You can change the size of the tablefootnotes by using any font switch you find in introductory books. In the example below i used Large and made it red, just to emphasize what changes.
Code: Select all
\documentclass[11pt, a4paper, oneside, onecolumn, openany]{book}
\usepackage{etoolbox}
\usepackage{parskip}
\usepackage{showframe}
\usepackage{mwe}
\usepackage{threeparttable}
\AtBeginEnvironment{tablenotes}{\Large\color{red}}%Make the
%tablenotes red and Large. Or \footnotesize ;-)
\newcommand{\species}[1]{\textit{#1}}%Helper command, keep it
%flexible
\begin{document}
\chapter{Test Chapter}
\label{chap:testB}
Computational models are mathematical models of systems such as
are found in biology, physics, weather systems etc. Such models
can be used to predict the behaviour of these systems in an
effort to develop interventions which help to control our
environment. By predicting weather systems we can safeguard
ourselves against extreme weather conditions or plan our crops to
avoid failures. In physics, models serve the purpose of
discovering the origins of the universe and predicting what the
future might hold for us. In biology, computational models serve
to provide a better understanding of the way our bodies work as
part of our effort to fight disease and prolong
life\footnote{stuff}.
\blindtext[2]
\begin{figure}[t]
\centering
\begin{threeparttable}
\begin{tabular}{c}
\includegraphics[width=.9\linewidth]{example-image-b}
\end{tabular}
\caption{From left to right: \species{Caenorhabditis
elegans}\tnote{a}, \species{Drosophila melanogaster}\tnote{b},
\species{Saccharomyces cerevisiae}, \species{Danio rerio}.}
\label{fig:model_organismsB}
\begin{tablenotes}
\item [a] A footnote
\item [b] Another footnote
\end{tablenotes}
\end{threeparttable}
\end{figure}
\end{document}
Concerning the other boxed stuff. Can you make a minimal working example, so i can see what is going on? The code defines new floating environments for programs and directory listings. Do you need this stuff, or is it rubbish from an old template?
