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GSR: Simulator - J-SPACE
| Attribute | Value |
|---|---|
| Title | J-SPACE |
| Short Description | J-SPACE: a Julia package for the simulation of spatial models of cancer evolution and of sequencing experiments |
| Long Description | 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. |
| Keywords | Cancer Evolution, Stochastic Simulation, Spatial dynamics, Next-generation sequencing |
| Version | 0.1.0 |
| Project Started | 2021 |
| Last Release | 3 years, 3 months ago |
| Homepage | https://github.com/BIMIB-DISCo/J-Space.jl |
| Citations | 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, July 8, 2022 [ Abstract, cited in PMC ] |
| GSR Certification | ✔ Accessibility |
| Last evaluated | Aug. 5, 2022 (1135 days ago) |
| Author verification | The basic description provided was derived from a website or publications by the GSR team and has not yet been verified by the simulation author. To modify this entry or add more information, propose changes to this simulator. |
| Attribute Category | Attribute |
|---|---|
| Target | |
| Type of Simulated Data | |
| Variations | |
| Simulation Method | |
| Input | |
| Data Type | |
| File format | |
| Output | |
| Data Type | Phylogenetic Tree, |
| Sequencing Reads | |
| File Format | Fasta or Fastq, SAM or BAM, Other, |
| Sample Type | |
| Phenotype | |
| Trait Type | |
| Determinants | |
| Evolutionary Features | |
| Demographic | |
| Population Size Changes | |
| Gene Flow | |
| Spatiality | |
| Life Cycle | |
| Mating System | |
| Fecundity | |
| Natural Selection | |
| Determinant | |
| Models | |
| Recombination | |
| Mutation Models | |
| Events Allowed | |
| Other | |
| Interface | |
| Development | |
| Tested Platforms | Windows, Linux and Unix, |
| Language | Other, |
| License | Other, |
| GSR Certification | Accessibility, Documentation, Support, |
Number of Primary Citations: 1
Number of Non-Primary Citations: 0
No example publication using J-SPACE has been provided.
Please propose new citations if you are aware of publications that use this software.