Publication

This software accompanies the publication From affinity selection to kinetic selection in germinal center modeling

^{Danial Lashgari1, Elena Merino Tjiero1, Michael Meyer-Hermann2,3, Marit J. van Gils 4, Huub Hoefsloot5#, Antoine H.C. van Kampen1,5,#*}

^{1 Bioinformatics Laboratory, Epidemiology and Data Science, Amsterdam Public Health research institute, Amsterdam Institute for Infection and Immunity, Amsterdam, the Netherlands. 2 Department for Systems Immunology and Braunschweig Integrated Centre of Systems Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany. 3 Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Braunschweig, Germany. 4 Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam, Academic Medical Center, University of Amsterdam, the Netherlands 5 Biosystems Data Analysis, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, the Netherlands.}

^{#Contributed equally
*Corresponding author:
Antoine H.C. van Kampen
Bioinformatics Laboratory
Epidemiology & Data Science
Amsterdam University Medical Centers
Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands
a.h.vankampen@amsterdamumc.nl (AvK)
tel. +31-20-5667096}

Software

This repository includes codes and nesseccary files for runing simulatios. The Agent-based model is based on [Meyer-Hermann et al., 2012] and [Robert et al., 2017].

Different scenarios can be modelled by codes provided in different folders: SC0: The Reference Scenario in the manuscript SC1: Scenario-1 in the manuscript SC2: SCenario-2 in the manuscript

All software is written in C++. All the parameters used are borrowed from the original model [Meyer-Hermann et al., 2012] except parameter $\theta$ that is explained in the manuscript. To change the parameters, use parameters.cpp

Run simulations

Run simulations Unix-based systems using following steps qmake KONKOFF.pro make run ./KONKOFF

Options

-s ^{"random seed": The default random seed is 1, when running simulations in parallel, this option can be used to assign random seeds for each run.}
-o ^{"Path of output folder": Specifies where the output files will be stored.}

References

• Meyer-Hermann, M., et al. (2012). "A theory of germinal center B cell selection, division, and exit." Cell Rep 2(1): 162-174.
• Robert, P. A., et al. (2017). "How to Simulate a Germinal Center." Methods Mol Biol 1623: 303-334.