MitoNetworksGenetics

Code associated with the article "Mitochondrial Network State Scales mtDNA Genetic Dynamics". See https://doi.org/10.1534/genetics.119.302423

Installation

Clone the repository

$ git clone --recursive https://github.com/ImperialCollegeLondon/MitoNetworksGenetics.git

to make sure you get the mitonetworks repository too. Much of the python code depends on the mitonetworks package which contains a set of helper functions and classes. To install this package, perform the following commands

$ cd mitonetworks
$ python setup.py sdist
$ pip install ./dist/mitonetworks-0.0.1.tar.gz

Figures

Alternative_control_laws

• Param_sweeps : Parameter sweeps for a set of replication/degradation rate functions, Figures S4B-I

Linear_Feedback_Control

• Ablate_fusion_fission : Figure S2B
• Deterministic_phase_portrait : Figures 2A,B and Figure S2A
• Quality_control/sel_fus/Analysis: Figure 4A
• Quality_control/QC_sweep: Figure S7
• Quality_control/sel_deg/Analysis : Figure 4B
• Stochastic_analysis/delta_sweep/Post_processing/Analysis: Figure 2G
• Stochastic_analysis/Fast_turnover: Figure S5
• Stochastic_analysis/kappa_sweep/Analysis: Figure 2F
• Stochastic_analysis/mu_sweep/Analysis: Figure 2E
• Stochastic_analysis/network_and_b_sweep/Post_processing/Analysis: Figure S3B,C,D,E, Figure S4A, and Figure 2H
• Stochastic_analysis/Nominal_parametrization/Analysis : Figure 2C,D and Figure S3A
• Stochastic_analysis/xi_sweep/Analysis : Figure S3E

Moran_infinite_sites

• Exploration of the infinite sites Moran model, Figure 3.

Simple_moran

• Exploration of a biallelic Moran model, Figure S6

Simple_Network_Process

• Deterministic treatment of a simple network process, Figure S1

Proofs

The following table summarizes the locations of the Mathematica proofs in the paper. LFC = linear feedback control.

Formula	Description	Directory
	LFC, Eq.(13)	Linear_Feedback_Control/Proof_Vh
	Alternative_control_laws, Eq.(13)	Alternative_control_laws/Vh_proofs
	Alternative_control_laws, Eq.(S72)	Alternative_control_laws/Vh_proofs
	, Eq.(13)	Alternative_model_vh_proof
	Deterministic steady state of LFC	Linear_Feedback_Control/Deterministic_Steady_State