The essential BYOM manual
The Build/Bring Your Own Model (BYOM) files represents a flexible platform to develop, simulate and fit models expressed as ordinary differential equations (ODEs). Make sure you are able to work with Matlab at a basic level. If your mastery of ODEs is rusty, you might want to read the refresher and make some exercises (see http://www.debtox.info/dynmodtox.html). Regularly check the BYOM web page to see if there are updates to the BYOM files or its packages.
The BYOM platform will take most of the difficult things away from you, so you can focus on modelling issues instead of programming issues. The script files in the examples directory demonstrate the use of BYOM, and can form the basis for your own experimentation. Do not modify the files in the examples directory too much; make a copy of these files into a new directory when you move to a new topic.
This manual starts with the essential things you need to know to get started with BYOM. More detailed background information, and guidance for how to start bending BYOM to your will, will be added in the future, step by step. If you are missing a certain functionality in BYOM, please let me know, and I will consider adding it in a future update.
Background knowledge. I assume you have a basic working knowledge of Matlab. That you know how to work with the editor and command window, kow how to define variables, vectors and matrices, and know how scripts and functions work. Also, it is really useful if you know how to work with the debugger. Otherwise, I suggest starting with the first two chapters of the Matlab primer from the Mathworks.
Thanks! I would like to thank the participants of the TKTD summerschool for using and commenting on BYOM, which has been a major driver to improve its functionality.
Contents of the manual:
- Getting started, installing BYOM and explainig the elements of a simple BYOM analysis.
- My first BYOM analysis, a walk through the full code of the simple example explained in the previous section.
- How to enter data sets, a more detailed guidance for entering less-straightforward data sets.
- To be written: entering parameters (ranges, log-scale, globals, priors, spline nodes).
- To be written: options for plotting data.
- To be written: sensitivity analyses and confidence intervals (profiles, Bayes, etc.).
Don't forget that all packages of BYOM have a walk through the code. You can find them on the BYOM web page. Use them to get more ideas on what BYOM can do for you.