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FindingPheno release #59

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FindingPheno release #59

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47 changes: 37 additions & 10 deletions README.md
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Expand Up @@ -9,17 +9,14 @@ This is a **Julia** package for fractional differential equations and ODEs. It p

Related work includes the independent [FractionalDiffEq](https://github.com/SciFracX/FractionalDiffEq.jl) Julia Package that provides solutions of differential equations with different fractional operators, and earlier tools that are available in [Matlab](https://www.dm.uniba.it/members/garrappa/software).

## Publications

The package development is linked with the following publications/preprints:

- Fdesolver: A Julia package for solving fractional differential equations M Khalighi, G Benedetti, L Lahti arXiv preprint, 2022. [arXiv:2212.12550](https://arxiv.org/abs/2212.12550)

- Ebola epidemic model with dynamic population and memory, F Ndaïrou, M Khalighi, and L Lahti, Chaos, Solitons \& Fractals, 170: 113361, 2023. [doi:10.1016/j.chaos.2023.113361](https://doi.org/10.1016/j.chaos.2023.113361)

- Three-species Lotka-Volterra model with respect to Caputo and Caputo-Fabrizio fractional operators. M Khalighi, L Eftekhari, S Hosseinpour, L Lahti. Symmetry 13 (3):368, 2021. [doi:10.3390/sym13030368](https://doi.org/10.3390/sym13030368)
The implemented models are generic and broadly applicable to modeling
multivariate signals from a single source or collected across multiple
sources. The dynamical models implemented in this package were
initially developed for modeling dynamics of interacting microbial
communities (Khalighi et al. 2022) but the models are more broadly
applicable and applicable to studying multi-omic and host-microbiome
interactions.

- Quantifying the impact of ecological memory on the dynamics of interacting communities. M Khalighi, G Sommeria-Klein, D Gonze, K Faust, L Lahti. bioRxiv 2021.09.01.458486 [doi:10.1101/2021.09.01.458486](https://doi.org/10.1101/2021.09.01.458486)


## Method
Expand Down Expand Up @@ -49,3 +46,33 @@ import Pkg; Pkg.add("FdeSolver")
```

A few methods on its usage are explained in [Examples](https://juliaturkudatascience.github.io/FdeSolver.jl/stable/examples/).


## Acknowledgments

We are grateful to all [contributors](https://github.com/JuliaTurkuDataScience/FdeSolver.jl/graphs/contributors). New issues and pull requests are welcome.

This research has received funding from
* the Horizon 2020 Programme of the European Union within the [FindingPheno project](https://www.findingpheno.eu/) under grant agreement No 952914.
* Research Council of Finland (grant 330887)

## Publications

**Kindly cite this work** as follows:

- Fdesolver: A Julia package for solving fractional differential equations M Khalighi, G Benedetti, L Lahti arXiv preprint, 2022. [arXiv:2212.12550](https://arxiv.org/abs/2212.12550)


The package development is further linked with the following publications/preprints:

- Quantifying the impact of ecological memory on the dynamics of interacting communities. M Khalighi, G Sommeria-Klein, D Gonze, K Faust, L Lahti. PLoS Computational Biology 18(6), 2022 [doi:10.1371/journal.pcbi.1009396](https://doi.org/10.1371/journal.pcbi.1009396)

- Three-species Lotka-Volterra model with respect to Caputo and Caputo-Fabrizio fractional operators. M Khalighi, L Eftekhari, S Hosseinpour, L Lahti. Symmetry 13 (3):368, 2021. [doi:10.3390/sym13030368](https://doi.org/10.3390/sym13030368)

- Ebola epidemic model with dynamic population and memory, F Ndaïrou, M Khalighi, and L Lahti, Chaos, Solitons \& Fractals, 170: 113361, 2023. [doi:10.1016/j.chaos.2023.113361](https://doi.org/10.1016/j.chaos.2023.113361)






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