J-SPACE: a Julia package for the simulation of spatial models of cancer evolution and of sequencing experiments Long Description (required)
J-SPACE is a Julia package to simulate the spatial growth and the genomic evolution of a cell population and the experiment of sequencing the genome of the sampled cells. Firstly, the software simulates the spatial dynamics of the cells as a continuous-time multi-type birth-death stochastic process on a graph employing different rules of interaction and an optimised Gillespie algorithm. After mimicking a spatial sampling of the tumour cells, J-SPACE returns the phylogenetic tree of the sample and simulates molecular evolution of the genome under the infinite-site models or a set of different substitution models. Ther is also the possibility of include indels. Finally, employing ART, J-SPACE generates the synthetic single-end, paired-/mate-pair end reads of the next-generation sequencing platforms. Cancer Evolution, Stochastic Simulation, Spatial dynamics, Next-generation sequencing https://github.com/BIMIB-DISCo/J-Space.jl
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Summary of Proposed Changes Current Citations/Applications
[Pubmed ID: 35804300 ],
Angaroni F, Guidi A, Ascolani G, d'Onofrio A, Antoniotti M, Graudenzi A ,
J-SPACE: a Julia package for the simulation of spatial models of cancer evolution and of sequencing experiments. ,
BMC Bioinformatics ,
07-08-2022 ,
https://www.ncbi.nlm.nih.gov/pubmed/?term=35804300, Primary Citation