From 2a452208e556207cec8fb61e5c90f50d7a7d048e Mon Sep 17 00:00:00 2001
From: "J.F.J. Laros" <j.f.j.laros@lumc.nl>
Date: Fri, 20 May 2011 17:18:26 +0000
Subject: [PATCH] Added a presentation, added acknowledgements.
git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@279 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1
---
doc/API/api.conf | 2 +-
.../Makefile | 1 +
.../allele.eps | 1 +
.../beamerthemelumc.sty | 1 +
.../gen2phen_logo.eps | 1 +
.../genes.eps | 1 +
.../lgtc_logo.eps | 1 +
.../lstBNF.tex | 1 +
.../lumc_logo.eps | 1 +
.../lumc_logo_small.eps | 1 +
.../nbic_logo.eps | 1 +
.../picture.tex | 1 +
.../presentation.tex | 524 ++++++++++++++++++
.../ul_logo.eps | 1 +
templates/about.html | 9 +
15 files changed, 546 insertions(+), 1 deletion(-)
create mode 120000 doc/Presentation_20-05-11_Utrecht_Mutalyzer2_project/Makefile
create mode 120000 doc/Presentation_20-05-11_Utrecht_Mutalyzer2_project/allele.eps
create mode 120000 doc/Presentation_20-05-11_Utrecht_Mutalyzer2_project/beamerthemelumc.sty
create mode 120000 doc/Presentation_20-05-11_Utrecht_Mutalyzer2_project/gen2phen_logo.eps
create mode 120000 doc/Presentation_20-05-11_Utrecht_Mutalyzer2_project/genes.eps
create mode 120000 doc/Presentation_20-05-11_Utrecht_Mutalyzer2_project/lgtc_logo.eps
create mode 120000 doc/Presentation_20-05-11_Utrecht_Mutalyzer2_project/lstBNF.tex
create mode 120000 doc/Presentation_20-05-11_Utrecht_Mutalyzer2_project/lumc_logo.eps
create mode 120000 doc/Presentation_20-05-11_Utrecht_Mutalyzer2_project/lumc_logo_small.eps
create mode 120000 doc/Presentation_20-05-11_Utrecht_Mutalyzer2_project/nbic_logo.eps
create mode 120000 doc/Presentation_20-05-11_Utrecht_Mutalyzer2_project/picture.tex
create mode 100644 doc/Presentation_20-05-11_Utrecht_Mutalyzer2_project/presentation.tex
create mode 120000 doc/Presentation_20-05-11_Utrecht_Mutalyzer2_project/ul_logo.eps
diff --git a/doc/API/api.conf b/doc/API/api.conf
index 3b307dd8..48ff9466 100644
--- a/doc/API/api.conf
+++ b/doc/API/api.conf
@@ -15,7 +15,7 @@ output: pdf
# target
# The path to the output directory. May be relative or absolute.
-target: api/
+target: doc/API/api
# docformat
# The default markup language for docstrings, for modules that do
diff --git a/doc/Presentation_20-05-11_Utrecht_Mutalyzer2_project/Makefile b/doc/Presentation_20-05-11_Utrecht_Mutalyzer2_project/Makefile
new file mode 120000
index 00000000..90684a51
--- /dev/null
+++ b/doc/Presentation_20-05-11_Utrecht_Mutalyzer2_project/Makefile
@@ -0,0 +1 @@
+/local/projects/presentation/trunk/Makefile
\ No newline at end of file
diff --git a/doc/Presentation_20-05-11_Utrecht_Mutalyzer2_project/allele.eps b/doc/Presentation_20-05-11_Utrecht_Mutalyzer2_project/allele.eps
new file mode 120000
index 00000000..d533e4f3
--- /dev/null
+++ b/doc/Presentation_20-05-11_Utrecht_Mutalyzer2_project/allele.eps
@@ -0,0 +1 @@
+../Presentation_05-01-10_Workdiscussion_Mutalyzer2/allele.eps
\ No newline at end of file
diff --git a/doc/Presentation_20-05-11_Utrecht_Mutalyzer2_project/beamerthemelumc.sty b/doc/Presentation_20-05-11_Utrecht_Mutalyzer2_project/beamerthemelumc.sty
new file mode 120000
index 00000000..f080c7a5
--- /dev/null
+++ b/doc/Presentation_20-05-11_Utrecht_Mutalyzer2_project/beamerthemelumc.sty
@@ -0,0 +1 @@
+/local/projects/presentation/trunk/beamerthemelumc.sty
\ No newline at end of file
diff --git a/doc/Presentation_20-05-11_Utrecht_Mutalyzer2_project/gen2phen_logo.eps b/doc/Presentation_20-05-11_Utrecht_Mutalyzer2_project/gen2phen_logo.eps
new file mode 120000
index 00000000..4d0481a6
--- /dev/null
+++ b/doc/Presentation_20-05-11_Utrecht_Mutalyzer2_project/gen2phen_logo.eps
@@ -0,0 +1 @@
+/local/projects/presentation/trunk/gen2phen_logo.eps
\ No newline at end of file
diff --git a/doc/Presentation_20-05-11_Utrecht_Mutalyzer2_project/genes.eps b/doc/Presentation_20-05-11_Utrecht_Mutalyzer2_project/genes.eps
new file mode 120000
index 00000000..eacd26db
--- /dev/null
+++ b/doc/Presentation_20-05-11_Utrecht_Mutalyzer2_project/genes.eps
@@ -0,0 +1 @@
+../Presentation_05-01-10_Workdiscussion_Mutalyzer2/genes.eps
\ No newline at end of file
diff --git a/doc/Presentation_20-05-11_Utrecht_Mutalyzer2_project/lgtc_logo.eps b/doc/Presentation_20-05-11_Utrecht_Mutalyzer2_project/lgtc_logo.eps
new file mode 120000
index 00000000..8e90373b
--- /dev/null
+++ b/doc/Presentation_20-05-11_Utrecht_Mutalyzer2_project/lgtc_logo.eps
@@ -0,0 +1 @@
+/local/projects/presentation/trunk/lgtc_logo.eps
\ No newline at end of file
diff --git a/doc/Presentation_20-05-11_Utrecht_Mutalyzer2_project/lstBNF.tex b/doc/Presentation_20-05-11_Utrecht_Mutalyzer2_project/lstBNF.tex
new file mode 120000
index 00000000..8645ea1c
--- /dev/null
+++ b/doc/Presentation_20-05-11_Utrecht_Mutalyzer2_project/lstBNF.tex
@@ -0,0 +1 @@
+../Presentation_24-02-11_HumGen_Mutalyzer2/lstBNF.tex
\ No newline at end of file
diff --git a/doc/Presentation_20-05-11_Utrecht_Mutalyzer2_project/lumc_logo.eps b/doc/Presentation_20-05-11_Utrecht_Mutalyzer2_project/lumc_logo.eps
new file mode 120000
index 00000000..e9937f89
--- /dev/null
+++ b/doc/Presentation_20-05-11_Utrecht_Mutalyzer2_project/lumc_logo.eps
@@ -0,0 +1 @@
+/local/projects/presentation/trunk/lumc_logo.eps
\ No newline at end of file
diff --git a/doc/Presentation_20-05-11_Utrecht_Mutalyzer2_project/lumc_logo_small.eps b/doc/Presentation_20-05-11_Utrecht_Mutalyzer2_project/lumc_logo_small.eps
new file mode 120000
index 00000000..290da08d
--- /dev/null
+++ b/doc/Presentation_20-05-11_Utrecht_Mutalyzer2_project/lumc_logo_small.eps
@@ -0,0 +1 @@
+/local/projects/presentation/trunk/lumc_logo_small.eps
\ No newline at end of file
diff --git a/doc/Presentation_20-05-11_Utrecht_Mutalyzer2_project/nbic_logo.eps b/doc/Presentation_20-05-11_Utrecht_Mutalyzer2_project/nbic_logo.eps
new file mode 120000
index 00000000..fcde8c20
--- /dev/null
+++ b/doc/Presentation_20-05-11_Utrecht_Mutalyzer2_project/nbic_logo.eps
@@ -0,0 +1 @@
+/local/projects/presentation/trunk/nbic_logo.eps
\ No newline at end of file
diff --git a/doc/Presentation_20-05-11_Utrecht_Mutalyzer2_project/picture.tex b/doc/Presentation_20-05-11_Utrecht_Mutalyzer2_project/picture.tex
new file mode 120000
index 00000000..eeed7e47
--- /dev/null
+++ b/doc/Presentation_20-05-11_Utrecht_Mutalyzer2_project/picture.tex
@@ -0,0 +1 @@
+../Presentation_24-02-11_HumGen_Mutalyzer2/picture.tex
\ No newline at end of file
diff --git a/doc/Presentation_20-05-11_Utrecht_Mutalyzer2_project/presentation.tex b/doc/Presentation_20-05-11_Utrecht_Mutalyzer2_project/presentation.tex
new file mode 100644
index 00000000..2907b0ed
--- /dev/null
+++ b/doc/Presentation_20-05-11_Utrecht_Mutalyzer2_project/presentation.tex
@@ -0,0 +1,524 @@
+\documentclass[slidestop]{beamer}
+
+\title{Project planning}
+\providecommand{\myConference}{NBIC BioAssist meeting}
+\providecommand{\myDate}{Friday, 20 May 2011}
+\author{Jeroen F. J. Laros}
+\providecommand{\myGroup}{Leiden Genome Technology Center}
+\providecommand{\myDepartment}{Department of Human Genetics}
+\providecommand{\myCenter}{Center for Human and Clinical Genetics}
+\providecommand{\lastCenterLogo}{
+ \raisebox{-0.1cm}{
+ \includegraphics[scale = 0.055]{lgtc_logo}
+ }
+}
+\providecommand{\lastRightLogo}{
+ \includegraphics[scale = 0.1]{nbic_logo}
+}
+
+\usetheme{lumc}
+
+\input{lstBNF.tex}
+\input{picture.tex}
+\setlength{\unitlength}{1pt}
+
+\begin{document}
+
+% This disables the \pause command, handy in the editing phase.
+%\renewcommand{\pause}{}
+
+% Make the title page.
+\bodytemplate
+
+% First page of the presentation.
+\section{Introduction}
+\begin{frame}
+ Common approaches:
+ \begin{itemize}
+ \item Just start.
+ \item Make sure the simple things work, the rest comes later.
+ \end{itemize}
+ \bigskip
+ \pause
+
+ However, it is likely that:
+ \begin{itemize}
+ \item Specific cases are solved, not parts of the problem.
+ \item Unscalable solution are made.
+ \item Unmaintainable solution are made.
+ \item Lots of time is spent on rewriting.
+ \begin{itemize}
+ \item Or worse, a stack of exceptions is made.
+ \end{itemize}
+ \item More time than needed is wasted.
+ \end{itemize}
+ \bigskip
+ \pause
+
+ Software needs to be \emph{designed}.
+\end{frame}
+
+\begin{frame}
+ Mutalyzer: a curational tool for \emph{Locus Specific Mutation Databases}
+ (LSDBs).
+
+ \bigskip
+ \begin{itemize}
+ \pause
+ \item Variant nomenclature checker applying \emph{Human Genome Variation
+ Society} (HGVS) guidelines.
+ \begin{itemize}
+ \item Is the syntax of the variant description valid?
+ \item Does the reference sequence exist?
+ \item Is the variant possible on this reference sequence?
+ \item Is this variant description the recommended one?
+ \end{itemize}
+ \pause
+ \item Basic effect prediction.
+ \begin{itemize}
+ \item Is the description of the transcript product as expected?
+ \item Is the predicted protein as expected?
+ \end{itemize}
+ \end{itemize}
+\end{frame}
+
+\section{HGVS nomenclature}
+\begin{frame}
+ \emph{Genomic} orientated positions:
+ \begin{center}
+ \bt{AL449423.14:g.[65449\_65463del;65564\color{yellow}T\color{white}>\color{yellow}C\color{white}]}
+ \end{center}
+ \pause
+ \bigskip
+ \emph{Coding sequence} orientated positions:
+ \begin{center}
+ \bt{AL449423.14(CDKN2A\_v001):c.[5\color{yellow}A\color{white}>\color{yellow}G\color{white}
+ ;106\_120del]}
+ \end{center}
+ \bigskip
+ \pause
+ \begin{itemize}
+ \item \bt{AL449423.14} -- reference sequence.
+ \item \bt{CDKN2A\_v001}$\;$ -- transcript variant \bt{1} of gene CDKN2A.
+ \item \bt{c.[5\color{yellow}A\color{white}>\color{yellow}G\color{white};106\_120del]}
+ \begin{itemize}
+ \item A \emph{substitution} at position \bt{5} counting from the start
+ codon.
+ \item A \emph{deletion} from position \bt{106} to position \bt{120}.
+ \end{itemize}
+ \end{itemize}
+\end{frame}
+
+\begin{frame}
+ \positionpicture
+
+ \renewcommand{\arraystretch}{1}
+ \begin{center}
+ \begin{tabular}{l|r|r|r}
+ Name & \bt{g.} & \bt{n.} & \bt{c.} \\
+ \hline
+ {\scriptsize Genomic start} & \bt{1} & \bt{100+d70} &
+ \bt{*10+d70} \\
+ {\scriptsize Genomic end} & \bt{300} & \bt{1-u50} &
+ \bt{-30-u50} \\
+ {\scriptsize Transcription start} & \bt{250} & \bt{1} & \bt{-30} \\
+ {\scriptsize Transcription end} & \bt{70} & \bt{100} & \bt{*10} \\
+ {\scriptsize CDS start} & \bt{220} & \bt{30} & \bt{1} \\
+ {\scriptsize CDS stop} & \bt{80} & \bt{90} & \bt{60} \\
+ \end{tabular}
+ \end{center}
+\end{frame}
+
+\begin{frame}
+ \positionpicture
+
+ \bt{c.} positions:
+ \bigskip
+ \begin{itemize}
+ \item Positions in introns are relative to the nearest exonic position.
+ \item Positions before the CDS are indicated with a \bt{-} sign.
+ \item Positions after the CDS are indicated with a \bt{*} sign.
+ \end{itemize}
+
+ \pause
+ \bigskip
+ Position \bt{-1} and \bt{1} are adjacent.
+
+ If \bt{60} is the last position of the CDS, then \bt{60} and \bt{*1} are
+ adjacent.
+\end{frame}
+
+\section{Mutalyzer 1.0.4}
+\begin{frame}
+ Organic growth:
+ \begin{itemize}
+ \item Developed in over four years by multiple people.
+ \item Originally a command line program.
+ \item Web interface added later.
+ \begin{itemize}
+ \item PHP scripts that call (exec) a python program.
+ \end{itemize}
+ \end{itemize}
+ \bigskip
+ \pause
+
+ Design flaws:
+ \begin{itemize}
+ \item Nomenclature rules interwoven with the code.
+ \item HTML output interwoven with the code.
+ \item No modularity (reuse of code is very hard).
+ \item Reference sequence parsing not abstracted
+ \begin{itemize}
+ \item Support for other reference sequences nearly impossible.
+ \end{itemize}
+ \item Nomenclature was not analysed / formalised.
+ \begin{itemize}
+ \item Regular expressions directly in code.
+ \item Virtually impossible to change (or read).
+ \end{itemize}
+ \end{itemize}
+\end{frame}
+
+\begin{frame}
+ Implementation flaws:
+ \begin{itemize}
+ \item Inheritance of types (delins on DNA $\Rightarrow$ delins on protein).
+ \item Disambiguation not general.
+ \item No support of up- / downstream exons.
+ \item Nothing was ever redesigned, only wrapped in loops.
+ \begin{itemize}
+ \item Debugging, altering code made impossible.
+ \item Speed drastically diminished.
+ \end{itemize}
+ \end{itemize}
+ \bigskip
+ \pause
+
+ Programming flaws:
+ \begin{itemize}
+ \item Excessive usage of exceptions.
+ \item Incomprehensible error messages.
+ \item Virtually no inline comment.
+ \item Non existent documentation (apart from the user manual).
+ \end{itemize}
+\end{frame}
+
+\begin{frame}
+ Feature requests:
+ \begin{itemize}
+ \item Solving all mentioned problems.
+ \item \color<2>{yellow}{Support for other reference files (LRG).}
+ \item \color<2>{yellow}{Programmatic access to internal functions.}
+ \item \color<2>{yellow}{Extension of HGVS nomenclature rules.}
+ \end{itemize}
+ \bigskip
+ \pause
+
+ Especially since:
+ \begin{itemize}
+ \item Interwoven nomenclature.
+ \item Interwoven interface.
+ \item Lack of documentation.
+ \end{itemize}
+ \bigskip
+ \pause
+
+ Throw away four years of work and start again.
+\end{frame}
+
+\section{Preparing for version 2.0}
+\begin{frame}
+ Preparations for a new version:
+ \begin{itemize}
+ \item Setting up two version control repositories.
+ \item Gathering all old versions and putting then under version control.
+ \begin{itemize}
+ \item Critical bugfixes until there is a new version.
+ \item Easy to search and track changes.
+ \item Point of reference for the new version.
+ \end{itemize}
+ \item Set up bugtracking systems.
+ \pause
+ \item Talking for months.
+ \begin{itemize}
+ \item Figuring out what the HGVS language is.
+ \item Formalising that language (BNF).
+ \item Semantic rules.
+ \end{itemize}
+ \item Identify and implement functional modules.
+ \item Designing interfaces (web (TAL), webservice, command line, \ldots).
+ \item Documentation (API (epydoc), TRM, User manual, \ldots).
+ \end{itemize}
+\end{frame}
+
+\begin{frame}
+ Although the complexity might seem low at first glance\ldots
+ \bigskip
+
+ Non-trivial problems can be found:
+ \begin{itemize}
+ \item Position systems.
+ \begin{itemize}
+ \item Reference sequence related peculiarities.
+ \end{itemize}
+ \item \only<2>{\color{yellow}}The HGVS nomenclature.\only<2>{\color{white}}
+ \item Parsing reference sequence files and their annotation.
+ \begin{itemize}
+ \item Keeping the option open for other formats (LRG).
+ \end{itemize}
+ \item Keeping track of positions after mutation.
+ \item \ldots
+ \end{itemize}
+\end{frame}
+
+\section{HGVS parser}
+\begin{frame}
+ The previous versions used \emph{regular expressions} for input parsing.
+ \begin{itemize}
+ \item The HGVS nomenclature turns out to be a \emph{context free} language.
+ \begin{itemize}
+ \item Strictly stronger than regular language.
+ \item Can not be parsed with a finite automaton.
+ \item No regular expressions.
+ \end{itemize}
+ \item The semantics of the HGVS is even more complex than the syntax.
+ \end{itemize}
+ \bigskip
+ \pause
+
+ These observations remind us of \emph{compiler construction}.
+ \begin{itemize}
+ \item We need a context free parser.
+ \item A parse tree must be generated.
+ \item And then there is the semantic checking.
+ \begin{itemize}
+ \item This should be the real focus of the project, the rest can be
+ solved with existing techniques.
+ \end{itemize}
+ \end{itemize}
+\end{frame}
+
+\begin{frame}[fragile]
+ Definition of a gene symbol.
+ \begin{lstlisting}[language = BNF, caption = {Abstract HGVS nomenclature}]
+ TransVar -> `_v' Number
+ ProtIso -> `_i' Number
+ GeneSymbol -> `(' Name (TransVar | ProtIso)? `)'
+ \end{lstlisting}
+
+ Gene name and optionally a transcript or isoform number.
+ \bigskip
+ \bigskip
+ \bigskip
+ \pause
+
+ \begin{lstlisting}[caption = {HGVS nomenclature in Python}]
+ TransVar = Suppress("_v") + Number("TransVar")
+ ProtIso = Suppress("_i") + Number("ProtIso")
+ GeneSymbol = Suppress('(') + \
+ Group(Name("GeneSymbol") + \
+ Optional(TransVar ^ ProtIso))("Gene") + \
+ Suppress(')')
+ \end{lstlisting}
+\end{frame}
+
+\begin{frame}[fragile]
+ After parsing, a nested python object (parse tree) is generated:
+ \bigskip
+ \pause
+
+ The generated object of \bt{(CDKN2A\_v001)}:
+ \begin{lstlisting}[caption = {Python object}]
+ Gene.GeneSymbol = CDKN2A
+ Gene.TransVar = 001
+ \end{lstlisting}
+ \bigskip
+ \pause
+
+ Complete BNF consists of $63$ production rules.
+ \bigskip
+ \medskip
+ \pause
+
+ \emph{
+ A formalized description of the standard human variant nomenclature will
+ improve sequence variant recognition in databases and literature.
+ }
+ \vspace{0.1cm}
+
+ \scriptsize{
+ Jeroen F. J. Laros$^1$, Andr\'e Blavier$^2$, Johan T. den Dunnen$^1$,
+ Peter E. M. Taschner$^1$
+ }
+ \vspace{0.1cm}
+
+ \tiny{
+ $^1$ Department of Human Genetics, Center for Human and Clinical Genetics,
+ Leiden University Medical Center, Leiden, Nederland
+ \vspace{-0.2cm}
+
+ $^2$ Interactive Biosoftware, Rouen, France
+ }
+\end{frame}
+
+\section{Interfaces}
+\begin{frame}
+
+ \begin{tabular}{l@{\ \ -\ \ }l}
+ Name checker & Full nomenclature / semantic check.\\
+ Syntax checker & Only nomenclature check.\\
+ Position converter & Mapping, lifting over (build / transcripts).\\
+ SNP converter & DbSNP rsId to HGVS.\\
+ Name generator & Point and click to make a description.\\
+ GenBank Uploader & Custom reference sequences.
+ \end{tabular}
+ \pause
+ \bigskip
+
+ Bulk / RPC interfaces:
+ \begin{itemize}
+ \item Upload a table (CSV, Excel, Open Office Spreadsheet):
+ \begin{itemize}
+ \item Name checker.
+ \item Name checker.
+ \item Syntax checker.
+ \item Position converter.
+ \item SNP converter.
+ \end{itemize}
+ \item Webservices (SOAP).
+ \begin{itemize}
+ \item $18$ functions available.
+ \end{itemize}
+ \end{itemize}
+\end{frame}
+
+\section{Components}
+\begin{frame}
+ \only<2->{\color{gray}}
+ \begin{tabular}{l@{\ \ -\ \ }l}
+ \color<2,3,4,5,7>{white}{Config} & Parsing config file.\\
+ \color<2,4>{white}{Crossmap} & Position conversions.\\
+ \color<2,4,7>{white}{Db} & Mapping, linking, queues, caching info.\\
+ \color<0,8>{white}{File} & CSV, Excel, OpenOffice tables.\\
+ \color<2,7>{white}{GenRecord} & Abstraction of annotated reference sequences.\\
+ \color<2,7>{white}{GBparser} & Instance of GenRecord (GenBank files).\\
+ \color<2>{white}{LRGparser} & Instance of GenRecord (LRG files).\\
+ \color<2,7>{white}{Misc} & \\
+ \color<2>{white}{Mutator} & Modify the reference sequence and annotation.\\
+ \color<2,3,4,5,6,7>{white}{Output} & Communication with the interfaces.\\
+ \color<2,3,4>{white}{Parser} & HGVS nomenclature parser.\\
+ \color<2,5,7>{white}{Retriever} & Retrieve / cache reference sequences.\\
+ \color<8>{white}{Scheduler} & Batch jobs scheduler.\\
+ \color<9>{white}{Serializers} & SOAP definitions of complex objects.
+ \end{tabular}
+ \only<2->{\color{white}}
+
+ \begin{center}
+ \only<2>{Name checker.}
+ \only<3>{Syntax checker.}
+ \only<4>{Position converter.}
+ \only<5>{SNP converter.}
+ \only<6>{Name generator.}
+ \only<7>{GenBank Uploader.}
+ \only<8>{Added when using a batch interface.}
+ \only<9>{Added when using webservices.}
+ \end{center}
+\end{frame}
+
+\section{Comparison to the old version}
+\begin{frame}
+ \begin{figure}
+ \colorbox{white} {
+ \includegraphics[scale = 0.65]{genes}
+ }
+ \caption{Runtime comparison}
+ \end{figure}
+ \vspace{-0.5cm}
+ A $229\times$ speedup was measured ($12min$ to $3s$).
+\end{frame}
+
+\begin{frame}
+ \begin{figure}
+ \colorbox{white} {
+ \includegraphics[scale = 0.65]{allele}
+ }
+ \caption{Scalability}
+ \end{figure}
+ \vspace{-0.5cm}
+ Overhead ($\pm 2.5s$): loading the reference sequence.
+\end{frame}
+
+\begin{frame}
+ Special focus on documentation.
+
+ \begin{table}
+ \begin{tabular}{l|l|l}
+ & 2.0 & 1.0.4 \\
+ \hline
+ User manual & $12$ pages & $12$ pages \\
+ TRM & $31$ pages & $-$ \\
+ API documentation & $215$ pages & $-$ \\
+ Total size & $493,\!816$ bytes & $367,\!836$ bytes \\
+ Code & $198,\!512$ bytes & $245,\!677$ bytes \\
+ Comment & $60\%$ & $33\%^*$ \\
+ Development time & $<1$ year & $>4$ years
+ \end{tabular}
+ \caption{Other characteristics.}
+ \end{table}
+
+ $^*$ Mostly discarded code.
+\end{frame}
+
+\section{Conclusions}
+\begin{frame}
+ Things to keep in mind:
+ \pause
+
+ \begin{itemize}
+ \item Do not get tempted to implement small exceptions.
+ \pause
+ \item Make a design.
+ \begin{itemize}
+ \item Requirements will change in the future.
+ \item Make your design capable to deal with these changes.
+ \end{itemize}
+ \item If requirements change, go back to your design.
+ \pause
+ \item Document everything.
+ \begin{itemize}
+ \item Especially your code.
+ \end{itemize}
+ \pause
+ \item Use a version control system.
+ \end{itemize}
+ \bigskip
+ \pause
+
+ Think before you start.
+\end{frame}
+
+\section{Questions?}
+\lastpagetemplate
+\begin{frame}
+ \begin{center}
+ Acknowledgements:
+ \bigskip
+ \bigskip
+
+ Martijn Vermaat\\
+ Gerben Stouten\\
+ Andr\'e Blavier\\
+ Gerard Schaafsma\\
+ Ivo Fokkema\\
+ Jacopo Celli\\
+ Peter Taschner\\
+ Johan den Dunnen
+ \bigskip
+ \bigskip
+ \bigskip
+
+ \bt{http://www.mutalyzer.nl/}
+ \end{center}
+\end{frame}
+
+\end{document}
diff --git a/doc/Presentation_20-05-11_Utrecht_Mutalyzer2_project/ul_logo.eps b/doc/Presentation_20-05-11_Utrecht_Mutalyzer2_project/ul_logo.eps
new file mode 120000
index 00000000..d49aa2da
--- /dev/null
+++ b/doc/Presentation_20-05-11_Utrecht_Mutalyzer2_project/ul_logo.eps
@@ -0,0 +1 @@
+/local/projects/presentation/trunk/ul_logo.eps
\ No newline at end of file
diff --git a/templates/about.html b/templates/about.html
index 4e2c70cb..185d818f 100644
--- a/templates/about.html
+++ b/templates/about.html
@@ -18,6 +18,15 @@
<li>Development of several smaller features and maintenance
programming is done by Martijn Vermaat.</li>
</ul>
+ Furthermore we would like to thank the following people for their
+ valuable work on previous versions that acted as a guideline for the
+ development of the current version:
+ <ul>
+ <li>Martin Wildeman.</li>
+ <li>Ernest van Ophuizen.</li>
+ <li>Corinne Bareil.</li>
+ <li>Gerben R. Stouten.</li>
+ </ul>
Specifications are given by Peter E. M. Taschner and Johan T. den
Dunnen.<br>
<br>
--
GitLab