Pinned Repositories
AntModels
Code to produce probability distributions for binary decision models, as well as stochastic simulations.
BinaryDecisionModel
Code for the time-dependent analytic solution of the mean-field binary decision model. Includes Monte Carlo verification of the solution, as well as ability to conduct model calibration via MLE.
Delayed-SSA-Models
Allows one to simulate the delayed stochastic simulation algorithm (in Julia) for the mechanistic and delayed-telegraph models of gene expression in https://www.biorxiv.org/content/10.1101/2021.06.08.447592v1.abstract.
Detailed-nRNA-Model
Stochastic simulation code for a detailed model of nascent RNA production in a cell, including delayed degradation time, gene replication, gene dosage compensation and cell division.
Ising
Here we detail the code necessary for the implementation of the analytic time-dependent solution of the mean-field Ising model. One can show using this code that the solution is correct compared to Monte-Carlo simulation, and can assess the mean-field approximation used against nearest neighbor interactions.
jamesholehouse.github.io
My personal website. Credit to LeNPaul for the Jekyll template.
OLDjamesholehouse.github.io
My personal website. Done using the Lagrange template of LeNPaul.
SSAandFSPexample
"How to" on running the SSA and FSP in Julia applied to genetic auto-regulation. Also, gives a short review of parameter inference using MLE and Bayesian methods.
Tanouchi-inference
We show using maximum likelihood inference (in Julia) that bacterial proteins are kept at an approximate homeostasis.
thermo-gene-expression
code for some figures in thermodynamics gene expression paper
jamesholehouse's Repositories
jamesholehouse/SSAandFSPexample
"How to" on running the SSA and FSP in Julia applied to genetic auto-regulation. Also, gives a short review of parameter inference using MLE and Bayesian methods.
jamesholehouse/Detailed-nRNA-Model
Stochastic simulation code for a detailed model of nascent RNA production in a cell, including delayed degradation time, gene replication, gene dosage compensation and cell division.
jamesholehouse/AntModels
Code to produce probability distributions for binary decision models, as well as stochastic simulations.
jamesholehouse/BinaryDecisionModel
Code for the time-dependent analytic solution of the mean-field binary decision model. Includes Monte Carlo verification of the solution, as well as ability to conduct model calibration via MLE.
jamesholehouse/Delayed-SSA-Models
Allows one to simulate the delayed stochastic simulation algorithm (in Julia) for the mechanistic and delayed-telegraph models of gene expression in https://www.biorxiv.org/content/10.1101/2021.06.08.447592v1.abstract.
jamesholehouse/Ising
Here we detail the code necessary for the implementation of the analytic time-dependent solution of the mean-field Ising model. One can show using this code that the solution is correct compared to Monte-Carlo simulation, and can assess the mean-field approximation used against nearest neighbor interactions.
jamesholehouse/jamesholehouse.github.io
My personal website. Credit to LeNPaul for the Jekyll template.
jamesholehouse/OLDjamesholehouse.github.io
My personal website. Done using the Lagrange template of LeNPaul.
jamesholehouse/Tanouchi-inference
We show using maximum likelihood inference (in Julia) that bacterial proteins are kept at an approximate homeostasis.
jamesholehouse/thermo-gene-expression
code for some figures in thermodynamics gene expression paper
jamesholehouse/volume-inference-take-2
Repo for the ABC inference on the gene expression models with nascent, nuclear and mature.