Minor formatting

Author: [email protected]

dsmts-models.tex

@@ -74,7 +74,7 @@ \subsubsection{dsmts--001--06}
 value is not determined by the model reactions but remains constant at
 its initial level. (ii) The death reaction is now:
 \[
-X \longrightarrow Sink 
+X \longrightarrow \mathtt{Sink}
 \]
 This model checks that the boundary condition attribute is
 handled correctly.
@@ -107,7 +107,7 @@ \subsubsection{dsmts--001--09}
 \addplots{dsmts-001-09}
 
 \subsubsection{dsmts--001--10}
-
+\sloppy
 Same as \verb$dsmts-001-01$, except that: (i) the \verb$Cell$
 compartment is declared to have \verb$size=1$ (ii)
 \verb$hasOnlySubstanceUnits$ is not declared to be true. Although many
@@ -194,7 +194,7 @@ \subsubsection{dsmts--001--19}
 \addplots{dsmts-001-19}
 
 
-
+\clearpage
 \subsection{dsmts--002 --- The immigration-death process}
 
 \subsubsection{dsmts--002--01}
@@ -291,6 +291,7 @@ \subsubsection{dsmts--002--10}
 
 \addplots{dsmts-002-10}
 
+\clearpage
 \subsection{dsmts--003 ---Dimerisation }
 
 \subsubsection{dsmts--003--01}
@@ -364,7 +365,7 @@ \subsubsection{dsmts--003--07}
 
 \addplots{dsmts-003-07}
 
-
+\clearpage
 \subsection{dsmts--004 --- The batch immigration-death process}
 
 \subsubsection{dsmts--004--01}

dsmts-userguide.tex

@@ -1,18 +1,15 @@
-\documentclass[12pt,a4paper]{article}
+\RequirePackage[l2tabu, orthodox]{nag}
+\documentclass[11pt,BCOR1mm,DIV18]{scrartcl}
+
 \usepackage{graphicx,url,amsmath,hyperref}
-\topmargin=-0.5in
-\oddsidemargin=0in
-\evensidemargin=0in
-\textwidth=6.5in
-\textheight=9.5in
 \newcommand{\addplots}[1]{{\par\includegraphics[width=0.5\textwidth]{#1-mean}\includegraphics[width=0.5\textwidth]{#1-sd}\par}}
 
 \title{SBML DSMTS --- User Guide}
 \author{T.~W.~Evans, C.~S.~Gillespie,  \href{http://www.staff.ncl.ac.uk/d.j.wilkinson/}{D.~J.~Wilkinson}\thanks{\texttt{[email protected]}}}
 \date{\today}
 
 \begin{document}
-\sf\maketitle
+\maketitle
 
 \section{Introduction} 
 
@@ -23,8 +20,9 @@ \section{Introduction}
 the simulation lots of times and check that the distribution of
 outcomes is correct. This can only be tested in a probabilistic way.
 The latest version of this test suite can be obtained from:
-\centerline{\url{http://dsmts.googlecode.com/}}
-
+\begin{center}
+\url{http://dsmts.googlecode.com/}
+\end{center}
 \noindent To cite the test suite:
 
 \noindent
@@ -42,7 +40,7 @@ \subsection{Aims and Scope of the Test Suite}
 function'' output is easy to map onto a regular time-grid either
 post-hoc, or during the simulation run itself. Further discussion of
 this issue can be found in Chapter~6 of
-Wilkinson~(2006)(\url{http://www.staff.ncl.ac.uk/d.j.wilkinson/smfsb/}),
+Wilkinson~(2006)\footnote{See \url{http://www.staff.ncl.ac.uk/d.j.wilkinson/smfsb/}},
 to which the reader is referred for further discussion of stochastic
 simulation generally, and the use of SBML for discrete stochastic
 models in particular.