Gene Regulatory Network Generator in Julia (JUGRNModelGenerator)

Introduction

The JUGRNModelGenerator.jl package is a code generation system that transforms simple JSON descriptions of the connectivity of gene regulatory networks into model code written in the Julia programming language. JUGRNModelGeneratorModelGenerator.jl has been used in the publications:

1. Tasseff R, Jensen H, Congleton J, Dai W, Rogers K, Sagar A, Yen A and J. Varner (2017) An Effective Model of the Retinoic Acid Induced Differentiation Program, Sci Reports, 7:14327 doi:10.1038/s41598-017-14523-5
2. Gould R, Bassen DM, Chakrabarti A, Varner JD and Butcher J (2016) Population Heterogeneity in the Epithelial to Mesenchymal Transition Is Controlled by NFAT and Phosphorylated Sp1. PLoS Comput Biol 12(12): e1005251. doi:10.1371/journal.pcbi.1005251
3. Adhikari A, Vilkhovoy M, Vadhin S, Lim HE and Varner JD (2020) Effective Biophysical Modeling of Cell Free Transcription and Translation Processes. Front. Bioeng. Biotechnol. 8:539081. doi: 10.3389/fbioe.2020.539081

to generate gene regulatory network code.

Installation and Requirements

JUGRNModelGenerator.jl is organized as a Julia package which can be installed in the package mode of Julia.

Start of the Julia REPL and enter the package mode using the ] key (to get back press the backspace or ^C keys). Then, at the prompt enter:

(v1.1) pkg> add JUGRNModelGenerator

This will install the JUGRNModelGenerator.jl package and the other required packages. JUGRNModelGenerator.jl requires Julia 1.6.x and above. JUGRNModelGenerator.jl is open source. You can download this repository as a zip file, or clone or pull it by using the command (from the command-line):

$ git pull https://github.com/varnerlab/JUGRNModelGenerator.jl.git

or

$ git clone https://github.com/varnerlab/JUGRNModelGenerator.jl.git