BYOM walkthrough

Author: Tjalling Jager
Date: November 2021
Web support: http://www.debtox.info/byom.html

Step-by-step walk through the code of the basic BYOM platform. This walk through is made with the 'publish' option in Matlab, which might also be very convenient to keep track of your work (as a modeller's log book). This walk through consists of the following files:

byom_bioconc_extra.m: a detailed example script, with a lot of text, and a lot of options shown.
byom_bioconc_start.m: a clean and quick example script (less text and less options).
derivatives.m: the actual model in the form of a system of ordinary differential equations (ODEs).
simplefun.m: the actual model in the form of a system of explicit functions (e.g., an analytical solution).
call_deri.m: calls derivatives.m or simplefun.m to calculate the model output. Here, the model output can be transformed to match the data, if needed.
byom_bioconc_parspace.m: a quick demonstration of the parameter-space explorer in BYOM for automatic optimisation and uncertainty analysis.
byom_bioconc_sim.m: a quick demonstration of the simulator. The SIMbyom package has way more details on this option.
pathdefine.m: a piece of code that searches for the engine directory, and adds it to the Matlab path. No need to make changes here, just make sure it is in every directory from which you run BYOM scripts.