README

This repository contains code and datasets from Kim Lab project to establish an agent-based mitochondria mutation dynamics model. The main assumption is that mitochondria genomes undergo multi-scale replication/hybridization dynamics. The scales are:

1. Replication of individual genomes organized into multiple nucleodes in a single organelle
2. Replication or fusion of individual mitochondria carrying multiple genomes
3. Replication of cells and division of mitochondria into daughter cells
4. Replication of the whole animal through the germline cells

We note that the codes are WORK-IN-PROGRESS and do not represent completed simulation platform.

Code Base

We have established three sets of codes

1. Original code written in Rust (RUST_mito folder)
2. Refactored code translated into python for CPUs (PythonCPU_mito folder)
3. Refactored code from python for GPUs (PythonGPU_mito folder) The code folders also contain starting mitochondrial genome in FASTA format (hg38.mito folder) derived from human genome annotation version 38, as well as parameter initiation file (param.ini)

Additional Data Tables (data_table folder)

We also include a table of key human genes involved in regulating mitochondrial replication (mtdna_gene_table.docx) and a list of human SNPs that are within the genes or gene regions of the mitochondrial replication genes (mtdna_snp_table.xlsx)d