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# CropMetaPop
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[[_TOC_]]
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## Presentation
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In the agricultural world where the major issue is to be able to produce steadily despite climatic, economic and environmental changes, the use of diversified agro-ecosystems (at the inner and intra-varietal level) is a major solution as they offer a better resilience when facing fluctuating environmental conditions. Among the elements that act on diversity dynamics, one can find the circulation of seeds between farmers.
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The objective of this project is to create a software allowing to simulate the evolution of a cultivated meta-population thanks to the different evolutionary forces (drift, selection, mutation, ...). The difference of this tool compared to others already existing is that we include our model in the farmer seed exchange point of view, which is modeled as a migration from a group of seeds of a population to an other.
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... | ... | @@ -11,48 +13,67 @@ In a first time, the simulations allowed to evaluate our model by comparing its |
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These first tests being comforting, the software will be used in a more intensive way in order to simulate more complex scenarios which would emphasize the role of certain parameters on cultivated diversity
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## Installation
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To install CropMetaPop,you can use the following command :
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`$ pip3 install cropmetapop`
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In order to use the command from the terminal without further commands, you might need to use sudo command (`$ sudo pip3 install cropmetapop`) to install the software.
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Please note that, if we demonstrate here how to install only **on *nix systems**, CropMetaPop can easily be installed **on Windows**. To do so, please refer to the documentation of the software.
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Please note that, if we demonstrate here how to install only \*_on nix systems_, CropMetaPop can easily be installed **on Windows**. To do so, please refer to the documentation of the software.
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## Quickstart
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To get a quick start with CropMetaPop, you can download [this example file](uploads/8f86c110408e3cdb2039e752fe759fa8/example.set), move into the directory you downloaded the file to, and run the program with :
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`$ cropmetapop example.set`
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## Documentation
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You can access the full documentation to install and use CropMetaPop by following these links, either in [HTML](uploads/7960449d87ed634a78e5f37524f8c07e/Documentation.html) or in [PDF](uploads/fc30f41c310fda71296d82bb05bfc695/Documentation.pdf).
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## Performance
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To get a glimpse at the performance of CropMetaPop, you can relate to the following table that accounts for run time and write time of the model in several situation.
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These simulations were run on a computer with an Intel i5-2400 with 8Gb of RAM.
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Simulations lasted for 30 generations, and only monolocus genotypes files were written along with seed transfer files if relevant.
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| number of replicates | number of populations | total number of loci | number of selected loci | number of alleles | colonisation + extinction | migration || Run time (s) | Write time (s) |
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| ------ | ------ | ------ | ------ | ------ | ------ | ------ | ------ | ------ |
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| 1 | 1 | 1 | 0 | 2 | No | No || 0.169 | 0.0007 |
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## Publications
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- **CropMetaPop : a population genetics program to simulate the evolution of crop metapopulations**, Mathieu Thomas, Anne Miramon, Abdel Kader Naino Jika, Baptiste Rouger, Frédéric Hospital, Camille Noûs, Isabelle Goldringer, DOI : https://doi.org/10.1101/2021.01.22.427853.
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- Click [here](uploads/43cd63fea6b86a2746e17d712320ffb7/dataCMP2021.zip) for associated data. These data are covered by the CC0 public domain licence. <img src="uploads/fb7aa1e6cf33dfaa023a4fc7705eca04/cc-zero.png" alt="drawing" width="75"/>
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To get a glimpse at the performance of CropMetaPop, you can relate to the following table that accounts for run time and write time of the model in several situation. These simulations were run on a computer with an Intel i5-2400 with 8Gb of RAM. Simulations lasted for 30 generations, and only monolocus genotypes files were written along with seed transfer files if relevant.
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| number of replicates | number of populations | total number of loci | number of selected loci | number of alleles | colonisation + extinction | migration | Run time (s) | Write time (s) |
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|----------------------|-----------------------|----------------------|-------------------------|-------------------|---------------------------|-----------|--------------|----------------|
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| 1 | 1 | 1 | 0 | 2 | No | No | 0.1690 | 0.0007 |
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| 1 | 1 | 1 | 1 | 2 | No | No | 0.5707 | 0.0007 |
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| 1 | 1 | 1 | 0 | 10 | No | No | 0.1838 | 0.0085 |
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| 1 | 1 | 1 | 1 | 10 | No | No | 21.5137 | 0.0041 |
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| 1 | 1 | 10 | 0 | 2 | No | No | 0.2527 | 0.0042 |
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| 1 | 1 | 10 | 5 | 2 | No | No | 6.2289 | 0.0042 |
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| 1 | 1 | 10 | 10 | 2 | No | No | 22.2663 | 0..0042 |
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| 1 | 10 | 1 | 0 | 2 | No | No | 1.6563 | 0.0041 |
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| 1 | 10 | 1 | 1 | 2 | No | No | 5.6159 | 0.0042 |
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| 1 | 10 | 10 | 0 | 2 | No | No | 2.4780 | 0.0466 |
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| 1 | 10 | 10 | 5 | 2 | No | No | 62.1955 | 0.0455 |
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| 10 | 10 | 10 | 5 | 2 | No | No | 6336.3737 | 0.4335 |
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| 10 | 10 | 10 | 5 | 2 | Yes | No | 561.0119 | 0.4351 |
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| 10 | 10 | 10 | 5 | 2 | No | Yes | 617.2233 | 0.4542 |
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| 10 | 10 | 10 | 5 | 2 | Yes | Yes | 554.2071 | 0.4305 |
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## Publications
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- **CropMetaPop : a population genetics program to simulate the evolution of crop metapopulations**, Mathieu Thomas, Anne Miramon, Abdel Kader Naino Jika, Baptiste Rouger, Frédéric Hospital, Camille Noûs, Isabelle Goldringer, DOI : https://doi.org/10.1101/2021.01.22.427853.
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- Click [here](uploads/43cd63fea6b86a2746e17d712320ffb7/dataCMP2021.zip) for associated data. These data are covered by the CC0 public domain licence. ![drawing](uploads/fb7aa1e6cf33dfaa023a4fc7705eca04/cc-zero.png)
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# Related softwares
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Several softwares have been developped in order to ease the use of CropMetaPop, either to create parameter files or to analyze the output data of the software.
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## CMPconfig
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This small software allows to design the main parameter file for the CropMetaPop model. It has a graphical interface that allows the user to enter values corresponding to most of the parameters available in the software. You can find it [here](https://forgemia.inra.fr/cropmetapop/cmpconfig).
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## CMPynalyser
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This is a small tool developed in Python3 that aims at analyzing the monolocus data output of CropMetaPop in order to compute a set of genetic and demographic indicators. It aims at being lightweight and fast. You can find it [here](https://forgemia.inra.fr/cropmetapop/CMPynalyser).
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## CMPanalyzeR
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This is a more complete tool than CMPynalyser that is developed in R. It aims at analyzing both monolocus and multilocus output data of CropMetaPop. It is designed to allow to compute a great number of genetic and demographic indicators. You can find it [here](https://forgemia.inra.fr/cropmetapop/cmpanalyzer)
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## CMPfitness
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This tool is designed to compute the fitnesses of the individuals in the CropMetaPop simulations. You can find it [here](https://forgemia.inra.fr/cropmetapop/cmpfitness)
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This tool is designed to compute the fitnesses of the individuals in the CropMetaPop simulations. You can find it [here](https://forgemia.inra.fr/cropmetapop/cmpfitness) |
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