T6ssSpaceTimeRedistribution

The correpsonding repository to interface Telegraph.jl, RandomWalker.jl and T6SSModellingStochasticTimerRW.jl and call the figures found in figures 3,4 and 5 in the paper: Space and time on the membrane: a model of Type VI secretion system redistribution.

tl;dr

For those not new to Julia

add https://github.com/fieldofnodes/Telegraph.jl
add https://github.com/fieldofnodes/RandomWalker.jl
add https://github.com/fieldofnodes/T6SSModellingStochasticTimerRW.jl

are needed, as well as Pluto and PlutoUI.

Open file: src/t6ss_space_time_redistribution_figure_generation.jl and execute code.

Download (clone) the repository

For this project, download the repository

git clone git@github.com:fieldofnodes/T6ssSpaceTimeRedistribution.git

Note my preferred cloning is through an SSH connection. Feel free to do so in another way. Once the repository is downloaded, navigate to the root folder such that

~/Projects/T6ssSpaceTimeRedistribution$

in an Ubuntu machine for example. Next the download of Julia is discussed.

Getting started with Julia

Download Julia with your favourite OS at the download page for www.julialang.org.

Once downloaded and installed, open Julia in a terminal session.

1. For MAC/Windows there will be an application icon, double click and a Julia session will commence.
2. In Linux based machines, the folder for the julia tar ball will have ~/julia/bin/ and the executable ./julia and a session will open.
   1. Alternatively add it to path to access from anywhere.
3. Please read instructions online at Julia for OS specific directions.

If all goes well a Julia session should appear as

REPL

Read, evaluate, print loop (REPL) is the terminal/shell interface to use with Julia.

julia>

To add a package press the ] in the terminal

julia> ]

the terminal will automatically change to

(@v1.8) pkg> 

Note that @v1.8 will appear if you open up Julia in any directory, to convert a current directory to a project, which is reccomented to ensure package versions are consitent and installed in desired places.

If not sure which directory Julia has been opened in then

pwd()

will display the current directory. If Julia is not opened in the desired directory then get the text version of the full directory and enter

cd("path/in/quotes/to/project")

then run

pwd()

and confirm correct directory. Then press ]

julia> ]

the terminal should read

(@v1.8) pkg> 

then type

(@v1.8) pkg> activate .

this will activate the current director as a project. As T6ssSpaceTimeRedistribution already contains the Manifest.toml and Project.toml files, Julia will read it is a project and will display

 (T6ssSpaceTimeRedistribution) pkg> 

This means Julia is opened at the correct directory. Next some package need to be installed.

Paper relevant package installations

This repository depends on three unregistered packages (unregistered as they have not requiest the general register to be accepted as a registered packaged,

1. Telegraph.jl
2. RandomWalker.jl
3. T6SSModellingStochasticTimerRW.jl

Still in the terminal,

add https://github.com/fieldofnodes/Telegraph.jl
add https://github.com/fieldofnodes/RandomWalker.jl
add https://github.com/fieldofnodes/T6SSModellingStochasticTimerRW.jl

Open up a favourite code editor and run src/t6ss_space_time_redistribution_figure_generation.jl