnas.1113019109)
https://github.com/jfdev001/plasmacelldiff

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Julia implementation of "Quantitative modeling of the terminal differentiation of B cells and mechanisms of lymphomagenesis" by Martinez2012 (https://doi.org/10.1073/pnas.1113019109)

• Host: GitHub
• URL: https://github.com/jfdev001/plasmacelldiff
• Owner: jfdev001
• Created: 2023-09-22T15:08:58.000Z (over 1 year ago)
• Default Branch: main
• Last Pushed: 2023-12-06T11:44:59.000Z (about 1 year ago)
• Last Synced: 2024-10-28T12:07:50.028Z (2 months ago)
• Language: Julia
• Size: 8.3 MB
• Stars: 0
• Watchers: 1
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

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README

        
# PlasmaCellDiff

Codebase implementing the germinal center exit pathway kinetic model, emphasizing bifurcation analysis through simulation, as introduced by Martinez et. al. (2012). Part of the masters course Bioinformatics 1 during period 1, 2023 at the University of Amsterdam. A summary of findings is contained in `frazier_jared_bioinformatics_report.pdf`.

# Installation

The only requirement is [Julia](https://julialang.org/), preferably version 1.9. Clone the repo and start a Julia REPL in the root directory

```shell

julia --project=path/to/PlasmaCellDiff

```

press `]` to enter Pkg mode. The REPL prompt should like

```shell

(PlasmaCellDiff) pkg>

```

Then instantiate the package to download the appropriate dependencies by

```shell

(PlasmaCellDiff) pkg> instantiate

```

Should you wish to re-run the notebooks that generate the figures, hit backspace to return to the regular REPL

```shell

julia> using IJulia

julia> notebook(dir="notebooks/")

```

then you can open notebooks and run them accordingly to reproduce the figures

in the `figures/` directory.

# Germinal Center Model

Note that $bcr_0$ and $cd_0$ could either be modelled with the Gaussian PDF

defined below, or they could simply be constant parameters of the model.

$$

\begin{aligned}

\frac{dp}{dt} &= \mu_p + \sigma_p \frac{k_b^2}{k_b^2 + b^2} + \sigma_p \frac{r^2}{k_r^2 + r^2} - \lambda_p p \\\\ % BLIMP1

\frac{db}{dt} &= \mu_b + \sigma_b \frac{k_p^2}{k_p^2 + p^2}\frac{k_b^2}{k_b^2 + b^2}\frac{k_r^2}{k_r^2 + r^2} - (\lambda_b + BCR)b \\\\ % BCL6

\frac{dr}{dt} &= \mu_r + \sigma_r \frac{r^2}{k_r^2 + r^2} + CD40 - \lambda_r r\\\\ % IRF4

BCR &= bcr_0 \frac{k_b^2}{k_b^2 + b^2} \\\\ % BCR

CD40 &= cd_0 \frac{k_b^2}{k_b^2 + b^2} \\\\ % CD40

bcr_0 &= BCR_{max} \frac{1}{\sigma_{BCR}\sqrt{2\pi}}\exp[-\frac{1}{2}(\frac{t - \mu_{BCR}}{\sigma_{BCR}})^2] \\\\ % Gaussian bcr0

cd_0 &= CD40_{max}\frac{1}{\sigma_{CD40}\sqrt{2\pi}}\exp[-\frac{1}{2}(\frac{t - \mu_{CD40}}{\sigma_{CD40}})^2] % Gaussian cd0

\end{aligned}

$$

# References

M. R. Martínez et al., Proceedings of the National Academy of Sciences, vol. 109, no. 7, pp. 2672–2677, 2012. doi:10.1073/pnas.1113019109

[Good Example of  Scientific Project in Julia: HighDimensionalComplexityEntropy](https://github.com/ikottlarz/HighDimensionalComplexityEntropy)

Datseris G. and Parlitz U. Chapter 1 - 4 from "Nonlinear Dynamics: A Concise Introduction Interlaced with Code"(2022). [github](https://github.com/JuliaDynamics/NonlinearDynamicsTextbook/tree/master). note: null clines, bifurcation analysis, stability analysis, lyapunov exponents.

Numerical bifurcation diagrams and bistable systems. Lecture notes from

computational biology at École normale supérieure de Paris.

url: http://www.normalesup.org/~doulcier/teaching/modeling/ (2018)