This repository contains the code to run the model associated with the paper titled "Timing matters in Macrophage / CD4+ T cell interactions: An agent-based model comparing Mycobacterium tuberculosis host-pathogen interactions between latently infected and naïve individuals"
This model was written using Repast Simphony (https://repast.github.io/). We have included all model files, the slurm scripts we used to run job arrays on the HPC, 2 parameter files (one for LTBI simulation and one for naive simulations). Post processing scripts and visualization codes can be found at Zenodo: .
The model runs with Repast Simphony version 2.8-2.11 and Java 11. The archived version of Repast Simphony can be downloaded at https://github.com/Repast/repast.simphony/releases. Next, follow the advice on this page https://repast.github.io/requirements.html to make sure you are using the correct Java version. Download Java 11 with hotspot from https://adoptopenjdk.net/. In Repast, select Eclipse -> Preferences -> Java -> Installed JREs -> Add…, then select adoptOpenJDK11, check, apply and close. Clone this repository, then in Repast File -> Open project from system files. The code can be run locally by using the gui that is opened with the green play button. Currently this model will produce ~500 MB files for TNF and IFN and does not output anything to AgentLocations or BacteriaLocations. The frequency of these outputs can be adjusted in the GUI.
To prepare the model, you must select 'Configure and launch batch runs' in the gui. Generate the batch parameter file and select 'Create model archive for batch runs'. This will create a jar file containing everything needed to run the model on the cluster, which is complete_model.jar in the output folder. This jar file needs to be uploaded to the cluster along with the submission script and wrapper. The slurm submission script is repast.slurm.array, which uses the wrapper repastwrapper_slurm.array.sh. Job name, array size, and account all need to be updated in these files. Unzip the jar, run 'chmod +x *.sh', and remove unrolledParamFile.txt and replace with a new parameter file (must be named unrolledParamFile.txt). Then submit the job array with 'sbatch repast.slurm.array'. After the model is finished running, navigate to the folder it was run in and run './outputcombiner.sh'. The data will be compiled in /combined_data/file-sink/.
- For Repast Testing: https://repast.github.io/docs/RepastModelTesting.pdf
- For Repast reference: https://repast.github.io/docs/RepastReference/RepastReference.html
- For Agent Based Modelling: https://www.tandfonline.com/doi/full/10.1057/jos.2016.7
- Quick Start Guide for Java: https://repast.github.io/docs/RepastJavaGettingStarted.pdf
For internal use: This model is commit (10aff55) on UpdatedLatentvsNaive branch in Repo TB-HIV-in-vitro.