Commit b36ccda6 authored by Jeroen F.J. Laros's avatar Jeroen F.J. Laros

Added lecture.

parent bdf85b3b
\documentclass[slidestop]{beamer}
\author{Jeroen F.J. Laros}
\title{The Journal of Open Source Software}
\providecommand{\mySubTitle}{}
\providecommand{\myConference}{Developers workdiscussion}
\providecommand{\myDate}{10-12-2018}
\providecommand{\myGroup}{}
\providecommand{\myDepartment}{Department of Human Genetics}
\providecommand{\myCenter}{Center for Human and Clinical Genetics}
\usetheme{lumc}
\begin{document}
% This disables the \pause command, handy in the editing phase.
%\renewcommand{\pause}{}
% Make the title slide.
\makeTitleSlide{\includegraphics[height=2.5cm]{joss_logo}}
% First page of the presentation.
\section{Introduction}
\makeTableOfContents
\section{Background}
\subsection{Binary file parsing}
\begin{pframe}
\begin{figure}[]
\begin{center}
\includegraphics[height=0.7\textheight]{fam_re}
\end{center}
\caption{A Cyrillic FAM file.}
\end{figure}
\end{pframe}
\begin{pframe}
\begin{figure}[]
\begin{center}
\includegraphics[height=0.3\textheight]{bin_parser_hld}
\end{center}
\caption{High level design of a general binary parser.}
\end{figure}
Specification separate from implementation.
\begin{itemize}
\item Specification of the basic types.
\item Specification of the global file structure.
\end{itemize}
\end{pframe}
\begin{pframe}
Structure: $259$ lines, types: $183$ lines.
\begin{lstlisting}[language=none, caption={Structure snippet.}]
- name: members
for: number_of_members
structure:
- name: surname
- name: forenames
- name: address
type: comment
- name: spouses
for: number_of_spouses
structure:
- name: id
type: int
- name: flags
type: relationship
- name: name
\end{lstlisting}
\end{pframe}
\begin{pframe}
Resulting output in YAML format.
\begin{lstlisting}[language=none, caption={Output snippet.}]
members:
- surname: 'Gambolputty'
forenames: 'Johann'
address: 'Ulm'
spouses:
- flags:
consanguineous: false
divorced: false
informal: false
separated: false
id: 2
name: ''
\end{lstlisting}
\end{pframe}
\subsection{Documentation}
\begin{pframe}
For larger projects, documentation hosting is highly advised.
\begin{itemize}
\item ReadTheDocs.
\end{itemize}
\bigskip
Improve visibility on GitHub:
\begin{itemize}
\item Fill in the \emph{project description} field.
\item Add \emph{topics} (tags).
\item Check the \emph{community profile} page.
\end{itemize}
\bigskip
\vfill
\permfoot{\url{https://bin-parser.readthedocs.io}}
\permfoot{\url{https://github.com/jfjlaros/bin-parser/community}}
\end{pframe}
\section{Journal of Open Source Software}
\subsection{What is JOSS?}
\begin{pframe}
\textit{The Journal of Open Source Software (JOSS) is a developer friendly
journal for research software packages.}
\bigskip
JOSS is:
\begin{itemize}
\item An academic journal (ISSN 2475-9066),
\item with a formal peer review process,
\item designed to \emph{improve the quality of the software submitted}.
\end{itemize}
\bigskip
\textit{We built this journal because we believe that after you've done the
hard work of writing great software, it shouldn't take weeks and months to
write a paper about your work.}
\end{pframe}
\section{Preparation}
\subsection{Prerequisites}
\begin{pframe}
What to do before submission:
\begin{itemize}
\item Software needs to be available in an open repository.
\item Needs to include an OSI approved Open Source license.
\item Author a short Markdown paper.
\begin{itemize}
\item Somewhere between $250$ and $1000$ words. % Mine was 251 words.
\end{itemize}
\end{itemize}
\vfill
\permfoot{\url{https://joss.readthedocs.io/en/latest/submitting.html}}
\end{pframe}
\subsection{Software requirements}
\begin{pframe}
Rules for software.
\begin{itemize}
\item The software should be Open Source.
\item The software should have an obvious research application.
\item You should be a major contributor to the software.
\item The software should be a significant contribution to the available
open source software.
\begin{itemize}
\item Enables some new research challenges to be addressed.
\item Makes addressing research challenges significantly better.
\item No minor ``utility'' packages e.g., ``thin'' API clients.
\end{itemize}
\item The software should be feature complete and designed for maintainable
extension.
\end{itemize}
\end{pframe}
\begin{pframe}
In addition, the software associated with your submission must:
\begin{itemize}
\item Be stored in a repository that can be cloned without registration.
\item Be stored in a repository that is browsable online without registration.
\item Have an issue tracker that is readable without registration.
\item Permit individuals to create issues/file tickets against your repository.
\end{itemize}
\end{pframe}
\section{The manuscript}
\subsection{Manuscript requirements}
\begin{pframe}
Paper should contain:
\begin{itemize}
\item A list of the authors of the software and their affiliations.
\item A summary describing the high-level functionality and purpose of the
software for a diverse, non-specialist audience.
\item A clear statement of need that illustrates the purpose of the software.
\item A list of key references including a link to the software archive.
\item Mentions (if applicable) of any ongoing research projects using the
software or recent scholarly publications enabled by it.
\end{itemize}
\end{pframe}
\begin{pframe}
\begin{lstlisting}[language=none, caption={Paper metadata.}]
title: General binary file parser.
tags:
- binary
- parser
- yaml
- json
- read write
authors:
- name: Jeroen F.J. Laros
orchid: 0000-0002-8715-7371
affiliation: 1
affiliations:
- name: Leiden University Medical Center,
index: 1
date: 5 June 2018
bibliography: paper.bib
\end{lstlisting}
\end{pframe}
\section{Submission}
\subsection{Submission process}
\begin{pframe}
You need an \emph{ORCID} account to submit a paper.
\begin{itemize}
\item One or more JOSS reviewers are assigned.
\item The Review is carried out in the ``reviews'' repository.
\item Authors respond to reviewer-raised issues on the submitted
repository’s issue tracker.
\begin{itemize}
\item Reviewers contributions must be acknowledged.
\end{itemize}
\item Deposit a copy of the repository with a data-archiving service such
as Zenodo or Figshare, issue a DOI for the archive.
\item After assignment of a DOI, your paper metadata is deposited in
CrossRef and listed on the JOSS website.
\end{itemize}
\vfill
\permfoot{\url{https://orcid.org/}}
\end{pframe}
\subsection{Example}
\begin{pframe}
Review of the binary parser package.
\vfill
\permfoot{\url{https://github.com/openjournals/joss-reviews/issues/766}}
\end{pframe}
\section{Result}
\begin{pframe}
\vspace{-1cm}
\begin{figure}[]
\begin{center}
\includegraphics[height=\textheight]{paper}
\end{center}
\end{figure}
\end{pframe}
% Make the acknowledgements slide.
\makeAcknowledgementsSlide{
\begin{tabular}{l}
Matthew Fernandez (reviewer) \\
Robert Haines (reviewer) \\
Daniel S. Katz (editor)
\end{tabular}
}
\end{document}
../../submodules/presentation/Makefile
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../../submodules/presentation/beamerthemelumc.sty
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../../submodules/presentation-pics/pics/bin_parser_hld.dia
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../../submodules/presentation-pics/pics/fam_re.ps
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../../submodules/presentation-pics/pics/joss_logo.jpg
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../../submodules/presentation/logos
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This diff is collapsed.
Subproject commit 0fdfa62033731733222d41c46513cfaa74e0aa88
Subproject commit 88b5a81641e02819df8c34d6332559c373902b8b
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