{"id":26902309,"url":"https://github.com/ntumitolab/mitochondria-retrograde-model","last_synced_at":"2025-06-20T10:33:33.047Z","repository":{"id":37041483,"uuid":"472207357","full_name":"ntumitolab/mitochondria-retrograde-model","owner":"ntumitolab","description":"Mitochondria Retrograde (RTG) Signalling model","archived":false,"fork":false,"pushed_at":"2024-04-08T01:31:37.000Z","size":10196,"stargazers_count":2,"open_issues_count":1,"forks_count":0,"subscribers_count":1,"default_branch":"main","last_synced_at":"2024-04-08T02:43:15.223Z","etag":null,"topics":["julia","jupyter-book","mitochondria","ode-model"],"latest_commit_sha":null,"homepage":"https://ntumitolab.github.io/mitochondria-retrograde-model/","language":"Julia","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/ntumitolab.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE.md","code_of_conduct":null,"threat_model":null,"audit":null,"citation":"CITATION.bib","codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null}},"created_at":"2022-03-21T06:06:18.000Z","updated_at":"2024-04-15T05:39:45.902Z","dependencies_parsed_at":"2024-04-15T05:53:52.382Z","dependency_job_id":null,"html_url":"https://github.com/ntumitolab/mitochondria-retrograde-model","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/ntumitolab/mitochondria-retrograde-model","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ntumitolab%2Fmitochondria-retrograde-model","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ntumitolab%2Fmitochondria-retrograde-model/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ntumitolab%2Fmitochondria-retrograde-model/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ntumitolab%2Fmitochondria-retrograde-model/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/ntumitolab","download_url":"https://codeload.github.com/ntumitolab/mitochondria-retrograde-model/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ntumitolab%2Fmitochondria-retrograde-model/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":260927228,"owners_count":23083981,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["julia","jupyter-book","mitochondria","ode-model"],"created_at":"2025-04-01T09:18:41.397Z","updated_at":"2025-06-20T10:33:28.022Z","avatar_url":"https://github.com/ntumitolab.png","language":"Julia","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Mitochodria Retrograde signalling ODE model\n\n\u003e Codes, data and notebooks for the manuscript titled \"Mathematical Modeling and Analysis of Mitochondrial Retrograde Signaling Dynamics\"\n\nForked from Steven's results: \u003chttps://github.com/ntumitolab/MitoRetroDynamics\u003e\n\n![Graphical abstract](https://user-images.githubusercontent.com/29009898/130342513-081f4592-3cc6-4468-ba3b-868416f3be6b.png)\n\n## Requirements\n\n1. Jupyter lab\n2. Julia (version 1.7+)\n3. IJulia\n\n### JupyterLab installation\n\nThe simulations are executed and displayed via JupyterLab. It is an IDE for literal programming. In this project, Julia kernel is used in Jupyterlab, and extra installation is needed to use Julia with Jupyterlab.\n\n```\npip3 install jupyterlab\n```\n\nSee https://jupyterlab.readthedocs.io/en/stable/getting_started/installation.html for further instruction.\n\n### Installing Julia\n\nJulia programming language runtime can be installed in the official website (https://julialang.org/downloads/)\n\n\n### IJulia\n\nIJulia (https://julialang.github.io/IJulia.jl/stable/manual/installation/) is a Julia package for kernel installation for Jupyter.\n\nThe installation requires Julia Package manager (Pkg, https://docs.julialang.org/en/v1/stdlib/Pkg/), which is a built-in package in Julia. To install IJulia, one needs to open Julia REPL (Read–eval–print loop) using the following command line.\n\n```\njulia\n```\n![Julia REPL](https://user-images.githubusercontent.com/29009898/130343508-7d8e5e18-7ca8-46f8-b3de-3e4910c42ff3.png)\n\nThe Julia REPL begins in the terminal after submitting `julia` command. The next step is to install IJulia with package manager (Pkg). Copy-paste the following code block to Julia REPL\n\n```julia\nusing Pkg\nPkg.add(\"IJulia\")\nPkg.build(\"IJulia\")\n```\n![IJulia installation with Pkg](https://user-images.githubusercontent.com/29009898/130343609-a997c935-a209-4364-8c5c-e2e62a3e42b0.png)\n\n### Enabling a multi-threaded kernel\n\nSome notebooks use multithread algorithms to speed up. The multithread process can be set by IJulia in Julia REPL.\n\n```julia\nusing IJulia\nIJulia.installkernel(\"Julia 8 Threads\", env=Dict(\n    \"JULIA_NUM_THREADS\" =\u003e \"8\",\n))\n```\n\nwhere `JULIA_NUM_THREADS` represents number of threads that can be used in the Julia process, and this can not be changed after a Julia process is initiated. Though the number of threads is set as `8`, it can be changed and usually depends on the hardware setup.\n\n## Set up of simulation environments\n\nOpen the project folder with terminal, and then in the Julia REPL prompt\n\n```julia\nusing Pkg\nPkg.activate(\".\")\nPkg.instantiate()\n```\n\n## Run notebooks\n\nIN the Julia REPL prompt\n\n```julia\nusing IJulia\nIJulia.jupyterlab(dir=pwd())\n```\n\nSelect the kernel with the name `Julia 8 Threads` to initiate Julia with multiple threads. After successfully initiation, one can see `Julia 8 Threads 1.6` located at the top right corner.\n\n![Jupyter screen shot](https://user-images.githubusercontent.com/29009898/130344079-b98a76f1-13c5-4b8c-a195-dd6f45bd5527.png)\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fntumitolab%2Fmitochondria-retrograde-model","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fntumitolab%2Fmitochondria-retrograde-model","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fntumitolab%2Fmitochondria-retrograde-model/lists"}