diff options
Diffstat (limited to 'tex/src')
| -rw-r--r-- | tex/src/figure-data-lineage.tex | 236 | ||||
| -rw-r--r-- | tex/src/figure-project-outline.tex | 229 | ||||
| -rw-r--r-- | tex/src/preamble-biblatex.tex | 9 | ||||
| -rw-r--r-- | tex/src/preamble-header.tex | 89 | ||||
| -rw-r--r-- | tex/src/preamble-necessary.tex | 90 | ||||
| -rw-r--r-- | tex/src/preamble-pgfplots.tex | 72 | ||||
| -rw-r--r-- | tex/src/preamble-style.tex | 257 | ||||
| -rw-r--r-- | tex/src/references.tex | 1530 |
8 files changed, 2157 insertions, 355 deletions
diff --git a/tex/src/figure-data-lineage.tex b/tex/src/figure-data-lineage.tex new file mode 100644 index 0000000..d849e8c --- /dev/null +++ b/tex/src/figure-data-lineage.tex @@ -0,0 +1,236 @@ +\newcommand{\paperpdf}{} +\newcommand{\papertex}{} +\newcommand{\projecttex}{} +\newcommand{\verifytex}{} +\newcommand{\initializetex}{} +\newcommand{\downloadtex}{} +\newcommand{\inputtwo}{} +\newcommand{\inputsconf}{} +\newcommand{\analysisonetex}{} +\newcommand{\outoneb}{} +\newcommand{\outonebdep}{} +\newcommand{\inputone}{} +\newcommand{\inputonedep}{} +\newcommand{\analysistwotex}{} +\newcommand{\outtwob}{} +\newcommand{\outtwobdep}{} +\newcommand{\analysisthreetex}{} +\newcommand{\analysisthreeouts}{} +\newcommand{\outtwoa}{} +\newcommand{\outtwoadep}{} +\newcommand{\outthreeadep}{} + + + + + +\begin{tikzpicture}[ + line width=1.5pt, + black!50, + text=black, +] + + %% Use small fonts + \footnotesize + + %% These white lines are only added to fix the vertical position of + %% the figure so it doesn't change as we add more boxes. + \draw [white] (-7.5,0) -- (7.4,0); + \draw [white] (0,-4.7) -- (0,5.7); + + %% top-make.mk + \node [at={(-0.05cm,2mm)}, + rectangle, + very thick, + text centered, + font=\ttfamily, + text width=2.8cm, + minimum height=7.8cm, + draw=green!50!black!50, + minimum width=\linewidth, + fill=black!10!green!2!white, + label={[shift={(0,-5mm)}]\texttt{top-make.mk}}] {}; + + %% Work-horse Makefiles. -5.6 -> -5.73 = -0.13 + \node (initializemk) [node-makefile, at={(-5.73cm,-1.3cm)}, + label={[shift={(0,-5mm)}]\texttt{initialize.mk}}] {}; + \node (downloadmk) [node-makefile, at={(-2.93cm,-1.3cm)}, + label={[shift={(0,-5mm)}]\texttt{download.mk}}] {}; + \node (analysis1mk) [node-makefile, at={(-0.13cm,-1.3cm)}, + label={[shift={(0,-5mm)}]\texttt{analysis1.mk}}] {}; + \node (analysis2mk) [node-makefile, at={(2.67cm,-1.3cm)}, + label={[shift={(0,-5mm)}]\texttt{analysis2.mk}}] {}; + \node (analysis2mk) [node-makefile, at={(5.47cm,-1.3cm)}, + label={[shift={(0,-5mm)}]\texttt{analysis3.mk}}] {}; + + %% verify.mk + \node [at={(-5.3cm,-2.8cm)}, + thick, + rectangle, + text centered, + font=\ttfamily, + text width=2.45cm, + minimum width=3.5cm, + minimum height=1.3cm, + draw=green!50!black!50, + fill=black!10!green!12!white, + label={[shift={(1cm,-5mm)}]\texttt{verify.mk}}] {}; + + %% Paper.mk + \node [at={(2.67cm,-2.8cm)}, + thick, + rectangle, + text centered, + text width=2.8cm, + minimum width=8.5cm, + minimum height=1.3cm, + draw=green!50!black!50, + fill=black!10!green!12!white, + font=\ttfamily, + label={[shift={(0,-5mm)}]\texttt{paper.mk}}] {}; + + %% paper.pdf + \ifdefined\paperpdf + \node (paperpdf) [node-terminal, at={(5.47cm,-2.9cm)}] {paper.pdf}; + \fi + + %% paper.tex + \ifdefined\papertex + \node (papertex) [node-nonterminal, at={(5.47cm,-4.2cm)}] {paper.tex}; + \draw [->] (papertex) -- (paperpdf); + \fi + + %% project.tex + \ifdefined\projecttex + \node (projecttex) [node-terminal, at={(-0.13cm,-2.9cm)}] {project.tex}; + \draw [->] (projecttex) -- (paperpdf); + \fi + + %% verify.tex + \ifdefined\verifytex + \node (verifytex) [node-terminal, at={(-5.73cm,-2.9cm)}] {verify.tex}; + \draw [->] (verifytex) -- (projecttex); + \fi + + %% Initialize.tex + \ifdefined\initializetex + \node (initializetex) [node-terminal, at={(-5.73cm,-0.8cm)}] {initialize.tex}; + \node (initialize-south) [node-point, at={(-5.73cm,-1.5cm)}] {}; + \draw [->] (initializetex) -- (verifytex); + \node [anchor=west, at={(-7.05cm,2.30cm)}] {Basic project info}; + \node [anchor=west, at={(-7.05cm,1.95cm)}] {(e.g., Git commit).}; + \node [anchor=west, at={(-7.05cm,1.10cm)}] {Also defines}; + \node [anchor=west, at={(-7.05cm,0.75cm)}] {project structure}; + \node [anchor=west, at={(-7.05cm,0.40cm)}] {(for \texttt{*.mk} files).}; + \fi + + %% download.tex + \ifdefined\downloadtex + \node (downloadtex) [node-terminal, at={(-2.93cm,-0.8cm)}] {download.tex}; + \draw [rounded corners, -] (downloadtex) |- (initialize-south); + \fi + + %% input-2.dat + \ifdefined\inputtwo + \node (input2) [node-terminal, at={(-2.93cm,1.1cm)}] {input2.dat}; + \draw [->] (input2) -- (downloadtex); + \fi + + %% INPUTS.conf + \ifdefined\inputsconf + \node (INPUTS) [node-nonterminal, at={(-2.93cm,4.6cm)}] {INPUTS.conf}; + \node (input2-west) [node-point, at={(-4.33cm,1.1cm)}] {}; + \draw [->,rounded corners] (INPUTS.west) -| (input2-west) |- (input2); + \fi + + %% analysis1.tex + \ifdefined\analysisonetex + \node (a1tex) [node-terminal, at={(-0.13cm,-0.8cm)}] {analysis1.tex}; + \draw [rounded corners, -] (a1tex) |- (initialize-south); + \fi + + %% out1b.dat + \ifdefined\outoneb + \node (out1b) [node-terminal, at={(-0.13cm,1.1cm)}] {out-1b.dat}; + \draw [->] (out1b) -- (a1tex); + \fi + + %% outonebdep + \ifdefined\outonebdep + \node (out1b-west) [node-point, at={(-1.53cm,1.1cm)}] {}; + \node (out1a) [node-terminal, at={(-0.13cm,2.7cm)}] {out-1a.dat}; + \node (a1conf1) [node-nonterminal, at={(-0.13cm,4.6cm)}] {param-1.conf}; + \draw [->] (input2) -- (out1b); + \draw [->] (out1a) -- (out1b); + \draw [->,rounded corners] (a1conf1.west) -| (out1b-west) |- (out1b); + \fi + + %% input1.dat + \ifdefined\inputone + \node (input1) [node-terminal, at={(-2.93cm,1.9cm)}] {input1.dat}; + \draw [->,rounded corners,] (input1.north) |- (out1a); + \fi + + %% input1 dependencies + \ifdefined\inputonedep + \node (input1-east) [node-point, at={(-1.53cm,1.9cm)}] {}; + \node (input1-west) [node-point, at={(-4.33cm,1.9cm)}] {}; + \draw [->,rounded corners] (INPUTS.west) -| (input1-west) |- (input1); + \fi + + %% analysis2.tex + \ifdefined\analysistwotex + \node (a2tex) [node-terminal, at={(2.67cm,-0.8cm)}] {analysis2.tex}; + \draw [rounded corners, -] (a2tex) |- (initialize-south); + \fi + + %% out-2b.dat + \ifdefined\outtwob + \node (out2b) [node-terminal, at={(2.67cm,0.3cm)}] {out-2b.dat}; + \draw [->] (out2b) -- (a2tex); + \fi + + %% out-2b dependencies + \ifdefined\outtwobdep + \draw [->,rounded corners,] (out1b.south) |- (out2b); + \fi + + %% analysis3.tex + \ifdefined\analysisthreetex + \node (a3tex) [node-terminal, at={(5.47cm,-0.8cm)}] {analysis3.tex}; + \draw [rounded corners, -] (a3tex) |- (initialize-south); + \fi + + %% Outputs of analysis3 + \ifdefined\analysisthreeouts + \node (out3a) [node-terminal, at={(5.47cm,2.7cm)}] {out-3a.dat}; + \node (out3b) [node-terminal, at={(5.47cm,1.1cm)}] {out-3b.dat}; + \node (a3tex-east) [node-point, at={(6.87cm,-0.8cm)}] {}; + \draw [->,rounded corners] (out3a.east) -| (a3tex-east) |- (a3tex); + \draw [->] (out3b) -- (a3tex); + \fi + + %% out-2a.dat + \ifdefined\outtwoa + \node (out2a) [node-terminal, at={(2.67cm,1.9cm)}] {out-2a.dat}; + \draw [->, rounded corners] (out2a.south) |- (out3b); + \fi + + %% Dependencies of out-2a + \ifdefined\outtwoadep + \node (a2conf1) [node-nonterminal, at={(2.67cm,5.3cm)}] {param-2a.conf}; + \node (a2conf2) [node-nonterminal, at={(2.67cm,4.6cm)}] {param-2b.conf}; + \node (out2a-west) [node-point, at={(1.27cm,1.9cm)}] {}; + \draw [->,rounded corners] (a2conf1.west) -| (out2a-west) |- (out2a); + \draw [->,rounded corners] (a2conf2.west) -| (out2a-west) |- (out2a); + \draw [->] (input1) -- (out2a); + \fi + + %% Dependencies of out-3a + \ifdefined\outthreeadep + \node (out3a-west) [node-point, at={(4.07cm,2.7cm)}] {}; + \node (a3conf1) [node-nonterminal, at={(5.47cm,4.6cm)}] {param-3.conf}; + \draw [->] (out1a) -- (out3a); + \draw [rounded corners] (a3conf1.west) -| (out3a-west) |- (out3a); + \fi +\end{tikzpicture} diff --git a/tex/src/figure-project-outline.tex b/tex/src/figure-project-outline.tex new file mode 100644 index 0000000..4cd933d --- /dev/null +++ b/tex/src/figure-project-outline.tex @@ -0,0 +1,229 @@ +% Copyright (C) 2018-2019 Mohammad Akhlaghi <mohammad@akhlaghi.org> +% +% This LaTeX source is free software: you can redistribute it and/or +% modify it under the terms of the GNU General Public License as +% published by the Free Software Foundation, either version 3 of the +% License, or (at your option) any later version. +% +% This LaTeX source is distributed in the hope that it will be useful, +% but WITHOUT ANY WARRANTY; without even the implied warranty of +% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU +% General Public License for more details. +% +% You should have received a copy of the GNU General Public License +% along with this LaTeX source. If not, see <https://www.gnu.org/licenses/>. + +%% Environment variables. +\newcommand{\allopacity}{1} +\newcommand{\sver}{} +\newcommand{\srep}{} +\newcommand{\dver}{} +\newcommand{\ddver}{} +\newcommand{\confopt}{} +\newcommand{\confenv}{} +\newcommand{\containers}{} +\newcommand{\db}{} +\newcommand{\calib}{} +\newcommand{\corr}{} +\newcommand{\runord}{} +\newcommand{\runopt}{} +\newcommand{\humanerr}{} +\newcommand{\confirmbias}{} +\newcommand{\depupdate}{} +\newcommand{\coauth}{} +\newcommand{\varsinpaper}{} +\newcommand{\recordinfo}{} +\newcommand{\softcite}{} +\newcommand{\prevchange}{} + +\begin{tikzpicture}[>=stealth, thick, black!50, text=black, + every new ->/.style={shorten >=1pt}, + hv path/.style={to path={-| (\tikztotarget)}}, + graphs/every graph/.style={edges=rounded corners}] + + \footnotesize + + %% This white line is only added to fix the vertical position of the + %% figure so it doesn't change as we add more boxes. + \draw [white] (0,-4.3) -- (0,3.8); + \draw [white] (-0.5,0) -- (12,0); + + %% Box showing containers. + \ifdefined\containers + \filldraw[orange!20!white, rounded corners=2mm] (-0.1,0.3) rectangle (5.6,3.8); + \draw (-0.1,3.65) node [anchor=west] {\scriptsize Existing solutions:}; + \draw (0,3.35) node [anchor=west] {\scriptsize Virtual machines}; + \draw (0,3.05) node [anchor=west] {\scriptsize Containers}; + \draw (0,2.75) node [anchor=west] {\scriptsize Package managers}; + \fi + + \graph[grow right sep, simple] { + { [nodes={yshift=7mm}] + soft/Software [gbox] -> build/Build [bbox], + hard/Hardware/data [gbox, yshift=-0.5cm] -- + p1 [coordinate, xshift=2cm, yshift=-0.5cm] + } -- [hv path] + p2 [coordinate] -> + srun/Run software on data [bbox] -> + paper/Paper [bbox] + }; + + \ifdefined\paperfinal + \node (happy) [inner sep=0pt, below=of paper, yshift=+8mm] + {\includegraphics[width=2cm]{img/happy-question.jpg}}; + \node (happyurl) [below=of happy, xshift=-9.5mm, yshift=+1cm] + {\tiny \url{https://heywhatwhatdidyousay.wordpress.com}}; + \node (qurl) [below=of happyurl, xshift=10.5mm, yshift=+1.2cm] + {\tiny \url{http://pngimages.net}}; + \else + \ifdefined\paperinit + \node (happy) [inner sep=0pt, below=of paper, yshift=+8mm] + {\includegraphics[width=2cm]{img/happy.jpg}}; + \node (happyurl) [below=of happy, xshift=-9.5mm, yshift=+1cm] + {\tiny \url{https://heywhatwhatdidyousay.wordpress.com}}; + \fi + \fi + + %% Software... + \let\ppopacity\undefined + \ifdefined\allopacity \newcommand{\ppopacity}{1} + \else \ifdefined\focusonpackages + \newcommand{\ppopacity}{1} + \else + \newcommand{\ppopacity}{0.3} + \fi + \fi + + \ifdefined\sver + \node (sver) + [rbox, above=of soft, yshift=-8mm, opacity=\ppopacity] + {What version?}; + \fi + \ifdefined\srep + \node (srep) + [rbox, above=of sver, yshift=-8mm, opacity=\ppopacity] + {Repository?}; + \fi + + %% Build + \ifdefined\dver + \node (dver) + [rbox, above=of build, yshift=-8mm, opacity=\ppopacity] + {Dependencies?}; + \fi + \ifdefined\ddver + \node (ddver) + [rbox, above=of dver, yshift=-8mm, opacity=\ppopacity] + {Dep. versions?}; + \fi + \ifdefined\confopt + \node (confopt) + [rbox, above=of ddver, yshift=-8mm, opacity=\ppopacity] + {Config options?}; + \fi + \ifdefined\confenv + \node (confenv) + [rbox, above=of confopt, yshift=-8mm, opacity=\ppopacity] + {Config environment?}; + \fi + + %% Hardware/data + \let\ppopacity\undefined + \ifdefined\allopacity \newcommand{\ppopacity}{1} + \else \ifdefined\focusonhardware + \newcommand{\ppopacity}{1} + \else + \newcommand{\ppopacity}{0.3} + \fi + \fi + \ifdefined\db + \node (db) + [rbox, below=of hard, yshift=+8mm, opacity=\ppopacity] + {Data base, or PID?}; + \fi + \ifdefined\calib + \node (calib) + [rbox, below=of db, yshift=+8mm, opacity=\ppopacity] + {Calibration/version?}; + \fi + \ifdefined\corr + \node (corr) + [rbox, below=of calib, yshift=+8mm, opacity=\ppopacity] + {Integrity?}; + \fi + + %% Run software ... + \let\ppopacity\undefined + \ifdefined\allopacity \newcommand{\ppopacity}{1} + \else \ifdefined\focusonrun + \newcommand{\ppopacity}{1} + \else + \newcommand{\ppopacity}{0.3} + \fi + \fi + \ifdefined\runord + \node (runord) + [rbox, above=of srun, yshift=-8mm, opacity=\ppopacity] + {What order?}; + \fi + \ifdefined\runopt + \node (runopt) + [rbox, above=of runord, yshift=-8mm, opacity=\ppopacity] + {Runtime options?}; + \fi + \ifdefined\humanerr + \node (humanerr) + [rbox, above=of runopt, yshift=-8mm, opacity=\ppopacity] + {Human error?}; + \fi + \ifdefined\confirmbias + \node (confirmbias) + [rbox, above=of humanerr, yshift=-8mm, opacity=\ppopacity] + {Confirmation bias?}; + \fi + \ifdefined\depupdate + \node (depupdate) + [rbox, below=of srun, yshift=+8mm, opacity=\ppopacity] + {Environment update?}; + \fi + \ifdefined\coauth + \node (coaut) + [rbox, below=of depupdate, yshift=+8mm, opacity=\ppopacity] + {In sync with coauthors?}; + \fi + + %% Paper ... + \let\ppopacity\undefined + \ifdefined\allopacity \newcommand{\ppopacity}{1} + \else \ifdefined\focusonpaper + \newcommand{\ppopacity}{1} + \else + \newcommand{\ppopacity}{0.3} + \fi + \fi + \ifdefined\varsinpaper + \node (varsinpaper) + [rbox, above=of paper, xshift=-1mm, yshift=-8mm, opacity=\ppopacity] + {Sync with analysis?}; + \fi + \ifdefined\recordinfo + \node (recordinfo) + [rbox, above=of varsinpaper, yshift=-8mm, opacity=\ppopacity] + {Report this info?}; + \fi + \ifdefined\softcite + \node (softcite) + [rbox, above=of recordinfo, yshift=-8mm, opacity=\ppopacity] + {Cited software?}; + \fi + \ifdefined\prevchange + \node (prevchange) + [rbox, above=of softcite, yshift=-8mm, opacity=\ppopacity] + {History recorded?}; + \fi + + \ifdefined\gitlogo + \node [inner sep=0pt, opacity=0.5] at (5.5,0) + {\includegraphics[width=10cm]{img/git.png}}; + \fi +\end{tikzpicture} diff --git a/tex/src/preamble-biblatex.tex b/tex/src/preamble-biblatex.tex index fc9f259..caa03b4 100644 --- a/tex/src/preamble-biblatex.tex +++ b/tex/src/preamble-biblatex.tex @@ -59,8 +59,8 @@ url=false, dashed=false, eprint=false, - maxbibnames=2, - minbibnames=1, + maxbibnames=10, + minbibnames=4, hyperref=true, maxcitenames=2, mincitenames=1, @@ -90,7 +90,8 @@ %% Set the color of the doi link to mymg (magenta) and the ads links %% to mypurp (or purple): \definecolor{mypurp}{cmyk}{0.75,1,0,0} -\newcommand{\doihref}[2]{\href{#1}{\color{magenta}{#2}}} +\definecolor{myblue}{rgb}{0,0.669,0.885} +\newcommand{\doihref}[2]{\href{#1}{\color{myblue}{#2}}} \newcommand{\adshref}[2]{\href{#1}{\color{mypurp}{#2}}} \newcommand{\blackhref}[2]{\href{#1}{\color{black}{#2}}} @@ -117,7 +118,7 @@ \usebibmacro{begentry}% \usebibmacro{author/translator+others}% \newunit% - \ifdefined\makethesis\printtext{\usebibmacro{title}}\fi% + \printtext{\usebibmacro{title}}% \newunit% \printtext[doilink]{\usebibmacro{journal}}% \addcomma% diff --git a/tex/src/preamble-header.tex b/tex/src/preamble-header.tex deleted file mode 100644 index 81a08b0..0000000 --- a/tex/src/preamble-header.tex +++ /dev/null @@ -1,89 +0,0 @@ -%% The headers: title, authors, top of pages and section title formatting -%% of the final LaTeX file are configured here. -% -%% Copyright (C) 2018-2020 Mohammad Akhlaghi <mohammad@akhlaghi.org> -% -%% This template is free software: you can redistribute it and/or modify it -%% under the terms of the GNU General Public License as published by the -%% Free Software Foundation, either version 3 of the License, or (at your -%% option) any later version. -% -%% This template is distributed in the hope that it will be useful, but -%% WITHOUT ANY WARRANTY; without even the implied warranty of -%% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU -%% General Public License for more details. -% -%% You should have received a copy of the GNU General Public License along -%% with this template. If not, see <http://www.gnu.org/licenses/>. - - - - - -%% General page header settings. -\usepackage{fancyhdr} -\pagestyle{fancy} -\lhead{\footnotesize{\scshape Draft paper}, {\footnotesize nnn:i (pp), Year Month day}} -\rhead{\scshape\footnotesize YOUR-NAME et al.} -\cfoot{\thepage} -\setlength{\voffset}{0.75cm} -\setlength{\headsep}{0.2cm} -\setlength{\footskip}{0.75cm} -\renewcommand{\headrulewidth}{0pt} - - - - - -%% Specific style for first page. -\fancypagestyle{firststyle} -{ - \lhead{\footnotesize{\scshape Draft paper}, nnn:i (pp), YYYY Month day\\ - \scriptsize \textcopyright YYYY, Your name. All rights reserved.} - \rhead{\footnotesize \footnotesize \today, \currenttime\\} -} - - - - - -%To set the style of the titles: -\usepackage{titlesec} -\titleformat{\section} - {\centering\normalfont\uppercase} - {\thesection.} - {0em} - { } -\titleformat{\subsection} - {\centering\normalsize\slshape} - {\thesubsection.} - {0em} - { } -\titleformat{\subsubsection} - {\centering\small\slshape} - {\thesubsubsection.} - {0em} - { } - - - - - -% Basic Document information that goes into the PDF meta-data. -\hypersetup -{ - pdfauthor={YOUR NAME}, - pdfsubject={A SHORT DESCRIPTION OF THE WORK}, - pdftitle={THE TITLE OF THIS PROJECT}, - pdfkeywords={SOME, KEYWORDS, FOR, THE, PDF} -} - - - - - -%% Title and author information -\usepackage{authblk} -\renewcommand\Authfont{\small\scshape} -\renewcommand\Affilfont{\footnotesize\normalfont} -\setlength{\affilsep}{0.2cm} diff --git a/tex/src/preamble-necessary.tex b/tex/src/preamble-necessary.tex deleted file mode 100644 index b6f5b55..0000000 --- a/tex/src/preamble-necessary.tex +++ /dev/null @@ -1,90 +0,0 @@ -%% Necessary (independent of style) macros for this project. -%% -%% These are a set of packages that have been commonly necessary in most -%% LaTeX usages. However, if any are not needed in your work, please feel -%% free to remove them. -% -%% Copyright (C) 2018-2020 Mohammad Akhlaghi <mohammad@akhlaghi.org> -% -%% This template is free software: you can redistribute it and/or modify it -%% under the terms of the GNU General Public License as published by the -%% Free Software Foundation, either version 3 of the License, or (at your -%% option) any later version. -% -%% This template is distributed in the hope that it will be useful, but -%% WITHOUT ANY WARRANTY; without even the implied warranty of -%% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU -%% General Public License for more details. -% -%% You should have received a copy of the GNU General Public License along -%% with this template. If not, see <http://www.gnu.org/licenses/>. - - - - - -%% Values from the analysis. -\input{tex/build/macros/project.tex} - - - - - -% Macros for to help in typing, remove them if you don't need them, but -% this can help as a demo on how you can simply writing of commonly used -% words that need special formatting (like software names). -\newcommand{\snsign}{{\small S}/{\small N}} -\newcommand{\originsoft}{\textsf{ORIGIN}} -\newcommand{\sextractor}{\textsf{SE\-xtractor}} -\newcommand{\noisechisel}{\textsf{Noise\-Chisel}} -\newcommand{\makecatalog}{\textsf{Make\-Catalog}} - - - - - -%% For highlighting updates. When this is set, text marked as \new -%% will be colored in dark green and text that is marked wtih \tonote -%% will be marked in dark red. -\ifdefined\highlightchanges -\newcommand{\new}[1]{\textcolor{green!60!black}{#1}} -\newcommand{\tonote}[1]{\textcolor{red!60!black}{[#1]}} -\else -\newcommand{\new}[1]{\textcolor{black}{#1}} -\newcommand{\tonote}[1]{{}} -\fi - - - - - -% Better than verbatim for displaying typed text. -\usepackage{alltt} - - - - - -% For arithmetic opertions within LaTeX -\usepackage[nomessages]{fp} - - - - - -%To add a code font to the text: -\usepackage{courier} - - - - - -%To add some enumerating styles -\usepackage{enumerate} - - - - - -%Including images if necessary -\usepackage{graphicx} diff --git a/tex/src/preamble-pgfplots.tex b/tex/src/preamble-pgfplots.tex index 0ffb294..3f467a6 100644 --- a/tex/src/preamble-pgfplots.tex +++ b/tex/src/preamble-pgfplots.tex @@ -67,7 +67,9 @@ %% slow with detailed plots). 2) You can use the PDFs of the individual %% plots for other purposes (for example to include in slides) cleanly. \usepackage{tikz} +\usetikzlibrary{graphs} \usetikzlibrary{external} +\usetikzlibrary{positioning} \tikzexternalize \tikzsetexternalprefix{tikz/} @@ -119,3 +121,73 @@ legend style = {font=\footnotesize}, label style = {font=\footnotesize} } + + + + + +%% Nodes in demo graphs +\tikzset{node-terminal/.style={ + rectangle, + very thick, + draw=blue!50, + text centered, + top color=white, + minimum size=6mm, + text width=2.1cm, + rounded corners=3mm, + bottom color=blue!20, + font=\ttfamily}} + +\tikzset{node-nonterminal/.style={ + rectangle, + very thick, + text centered, + top color=white, + text width=2.1cm, + minimum size=6mm, + draw=green!50!black!50, + bottom color=green!80!black!50, + font=\ttfamily}} + +\tikzset{node-makefile/.style={ + thick, + rectangle, + anchor=south, + minimum width=2.6cm, + minimum height=5cm, + draw=green!50!black!50, + fill=black!10!green!12!white, +}} + +\tikzset{node-point/.style={ + circle, + black!50, + inner sep=0pt, + minimum size=0pt, + fill=white}} + +\tikzset{ bbox/.style={ + rectangle, + minimum width=2.5cm, + rounded corners=2mm, + very thick,draw=blue!50, + top color=white, + bottom color=blue!20 } } + +\tikzset{ rbox/.style={ + rectangle, + dotted, + minimum width=2.5cm, + rounded corners=2mm, + very thick,draw=red!50!black!50, + top color=white, + bottom color=red!50!black!20 } } + +\tikzset{ gbox/.style={ + rectangle, + minimum width=2.5cm, + very thick, + draw=green!50!black!50, + top color=white, + bottom color=green!50!black!20 } } diff --git a/tex/src/preamble-style.tex b/tex/src/preamble-style.tex index 95fafc8..e843903 100644 --- a/tex/src/preamble-style.tex +++ b/tex/src/preamble-style.tex @@ -1,152 +1,125 @@ -%% General paper's style settings. -%% -%% This preamble can be completely ignored when including this TeX file in -%% another style. This is done because this LaTeX build is meant to be an -%% initial/internal phase or part of a larger effort, so it has a basic -%% style defined here as a preamble. To ignore it, uncomment or delete the -%% respective line in `paper.tex'. -%% -%% Copyright (C) 2019-2020 Mohammad Akhlaghi <mohammad@akhlaghi.org> -% -%% This template is free software: you can redistribute it and/or modify it -%% under the terms of the GNU General Public License as published by the -%% Free Software Foundation, either version 3 of the License, or (at your -%% option) any later version. -% -%% This template is distributed in the hope that it will be useful, but -%% WITHOUT ANY WARRANTY; without even the implied warranty of -%% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU -%% General Public License for more details. -% -%% You should have received a copy of the GNU General Public License along -%% with this template. If not, see <http://www.gnu.org/licenses/>. - - - - - -%% Font. +%% Set the page margins (use `showframe' to see the sides). +%% A4 is 210mm x 297mm +\usepackage[a4paper]{geometry} + +%% Horizontal space of text: total is 210mm +\setlength{\hoffset}{0mm} % remaining: 190mm +\setlength{\textwidth}{155mm} % remaining: 160mm +\setlength{\marginparsep}{0pt} +\setlength{\marginparwidth}{0pt} +\setlength{\oddsidemargin}{0pt} + +%% Vertical space of text: total is 297mm. +\setlength{\voffset}{-15.4mm} % remaining: 287mm (== 10mm (1 inch + \hoffset). +\setlength{\topmargin}{0mm} % remaining: 287mm. +\setlength{\headheight}{10mm} % remaining: 277mm. +\setlength{\headsep}{10mm} % remaining: 272mm. +\setlength{\textheight}{245mm} % remaining: 22mm. +\setlength{\footskip}{7mm} % remaining: 10mm. + +%% To see the layout, add a `\layout' right after `\begin{document}'. +\usepackage{layout} + +%% To allow a prefix to the enumeration. +\usepackage{enumitem} + +%% Horizontal line with spacing +\newcommand{\horizontalline}{\vspace{3mm}\hrule\vspace{3mm}} + +%% Custom title format +\usepackage{setspace} +\makeatletter +\renewcommand{\maketitle}{\bgroup\setlength{\parindent}{0pt} + \begin{flushleft} + {\mpbold RESEARCH PAPER} + + \vspace{3mm} + {\LARGE\mpmedium \@title} + + \vspace{2mm} + \@author + \end{flushleft}\egroup + \horizontalline +} +\makeatother + +%% For authors and affiliations +\newcommand{\authoraffil}[2]{#1\textsuperscript{\mplight#2}} + +%% Spacing before and after section titles. +%% Format: \titlespacing*{<command>}{<left>}{<before-sep>}{<after-sep>} +\usepackage{titlesec} +\titlespacing*{\section}{0pt}{10pt plus 0pt minus 0pt}{0pt plus 0pt minus 0pt} +\titlespacing*{\subsection}{0pt}{10pt plus 0pt minus 0pt}{0pt plus 0pt minus 0pt} +\titlespacing*{\subsubsection}{0pt}{10pt plus 0pt minus 0pt}{0pt plus 0pt minus 0pt} +\titleformat{\section}{\large\scshape\bf}{\thesection.{ }}{0pt}{} +\titleformat{\subsection}{\bfseries\itshape}{\thesubsection.{ }}{0pt}{} +\titleformat{\subsubsection}{\bfseries\itshape}{\thesubsubsection.{ }}{0pt}{} + +%% Set the font. +%% After downloading, put the font in `/usr/share/fonts/TTF'. +%% https://www.fontspace.com/m-fonts/m-2p +%% Also for M+: https://mplus-fonts.osdn.jp/about-en.html +%% https://www.fontpalace.com/font-download/Memento/ +\usepackage{fontspec} \usepackage[T1]{fontenc} -\usepackage{newtxtext} -\usepackage{newtxmath} - - - - - -%% Print size -\usepackage[a4paper, includeheadfoot, body={18.7cm, 24.5cm}]{geometry} - - - - - -%% Set the distance between the columns if two columns: -\setlength{\columnsep}{0.75cm} - - - - - -% To allow figures to take up more space on the top of the page: -\renewcommand{\topfraction}{.99} -\renewcommand{\bottomfraction}{.7} -\renewcommand{\textfraction}{.05} -\renewcommand{\floatpagefraction}{.99} -\renewcommand{\dbltopfraction}{.99} -\renewcommand{\dblfloatpagefraction}{.99} -\setcounter{topnumber}{1} -\setcounter{bottomnumber}{0} -\setcounter{totalnumber}{2} -\setcounter{dbltopnumber}{1} - - - - - -%% Color related settings: -\usepackage{xcolor} -\color{black} % Text color -\definecolor{DarkBlue}{RGB}{0,0,90} - - - - - - -% figure and figure* ordering correction: -\usepackage{fixltx2e} - - - - - -%% For editing the caption appearence. The `setspace' package defines -%% the `stretch' variable. `abovecaptionskip' is the distance between -%% the figure and the caption. -\usepackage{setspace, caption} -\captionsetup{font=footnotesize, labelfont={color=DarkBlue,bf}, skip=1pt} -\captionsetup[figure]{font={stretch=1, small}} -\setlength{\abovecaptionskip}{3pt plus 1pt minus 1pt} -\setlength{\belowcaptionskip}{-1.25em} - - - - - - -%% To make the footnotes align: -\usepackage[hang]{footmisc} -\setlength\footnotemargin{10pt} - - - - - -%For including time in the title: -\usepackage{datetime} - - - - - -%To make links to webpages and include document information in the -%properties of the PDF +\usepackage{Alegreya} +\newfontfamily\mplight{AlegreyaSans-Light} +\newfontfamily\mpbold{AlegreyaSans-Bold} +\newfontfamily\mpmedium{AlegreyaSans-Medium} +\newfontfamily\mpregular{AlegreyaSans-Regular} + +%% For highlighting updates. When this is set, text marked as \new +%% will be colored in dark green and text that is marked wtih \tonote +%% will be marked in dark red. +\ifdefined\highlightchanges +\newcommand{\new}[1]{\textcolor{green!60!black}{#1}} +\newcommand{\tonote}[1]{\textcolor{red!60!black}{[#1]}} +\else +\newcommand{\new}[1]{\textcolor{black}{#1}} +\newcommand{\tonote}[1]{{}} +\fi + +%% To have links. \usepackage[ colorlinks, - urlcolor=blue, - citecolor=blue, - linkcolor=blue, + urlcolor=gray, + citecolor=gray, + linkcolor=gray, linktocpage]{hyperref} \renewcommand\UrlFont{\rmfamily} +%% To include figures. +\usepackage{graphicx} +%% To manage captions. +\usepackage[font={footnotesize}]{caption} +%% To use colors. +\usepackage{xcolor} - -%% Define the abstract environment -\renewenvironment{abstract} - {\vspace{-0.5cm}\small% - \list{}{% - \setlength{\leftmargin}{2cm}% - \setlength{\rightmargin}{\leftmargin}% - }% - \item\relax} - {\endlist} - - - - - -%% To keep the main page's code clean. -\newcommand{\includeabstract}[1]{% -\twocolumn[% - \begin{@twocolumnfalse}% - \maketitle% - \begin{abstract}% - #1% - \end{abstract}% - \vspace{1cm}% - \end{@twocolumnfalse}% - ]% +%% Header and footer style. +\usepackage{lastpage} +\usepackage{fancyhdr} +\pagestyle{fancy} +\lhead{\mplight\footnotesize Art.XX, page {\thepage} of \pageref{LastPage}} +\chead{} +\rhead{\mplight\footnotesize Akhlaghi et al; Reproducible paper template} +\lfoot{} +\cfoot{} +\rfoot{} +\renewcommand\headrulewidth{0.0pt} +\renewcommand\footrulewidth{0.0pt} +\fancypagestyle{firstpage} { + \lhead{\includegraphics[width=3.5cm]{tex/img/codata.png}} + \chead{} + \rhead{\mplight\footnotesize + Akhlaghi, M, et al. 2019. Reproducible paper template\\ + \emph{Data Science Journal}, VV, NN, pp.1-N,\\ + DOI: https://doi.org/10.5334/dsj-XXXX-XXX} + \lfoot{} + \cfoot{} + \rfoot{} + \renewcommand\headrulewidth{0.1pt} + \renewcommand\footrulewidth{0.0pt} } diff --git a/tex/src/references.tex b/tex/src/references.tex index 02a7d50..0f8171b 100644 --- a/tex/src/references.tex +++ b/tex/src/references.tex @@ -1,33 +1,1503 @@ -%% Non-software BibTeX entries. The software-specific BibTeX entries are -%% stored in a `*.tex' file under the `tex/dependencies' directory. -% -%% Copyright (C) 2018-2020 Mohammad Akhlaghi <mohammad@akhlaghi.org> -% -%% Copying and distribution of this file, with or without modification, -%% are permitted in any medium without royalty provided the copyright -%% notice and this notice are preserved. This file is offered as-is, -%% without any warranty. +@ARTICLE{gibney20, + author = {Elizabeth Gibney}, + title = {This AI researcher is trying to ward off a reproducibility crisis}, + year = {2020}, + journal = {Nature}, + volume = {577}, + pages = {14}, + doi = {10.1038/d41586-019-03895-5}, +} + + + + + +@ARTICLE{munafo19, + author = {Marcus Munaf\'o}, + title = {Raising research quality will require collective action}, + year = {2019}, + journal = {Nature}, + volume = {576}, + pages = {183}, + doi = {10.1038/d41586-019-03750-7}, +} + + + + + +@ARTICLE{jones19, + author = {{Jones}, M.~G. and {Verdes-Montenegro}, L. and {Damas-Segovia}, A. and + {Borthakur}, S. and {Yun}, M. and {del Olmo}, A. and {Perea}, J. and + {Rom{\'a}n}, J. and {Luna}, S. and {Lopez Gutierrez}, D. and + {Williams}, B. and {Vogt}, F.~P.~A. and {Garrido}, J. and + {Sanchez}, S. and {Cannon}, J. and {Ram{\'\i}rez-Moreta}, P.}, + title = "{Evolution of compact groups from intermediate to final stages. A case study of the H I content of HCG 16}", + journal = {Astronomy \& Astrophysics}, + eprint = {1910.03420}, + keywords = {galaxies: groups: individual: HCG 16, galaxies: interactions, galaxies: evolution, galaxies: ISM, radio lines: galaxies}, + year = "2019", + month = "Dec", + volume = {632}, + eid = {A78}, + pages = {A78}, + doi = {10.1051/0004-6361/201936349}, + adsurl = {https://ui.adsabs.harvard.edu/abs/2019A&A...632A..78J}, + adsnote = {Provided by the SAO/NASA Astrophysics Data System} +} + + + + + +@ARTICLE{banek19, + author = {{Banek}, Christine and {Thornton}, Adam and {Economou}, Frossie and + {Fausti}, Angelo and {Krughoff}, K. Simon and {Sick}, Jonathan}, + title = "{Why is the LSST Science Platform built on Kubernetes?}", + journal = {Proceedings of ADASS XXIX}, + volume = {arXiv}, + keywords = {Astrophysics - Instrumentation and Methods for Astrophysics}, + year = "2019", + month = "Nov", + eid = {arXiv:1911.06404}, + pages = {1911.06404}, +archivePrefix = {arXiv}, + eprint = {1911.06404}, + primaryClass = {astro-ph.IM}, + adsurl = {https://ui.adsabs.harvard.edu/abs/2019arXiv191106404B}, + adsnote = {Provided by the SAO/NASA Astrophysics Data System} +} + + + + + +@ARTICLE{infante19, + author = {{Infante-Sainz}, Ra{\'u}l and {Trujillo}, Ignacio and + {Rom{\'a}n}, Javier}, + title = "{The Sloan Digital Sky Survey extended Point Spread Functions}", + journal = {MNRAS}, + volume = {arXiv}, + keywords = {Astrophysics - Instrumentation and Methods for Astrophysics, Astrophysics - Astrophysics of Galaxies}, + year = "2019", + month = "Nov", + eid = {arXiv:1911.01430}, + pages = {1911.01430}, +archivePrefix = {arXiv}, + eprint = {1911.01430}, + primaryClass = {astro-ph.IM}, + adsurl = {https://ui.adsabs.harvard.edu/abs/2019arXiv191101430I}, + adsnote = {Provided by the SAO/NASA Astrophysics Data System} +} + + + + + +@ARTICLE{fineberg19, + author = {Harvey V. Fineberg and David B. Allison and Lorena A. Barba and Dianne Chong and David L. Donoho and Juliana Freire and Gerald Gabrielse and Constantine Gatsonis and Edward Hall and Thomas H. Jordan and Dietram A. Scheufele and Victoria Stodden and Simine Vazire, Timothy D. Wilson and Wendy Wood and Jennifer Heimberg and Thomas Arrison and Michael Cohen and Michele Schwalbe and Adrienne Stith Butler and Barbara A. Wanchisen and Tina Winters and Rebecca Morgan and Thelma Cox and Lesley Webb and Garret Tyson and Erin Hammers Forstag}, + title = {Reproducibility and Replicability in Science}, + journal = {The National Academies Press}, + year = 2019, + pages = {1}, + doi = {10.17226/25303}, +} + + + + + +@ARTICLE{akhlaghi19, + author = {{Akhlaghi}, Mohammad}, + title = "{Carving out the low surface brightness universe with NoiseChisel}", + journal = {IAU Symposium 355}, + volume = {arXiv}, + keywords = {Astrophysics - Instrumentation and Methods for Astrophysics, Astrophysics - Astrophysics of Galaxies, Computer Science - Computer Vision and Pattern Recognition}, + year = "2019", + month = "Sep", + eid = {arXiv:1909.11230}, + pages = {1909.11230}, +archivePrefix = {arXiv}, + eprint = {1909.11230}, + primaryClass = {astro-ph.IM}, + adsurl = {https://ui.adsabs.harvard.edu/abs/2019arXiv190911230A}, + adsnote = {Provided by the SAO/NASA Astrophysics Data System} +} + + + + + +@ARTICLE{cribbs19, + author = {Cribbs, AP and Luna-Valero, S and George, C and Sudbery, IM and Berlanga-Taylor, AJ and Sansom, SN and Smith, T and Ilott, NE and Johnson, J and Scaber, J and Brown, K and Sims, D and Heger, A}, + title = {CGAT-core: a python framework for building scalable, reproducible computational biology workflows [version 2; peer review: 1 approved, 1 approved with reservations]}, + journal = {F1000Research}, + year = 2019, + volume = 8, + pages = {377}, + doi = {10.12688/f1000research.18674.2}, +} + + + + + +@ARTICLE{brinckman19, +author = "Adam Brinckman and Kyle Chard and Niall Gaffney and Mihael Hategan and Matthew B. Jones and Kacper Kowalik and Sivakumar Kulasekaran and Bertram Ludäscher and Bryce D. Mecum and Jarek Nabrzyski and Victoria Stodden and Ian J. Taylor and Matthew J. Turk and Kandace Turner", + title = {Computing environments for reproducibility: Capturing the ``Whole Tale''}, + journal = {Future Generation Computer Systems}, + year = 2019, + volume = 94, + pages = 854, + doi = {10.1016/j.future.2017.12.029}, +} + + + + + +@ARTICLE{uhse19, + author = {Uhse, Simon and Pflug, Florian G. and {von Haeseler}, Arndt and Djamei, Armin}, + title = {Insertion Pool Sequencing for Insertional Mutant Analysis in Complex Host‐Microbe Interactions}, + journal = {Current Protocols in Plant Biology}, + volume = {4}, + year = "2019", + month = "July", + pages = {e20097}, + doi = {10.1002/cppb.20097}, +} + + + + + +@ARTICLE{alliez19, + author = {{Alliez}, Pierre and {Di Cosmo}, Roberto and {Guedj}, Benjamin and + {Girault}, Alain and {Hacid}, Mohand-Said and {Legrand}, Arnaud and + {Rougier}, Nicolas P.}, + title = "{Attributing and Referencing (Research) Software: Best Practices and Outlook from Inria}", + journal = {Computing in Science \& Engineering}, + volume = {22}, + keywords = {Computer Science - Digital Libraries, Computer Science - Software Engineering}, + year = "2019", + month = "May", + pages = {39}, +archivePrefix = {arXiv}, + eprint = {1905.11123}, + primaryClass = {cs.DL}, + doi = {10.1109/MCSE.2019.2949413}, + adsurl = {https://ui.adsabs.harvard.edu/abs/2019arXiv190511123A}, + adsnote = {Provided by the SAO/NASA Astrophysics Data System} +} + + + + + +@ARTICLE{kneller19, + author = {Kneller,Gerald R. and Hinsen,Konrad}, + title = {Memory effects in a random walk description of protein structure ensembles}, + journal = {The Journal of Chemical Physics}, + volume = {150}, + year = {2019}, + pages = {064911}, + doi = {10.1063/1.5054887}, +} + + + + + +@ARTICLE{plesser18, + author = {Hans E. Plesser}, + title = {Reproducibility vs. Replicability: A Brief History of a Confused Terminology}, + journal = {Frontiers in Neuroinformatics}, + volume = {11}, + year = {2018}, + pages = {76}, + doi = {10.3389/fninf.2017.00076}, +} + + + + + +@ARTICLE{zhang18, + author = {{Zhang}, Zhi-Yu and {Romano}, D. and {Ivison}, R.~J. and + {Papadopoulos}, Padelis P. and {Matteucci}, F.}, + title = "{Stellar populations dominated by massive stars in dusty starburst galaxies across cosmic time}", + journal = {Nature}, + keywords = {Astrophysics - Astrophysics of Galaxies}, + year = "2018", + month = "Jun", + volume = {558}, + number = {7709}, + pages = {260}, + doi = {10.1038/s41586-018-0196-x}, +archivePrefix = {arXiv}, + eprint = {1806.01280}, + primaryClass = {astro-ph.GA}, + adsurl = {https://ui.adsabs.harvard.edu/abs/2018Natur.558..260Z}, + adsnote = {Provided by the SAO/NASA Astrophysics Data System} +} + + + + + +@ARTICLE{smart18, + author = {{Smart}, A.G.}, + title = {The war over supercooled water}, + journal = {Physics Today}, + volume = {Aug}, + year = "2018", + pages = {DOI:10.1063/PT.6.1.20180822a}, + doi = {10.1063/PT.6.1.20180822a}, +} + + + + + +@ARTICLE{kaiser18, + author = {{Kaiser}, J.}, + title = {Plan to replicate 50 high-impact cancer papers shrinks to just 18}, + journal = {Science}, + volume = {Jul}, + year = "2018", + pages = {31}, + doi = {10.1126/science.aau9619}, +} + + + + + +@ARTICLE{dicosmo18, + author = {{Di Cosmo}, Roberto and {Gruenpeter}, Morane and {Zacchiroli}, Stefano}, + title = {Identifiers for Digital Objects: The case of software source code preservation}, + journal = {Proceedings of iPRES 2018}, + year = "2018", + pages = {204.4}, + doi = {10.17605/osf.io/kde56}, +} + + + + + +@ARTICLE{gruning18, + author = {Gr\"uning, Bj\"orn and Chilton, John and K\"oster, Johannes and Dale, Ryan and Soranzo, Nicola and {van den Beek}, Marius and Goecks, Jeremy and Backofen, Rolf and Nekrutenko, Anton and Taylor, James}, + title = {Practical Computational Reproducibility in the Life Sciences}, + journal = {Cell Systems}, + volume = 6, + year = "2018", + pages = {631. bioRxiv:\href{https://www.biorxiv.org/content/10.1101/200683v2}{200683}}, + doi = {10.1016/j.cels.2018.03.014}, +} + + + + + +@ARTICLE{allen18, + author = {{Allen}, Alice and {Teuben}, Peter J. and {Ryan}, P. Wesley}, + title = "{Schroedinger's Code: A Preliminary Study on Research Source Code Availability and Link Persistence in Astrophysics}", + journal = {The Astrophysical Journal Supplement Series}, + keywords = {methods: numerical, Astrophysics - Instrumentation and Methods for Astrophysics, Computer Science - Digital Libraries}, + year = "2018", + month = "May", + volume = {236}, + number = {1}, + eid = {10}, + pages = {10}, + doi = {10.3847/1538-4365/aab764}, +archivePrefix = {arXiv}, + eprint = {1801.02094}, + primaryClass = {astro-ph.IM}, + adsurl = {https://ui.adsabs.harvard.edu/abs/2018ApJS..236...10A}, + adsnote = {Provided by the SAO/NASA Astrophysics Data System} +} + + + + + +@ARTICLE{burrell18, + author = {{Burrell}, A.G. and {Halford}, A. and {Klenzing}, J. and {Stoneback}, R.A. and {Morley}, S.K. and {Annex}, A.M. and {Laundal}, K.M. and {Kellerman}, A.C. and {Stansby}, D. and {Ma}, J.}, + title = {Snakes on a Spaceship—An Overview of Python in Heliophysics}, + journal = {Journal of Geophysical Research: Space Physics}, + volume = {123}, + year = "2018", + pages = {384}, + doi = {10.1029/2018JA025877}, +} + + + + + +@article{stodden18, + author = {{Stodden}, V. and {Seiler}, J. and {Ma}, Z.}, + title = {An empirical analysis of journal policy effectiveness for computational reproducibility}, + volume = {115}, + number = {11}, + pages = {2584}, + year = {2018}, + doi = {10.1073/pnas.1708290115}, + issn = {0027-8424}, + URL = {https://www.pnas.org/content/115/11/2584}, + journal = {Proceedings of the National Academy of Sciences} +} + + + + + +@article {fanelli18, + author = {{Fanelli}, D.}, + title = {Opinion: Is science really facing a reproducibility crisis, and do we need it to?}, + volume = {115}, + number = {11}, + pages = {2628}, + year = {2018}, + doi = {10.1073/pnas.1708272114}, + publisher = {National Academy of Sciences}, + issn = {0027-8424}, + URL = {https://www.pnas.org/content/115/11/2628}, + journal = {Proceedings of the National Academy of Sciences} +} + + + + + + +@ARTICLE{lewis18, + author = {{Lewis}, L.M. and {Edwards}, M.C. and {Meyers}, Z.R. and {Conover Talbot}, C. and {Hao}, H. and {Blum}, D. }, + title = "{Replication Study: Transcriptional amplification in tumor cells with elevated c-Myc}", + journal = {eLife}, + volume = {7}, + year = "2018", + month = "January", + pages = {e30274}, + doi = {10.7554/eLife.30274}, +} + + + + + +@ARTICLE{akhlaghi18b, + author = {{Akhlaghi}, Mohammad and {Bacon}, Roland and {Inami}, Hanae}, + title = "{MUSE HUDF survey I \& II, Sections 7.3 \& 3.4: photometry for objects with no prior broad-band segmentation map}", + journal = {Zenodo}, + pages = {DOI:10.5281/zenodo.1164774}, + year = "2018", + month = "February", + doi = {10.5281/zenodo.1164774}, +} + + + + + +@ARTICLE{akhlaghi18a, + author = {{Akhlaghi}, Mohammad and {Bacon}, Roland}, + title = "{MUSE HUDF survey I, Section 4: data and reproduction pipeline for photometry and astrometry}", + journal = {Zenodo}, + pages = {DOI:10.5281/zenodo.1163746}, + year = "2018", + month = "January", + doi = {10.5281/zenodo.1163746}, +} + + + + + +@ARTICLE{leek17, + author = {Jeffrey T. Leek and Leah R. Jager}, + title = {Is Most Published Research Really False?}, + journal = {Annual Review of Statistics and Its Application}, + volume = {4}, + year = {2017}, + pages = {109}, + doi = {10.1146/annurev-statistics-060116-054104}, +} + + + + + +@ARTICLE{reich17, + author = {Michael Reich and Thorin Tabor and Ted Liefeld and Helga Thorvaldsdóttir and Barbara Hill and Pablo Tamayo and Jill P. Mesirov}, + title = {The GenePattern Notebook Environment}, + journal = {Cell Systems}, + year = {2017}, + volume = {5}, + pages = {149}, + doi = {10.1016/j.cels.2017.07.003}, +} + + + + + +@ARTICLE{becker17, + author = {Gabriel Becker and Cory Barr and Robert Gentleman and Michael Lawrence}, + title = {Enhancing Reproducibility and Collaboration via Management of R Package Cohorts}, + journal = {Journal of Statistical Software, Articles}, + volume = {82}, + pages = 1, + year = "2017", +archivePrefix = {arXiv}, + eprint = {1501.02284}, + doi = {10.18637/jss.v082.i01}, + adsurl = {https://ui.adsabs.harvard.edu/abs/2015arXiv150102284B}, +} + + + + + +@ARTICLE{jenness17, + author = {{Jenness}, Tim}, + title = "{Modern Python at the Large Synoptic Survey Telescope}", + journal = {ADASS 27}, + year = "2017", + month = "Dec", + eid = {arXiv:1712.00461}, + pages = {arXiv:1712.00461}, +archivePrefix = {arXiv}, + eprint = {1712.00461}, + primaryClass = {astro-ph.IM}, + adsurl = {https://ui.adsabs.harvard.edu/abs/2017arXiv171200461J}, + adsnote = {Provided by the SAO/NASA Astrophysics Data System} +} + + + + + +@article{bezanson17, + title={Julia: A fresh approach to numerical computing}, + author={Bezanson, Jeff and Edelman, Alan and Karpinski, Stefan and Shah, Viral B}, + journal={SIAM {R}eview}, + volume={59}, + number={1}, + pages={65}, + year={2017}, + archivePrefix={arXiv}, + eprint={1411.1607}, + publisher={SIAM}, + doi={10.1137/141000671}, + adsurl = {https://ui.adsabs.harvard.edu/abs/2014arXiv1411.1607B}, +} + + + + + +@ARTICLE{melson17, + author = {{Melsen}, L.A. and {Torfs}, P.J.J.F and {Uijlenhoet}, R. and {Teuling}, A.J.}, + title = {Comment on “Most computational hydrology is not reproducible, so is it really science?” by Christopher Hutton et al.}, + journal = {Water Resources Research}, + volume = 53, + pages = {2568}, + year = {2017}, + doi = {10.1002/2016WR020208}, +} + + + + + +@ARTICLE{munafo17, + author = {{Munaf\'o}, M.R. and {Nosek}, B.A. and {Bishop}, D.V.M. and {Button}, K.S. and {Chambers}, C.D. and {Percie du Sert}, N. and {Simonsohn}, U. and {Wagenmakers}, E.J. and {Ware}, J.J. {Ioannidis}, J.P.A.}, + title = {A manifesto for reproducible science}, + journal = {Nature Human Behaviour}, + volume = 1, + pages = {21}, + year = {2017}, + doi = {10.1038/s41562-016-0021}, +} + + + + + +@ARTICLE{jimenez17, + title={The popper convention: Making reproducible systems evaluation practical}, + author = {{Jimenez}, I. and {Sevilla}, M. and {Watkins}, N. and {Maltzahn}, C. and {Lofstead}, J. and {Mohror}, K. and {Arpaci-Dusseau}, A. and {Arpaci-Dusseau}, R.}, + journal = {IEEE IPDPSW}, + pages = {1561}, + year = {2017}, + doi = {10.1109/IPDPSW.2017.157}, +} + + + + @ARTICLE{bacon17, - author = {{Bacon}, R. and {Conseil}, S. and {Mary}, D. and {Brinchmann}, J. and - {Shepherd}, M. and {Akhlaghi}, M. and {Weilbacher}, P.~M. and - {Piqueras}, L. and {Wisotzki}, L. and {Lagattuta}, D. and {Epinat}, B. and - {Guerou}, A. and {Inami}, H. and {Cantalupo}, S. and {Courbot}, J.~B. and - {Contini}, T. and {Richard}, J. and {Maseda}, M. and {Bouwens}, R. and - {Bouch{\'e}}, N. and {Kollatschny}, W. and {Schaye}, J. and - {Marino}, R.~A. and {Pello}, R. and {Herenz}, C. and {Guiderdoni}, B. and - {Carollo}, M.}, - title = "{The MUSE Hubble Ultra Deep Field Survey. I. Survey description, data reduction, and source detection}", - journal = {A\&A}, -archivePrefix = "arXiv", - eprint = {1710.03002}, - keywords = {galaxies: distances and redshifts, galaxies: high-redshift, cosmology: observations, methods: data analysis, techniques: imaging spectroscopy, galaxies: formation}, - year = 2017, - month = nov, - volume = 608, - eid = {A1}, - pages = {A1}, - doi = {10.1051/0004-6361/201730833}, - adsurl = {http://adsabs.harvard.edu/abs/2017A\%26A...608A...1B}, - adsnote = {Provided by the SAO/NASA Astrophysics Data System} + author = {{Bacon}, Roland and {Conseil}, Simon and {Mary}, David and + {Brinchmann}, Jarle and {Shepherd}, Martin and {Akhlaghi}, Mohammad and + {Weilbacher}, Peter M. and {Piqueras}, Laure and {Wisotzki}, Lutz and + {Lagattuta}, David and {Epinat}, Benoit and {Guerou}, Adrien and + {Inami}, Hanae and {Cantalupo}, Sebastiano and + {Courbot}, Jean Baptiste and {Contini}, Thierry and {Richard}, Johan and + {Maseda}, Michael and {Bouwens}, Rychard and {Bouch{\'e}}, Nicolas and + {Kollatschny}, Wolfram and {Schaye}, Joop and {Marino}, Raffaella Anna and + {Pello}, Roser and {Herenz}, Christian and {Guiderdoni}, Bruno and + {Carollo}, Marcella}, + title = "{The MUSE Hubble Ultra Deep Field Survey. I. Survey description, data reduction, and source detection}", + journal = {Astronomy \& Astrophysics}, + keywords = {galaxies: distances and redshifts, galaxies: high-redshift, cosmology: observations, methods: data analysis, techniques: imaging spectroscopy, galaxies: formation, Astrophysics - Astrophysics of Galaxies}, + year = "2017", + month = "Nov", + volume = {608}, + eid = {A1}, + pages = {A1}, + doi = {10.1051/0004-6361/201730833}, +archivePrefix = {arXiv}, + eprint = {1710.03002}, + primaryClass = {astro-ph.GA}, + adsurl = {https://ui.adsabs.harvard.edu/abs/2017A\&A...608A...1B}, + adsnote = {Provided by the SAO/NASA Astrophysics Data System} +} + + + + + +@ARTICLE{smith16, + author = {Arfon M. Smith and Daniel S. Katz and Kyle E. Niemeyer}, + title = {Software citation principles}, + journal = {PeerJ Computer Science}, + volume = {2}, + year = {2016}, + pages = {e86}, + doi = {10.7717/peerj-cs.86}, +} + + + + + +@ARTICLE{ziemann16, + author = {Mark Ziemann and Yotam Eren and Assam El-Osta}, + title = {Gene name errors are widespread in the scientific literature}, + journal = {Genome Biology}, + volume = {17}, + year = {2016}, + pages = {177}, + doi = {10.1186/s13059-016-1044-7}, +} + + + + + +@ARTICLE{hinsen16, + author = {Konrad Hinsen}, + title = {Scientific notations for the digital era}, + journal = {The Self Journal of Science}, + year = {2016}, + pages = {1: arXiv:\href{https://arxiv.org/abs/1605.02960}{1605.02960}}, +} + + + + + +@ARTICLE{kluyver16, + author = {Thomas Kluyver and Benjamin Ragan-Kelley and Fernando Pérez and Brian Granger and Matthias Bussonnier and Jonathan Frederic and Kyle Kelley and Jessica Hamrick and Jason Grout and Sylvain Corlay and Paul Ivanov and Damián Avila and Safia Abdalla and Carol Willing}, + title = "{Jupyter Notebooks – a publishing format for reproducible computational workflows}", + journal = {Positioning and Power in Academic Publishing: Players, Agents and Agendas}, + year = {2016}, + pages = {87}, + doi = {10.3233/978-1-61499-649-1-87}, +} + + + + + +@ARTICLE{baker16, + author = {{Baker}, M.}, + title = "{Is there a reproducibility crisis?}", + journal = {Nature}, + volume = {533}, + year = "2016", + month = "May", + pages = {452}, + doi = {10.1038/533452a}, +} + + + + + +@ARTICLE{wilkinson16, + author = { {Wilkinson}, M.D and {Dumontier}, M. and {Aalbersberg}, I.J. and {Appleton}, G. and {Axton}, M. and {Baak}, A. and {Blomberg}, N. and {Boiten}, J. and {da Silva Santos}, L.B and {Bourne}, P.E. and {Bouwman}, J. and {Brookes}, A.J. and {Clark}, T. and {Crosas}, M. and {Dillo}, I. and {Dumon}, O. and {Edmunds}, S. and {Evelo}, C. and {Finkers}, R. and {Gonzalez-Beltran}, A. and {Gray}, A.J.G. and {Groth}, P. and {Goble}, C. and {Grethe}, Jeffrey S. and {Heringa}, J. and {’t Hoen}, P.A.C and {Hooft}, R. and {Kuhn}, T. and {Kok}, R. and {Kok}, J. and {Lusher}, S. and {Martone}, M. and {Mons}, A. and {Packer}, A. and {Persson}, B. and {Rocca-Serra}, P. and {Roos}, M. and {van Schaik}, R. and {Sansone}, S. and {Schultes}, E. and {Sengstag}, T. and {Slater}, T. and {Strawn}, G. and {Swertz}, M. and {Thompson}, M. and {van der Lei}, J. and {van Mulligen}, E. and {Velterop}, J. and {Waagmeester}, A. and {Wittenburg}, P. and {Wolstencroft}, K. and {Zhao}, J. and {Mons}, B.}, + title = "{The FAIR Guiding Principles for scientific data management and stewardship}", + journal = {Scientific Data}, + year = 2016, + month = mar, + volume = 3, + pages = {160018}, + doi = {10.1038/sdata.2016.18}, +} + + + + +@ARTICLE{hutton16, + author = {{Hutton}, C. and {Wagener}, T. and {Freer}, J. and {Han}, D. and {Duffy}, C. and {Arheimer}, B.}, + title = {Most computational hydrology is not reproducible, so is it really science?}, + journal = {Water Resources Research}, + year = {2016}, + volume = 52, + pages = {7548}, + doi = {10.1002/2016WR019285}, +} + + + + + +@ARTICLE{topalidou16, + author = {{Topalidou}, M. and {Leblois}, A. and {Boraud}, T. and {Rougier}, N.P.}, + title = {A long journey into reproducible computational neuroscience}, + journal = {Frontiers in Computational Neuroscience}, + year = {2016}, + volume = 9, + pages = {30}, + doi = {10.3389/fncom.2015.00030}, +} + + + + + +@ARTICLE{gil16, + author = {{Gil}, Yolanda and {David}, C.H. and {Demir}, I. and {Essawy}, B.T. and {Fulweiler}, R.W. and {Goodall}, J.L. and {Karlstrom}, L. and {Lee}, H. and {Mills}, H.J. and {Oh}, J. and {Pierce}, S.A. and {Pope}, A. and {Tzeng}, M.W. and {Villamizar}, S.R. and {Yu}, X}, + title = {Toward the Geoscience Paper of the Future: Best practices for documenting and sharing research from data to software to provenance}, + journal = {Earth and Space Science}, + year = 2016, + volume = 3, + pages = {388}, + doi = {10.1002/2015EA000136}, +} + + + + + +@ARTICLE{horvath15, + author = {Steve Horvath}, + title = {Erratum to: DNA methylation age of human tissues and cell types}, + journal = {Genome Biology}, + volume = {16}, + pages = {96}, + year = {2015}, + doi = {10.1186/s13059-015-0649-6}, +} + + + + + +@ARTICLE{chang15, + author = {Andrew C. Chang and Phillip Li}, + title = {Is Economics Research Replicable? Sixty Published Papers from Thirteen Journals Say ``Usually Not''}, + journal = {Finance and Economics Discussion Series 2015-083}, + year = {2015}, + pages = {1}, + doi = {10.17016/FEDS.2015.083}, +} + + + + + +@ARTICLE{schaffer15, + author = {Jonathan Schaffer}, + title = {What Not to Multiply Without Necessity}, + journal = {Australasian Journal of Philosophy}, + volume = {93}, + pages = {644}, + year = {2015}, + doi = {10.1080/00048402.2014.992447}, +} + + + + + +@ARTICLE{clarkso15, + author = "Chris Clarkson and Mike Smith and Ben Marwick and Richard Fullagar and Lynley A. Wallis and Patrick Faulkner and Tiina Manne and Elspeth Hayes and Richard G. Roberts and Zenobia Jacobs and Xavier Carah and Kelsey M. Lowe and Jacqueline Matthews and S. Anna Florin", + title = {The archaeology, chronology and stratigraphy of Madjedbebe (Malakunanja II): A site in northern Australia with early occupation}, + journal = {Journal of Human Evolution}, + year = 2015, + volume = 83, + pages = 46, + doi = {10.1016/j.jhevol.2015.03.014}, +} + + + + + +@ARTICLE{meng15, + author = {Haiyan Meng and Rupa Kommineni and Quan Pham and Robert Gardner and Tanu Malik and Douglas Thain}, + title = {An invariant framework for conducting reproducible computational science}, + journal = {Journal of Computational Science}, + year = 2015, + volume = 9, + pages = 137, + doi = {10.1016/j.jocs.2015.04.012}, +} + + + + + +@ARTICLE{gamblin15, + author = {Gamblin, Todd and LeGendre, Matthew and Collette, Michael R. and Lee, Gregory L. and Moody, Adam and {de Supinski}, Bronis R. and Futral, Scott}, + title = {The Spack package manager: bringing order to HPC software chaos}, + journal = {IEEE SC15}, + year = 2015, + volume = 1, + pages = {1}, + doi = {10.1145/2807591.2807623}, +} + + + + +@ARTICLE{akhlaghi15, + author = {{Akhlaghi}, M. and {Ichikawa}, T.}, + title = "{Noise-based Detection and Segmentation of Nebulous Objects}", + journal = {The Astrophysical Journal Supplement Series}, + archivePrefix = "arXiv", + eprint = {1505.01664}, + primaryClass = "astro-ph.IM", + keywords = {galaxies: irregular, galaxies: photometry, galaxies: structure, methods: data analysis, techniques: image processing, techniques: photometric}, + year = 2015, + month = sep, + volume = 220, + eid = {1}, + pages = {1}, + doi = {10.1088/0067-0049/220/1/1}, + adsurl = {https://ui.adsabs.harvard.edu/abs/2015ApJS..220....1A}, + adsnote = {Provided by the SAO/NASA Astrophysics Data System} +} + + + + + +@ARTICLE{courtes15, + author = {{Court{\`e}s}, Ludovic and {Wurmus}, Ricardo}, + title = "{Reproducible and User-Controlled Software Environments in HPC with Guix}", + journal = {Euro-Par}, + volume = {9523}, + keywords = {Computer Science - Distributed, Parallel, and Cluster Computing, Computer Science - Operating Systems, Computer Science - Software Engineering}, + year = "2015", + month = "Jun", + eid = {arXiv:1506.02822}, + pages = {arXiv:1506.02822}, +archivePrefix = {arXiv}, + eprint = {1506.02822}, + primaryClass = {cs.DC}, + doi = {10.1007/978-3-319-27308-2_47}, + adsurl = {https://ui.adsabs.harvard.edu/abs/2015arXiv150602822C}, + adsnote = {Provided by the SAO/NASA Astrophysics Data System} +} + + + + + +@ARTICLE{hinsen15, + author = {{Hinsen}, K.}, + title = {ActivePapers: a platform for publishing and archiving computer-aided research}, + journal = {F1000Research}, + year = 2015, + volume = 3, + pages = {289}, + doi = {10.12688/f1000research.5773.3}, +} + + + + + +@ARTICLE{belhajjame15, + author = {{Belhajjame}, K. and {Zhao}, Z. and {Garijo}, D. and {Gamble}, M. and {Hettne}, K. and {Palma}, R. and {Mina}, E. and {Corcho}, O. and {Gómez-Pérez}, J.M. and {Bechhofer}, S. and {Klyne}, G. and {Goble}, C}, + title = "{Using a suite of ontologies for preserving workflow-centric research objects}", + journal = {Journal of Web Semantics}, + year = 2015, + volume = 32, + pages = {16}, + doi = {10.1016/j.websem.2015.01.003}, +} + + + + + +@ARTICLE{bechhofer13, + author = {{Bechhofer}, S. and {Buchan}, I. and {De Roure}, D. and {Missier}, P. and {Ainsworth}, J. and {Bhagat}, J. and Couch, P. and Cruickshank, D. and {Delderfield}, M and Dunlop, I. and {Gamble}, M. and {Michaelides}, D. and {Owen}, S. and {Newman}, D. and {Sufi}, S. and {Goble}, C}, + title = "{Why linked data is not enough for scientists}", + journal = {Future Generation Computer Systems}, + year = 2013, + volume = 29, + pages = {599}, + doi = {10.1016/j.future.2011.08.004}, +} + + + + + +@ARTICLE{peng15, + author = {{Peng}, R.D.}, + title = {The reproducibility crisis in science: A statistical counterattack}, + journal = {Significance}, + year = 2015, + month = jun, + volume = 12, + pages = {30}, + doi = {10.1111/j.1740-9713.2015.00827.x}, +} + + + + + +@ARTICLE{herndon14, + author = {Thomas Herndon and Michael Ash and Robert Pollin}, + title = {Does high public debt consistently stifle economic growth? A critique of Reinhart and Rogoff}, + journal = {Cambridge Journal of Economics}, + year = {2014}, + month = {dec}, + volume = {38}, + pages = {257}, + doi = {10.1093/cje/bet075}, +} + + + + + +@ARTICLE{easterbrook14, + author = {{Easterbook}, S.}, + title = {Open code for open science?}, + journal = {Nature Geoscience}, + year = 2014, + month = oct, + volume = 7, + pages = {779}, + doi = {10.1038/ngeo2283}, +} + + + + + +@ARTICLE{fomel13, + author = {Sergey Fomel and Paul Sava and Ioan Vlad and Yang Liu and Vladimir Bashkardin}, + title = {Madagascar: open-source software project for multidimensional data analysis and reproducible computational experiments}, + journal = {Journal of open research software}, + year = {2013}, + volume = {1}, + pages = {e8}, + doi = {10.5334/jors.ag}, +} + + + + + +@ARTICLE{sandve13, + author = {{Sandve}, G.K. and {Nekrutenko}, A. and {Taylor}, J. and {Hovig}, E.}, + title = {Ten Simple Rules for Reproducible Computational Research}, + journal = {PLoS Computational Biology}, + year = 2013, + month = oct, + volume = 9, + pages = {e1003285}, + doi = {10.1371/journal.pcbi.1003285}, +} + + + + + +@ARTICLE{malik13, + author = {Tanu Malik and Quan Pham and Ian Foster}, + title = {SOLE: Towards Descriptive and Interactive Publications}, + journal = {Implementing Reproducible Research}, + year = 2013, + volume = {Chapter 2}, + pages = {1. URL: \url{https://osf.io/ns2m3}}, +} + + + + + +@ARTICLE{gronenschild12, + author = {Ed H. B. M. Gronenschild and Petra Habets and Heidi I. L. Jacobs and Ron Mengelers and Nico Rozendaal and Jim van Os and Machteld Marcelis}, + title = {The Effects of FreeSurfer Version, Workstation Type, and Macintosh Operating System Version on Anatomical Volume and Cortical Thickness Measurements}, + journal = {PLoS ONE}, + volume = {7}, + year = {2012}, + pages = {e38234}, + doi = {10.1371/journal.pone.0038234}, +} + + + + + +@ARTICLE{pham12, + author = {Quan Pham and Tanu Malik and Ian Foster and Roberto {Di Lauro} and Raffaele Montella}, + title = {SOLE: Linking Research Papers with Science Objects}, + journal = {Provenance and Annotation of Data and Processes (IPAW)}, + year = {2012}, + pages = {203}, + doi = {10.1007/978-3-642-34222-6_16}, +} + + + + + +@ARTICLE{davison12, + author = {Andrew Davison}, + title = {Automated Capture of Experiment Context for Easier Reproducibility in Computational Research}, + journal = {Computing in Science \& Engineering}, + volume = {14}, + year = {2012}, + pages = {48}, + doi = {10.1109/MCSE.2012.41}, +} + + + + + +@ARTICLE{zhao12, + author = {Jun Zhao and Jose Manuel Gomez-Perez and Khalid Belhajjame and Graham Klyne and Esteban Garcia-Cuesta and Aleix Garrido and Kristina Hettne and Marco Roos and David {De Roure} and Carole Goble}, + title = {Why workflows break — Understanding and combating decay in Taverna workflows}, + journal = {IEEE 8th International Conference on E-Science}, + year = {2012}, + pages = {1}, + doi = {10.1109/eScience.2012.6404482}, +} + + + + +@ARTICLE{vangorp11, + author = {Pieter {Van Gorp} and Steffen Mazanek}, + title = {SHARE: a web portal for creating and sharing executable research}, + journal = {Procedia Computer Science}, + year = 2011, + volume = 4, + pages = {589}, + doi = {10.1016/j.procs.2011.04.062}, +} + + + + + +@ARTICLE{hinsen11, + author = {{Hinsen}, Konrad}, + title = {A data and code model for reproducible research and executable papers}, + journal = {Procedia Computer Science}, + year = 2011, + volume = 4, + pages = {579}, + doi = {10.1016/j.procs.2011.04.061}, +} + + + + + +@ARTICLE{limare11, + author = {Nicolas Limare and Jean-Michel Morel}, + title = {The IPOL Initiative: Publishing and Testing Algorithms on Line for +Reproducible Research in Image Processing}, + journal = {Procedia Computer Science}, + year = 2011, + volume = 4, + pages = {716}, + doi = {10.1016/j.procs.2011.04.075}, +} + + + + + +@ARTICLE{gavish11, + author = {Matan Gavish and David L. Donoho}, + title = {A Universal Identifier for Computational Results}, + journal = {Procedia Computer Science}, + year = 2011, + volume = 4, + pages = {637}, + doi = {10.1016/j.procs.2011.04.067}, +} + + + + +@ARTICLE{gabriel11, + author = {Ann Gabriel and Rebecca Capone}, + title = {Executable Paper Grand Challenge Workshop}, + journal = {Procedia Computer Science}, + volume = {4}, + year = {2011}, + pages = {577}, + doi = {10.1016/j.procs.2011.04.060}, +} + + + + + +@ARTICLE{nowakowski11, + author = {Piotr Nowakowski and Eryk Ciepiela and Daniel Har\k{e}\.{z}lak and Joanna Kocot and Marek Kasztelnik and Tomasz Barty\'nski and Jan Meizner and Grzegorz Dyk and Maciej Malawski}, + title = {The Collage Authoring Environment}, + journal = {Procedia Computer Science}, + volume = {4}, + year = {2011}, + pages = {608}, + doi = {j.procs.2011.04.064}, +} + + + + + +@ARTICLE{peng11, + author = {{Peng}, R.D.}, + title = {Reproducible Research in Computational Science}, + journal = {Science}, + year = 2011, + month = dec, + volume = 334, + pages = {1226}, + doi = {10.1126/science.1213847}, +} + + + + + +@ARTICLE{pence10, + author = {{Pence}, W.~D. and {Chiappetti}, L. and {Page}, C.~G. and {Shaw}, R.~A. and + {Stobie}, E.}, + title = "{Definition of the Flexible Image Transport System (FITS), version 3.0}", + journal = {Astronomy and Astrophysics}, + keywords = {instrumentation: miscellaneous, methods: miscellaneous, techniques: miscellaneous, reference systems, standards, astronomical databases: miscellaneous}, + year = "2010", + month = "Dec", + volume = {524}, + eid = {A42}, + pages = {A42}, + doi = {10.1051/0004-6361/201015362}, + adsurl = {https://ui.adsabs.harvard.edu/abs/2010A\&A...524A..42P}, + adsnote = {Provided by the SAO/NASA Astrophysics Data System} +} + + + + + +@ARTICLE{goecks10, + author = {Jeremy Goecks and Anton Nekrutenko and James Taylor}, + title = {Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences}, + journal = {Genome Biology}, + year = 2010, + volume = 11, + pages = {R86}, + doi = {10.1186/gb-2010-11-8-r86}, +} + + + + + +@ARTICLE{merali10, + author = {Zeeya Merali}, + title = {Computational science: ...Error}, + journal = {Nature}, + year = 2010, + volume = 467, + pages = {775}, + doi = {10.1038/467775a}, +} + + + + + +@ARTICLE{casadevall10, + author = {{Casadevall}, A. and {Fang}, F.C}, + title = {Reproducible Science}, + journal = {Infection and Immunity}, + year = 2010, + volume = 78, + pages = {4972}, + doi = {10.1128/IAI.00908-10}, +} + + + + + +@ARTICLE{mesirov10, + author = {{Mesirov}, J.P.}, + title = {Accessible Reproducible Research}, + journal = {Science}, + year = 2010, + volume = 327, + pages = {415}, + doi = {10.1126/science.1179653}, +} + + + + + +@ARTICLE{ioannidis2009, + author = {John P. A. Ioannidis and David B. Allison and Catherine A. Ball and Issa Coulibaly and Xiangqin Cui and Aedín C Culhane and Mario Falchi and Cesare Furlanello and Laurence Game and Giuseppe Jurman and Jon Mangion and Tapan Mehta and Michael Nitzberg and Grier P. Page and Enrico Petretto and Vera {van Noort}}, + title = {Repeatability of published microarray gene expression analyses}, + journal = {Nature Genetics}, + year = {2009}, + volume = {41}, + pages = {149}, + doi = {10.1038/ng.295}, +} + + + + + +@ARTICLE{fomel09, + author = {Sergey Fomel and Jon F. Claerbout}, + title = {Reproducible Research}, + journal = {Computing in Science Engineering}, + year = {2009}, + volume = {11}, + pages = {5}, + doi = {10.1109/MCSE.2009.14}, +} + + + + + +@ARTICLE{baggerly09, + author = {Keith A. Baggerly and Kevin R Coombes}, + title = {Deriving chemosensitivity from cell lines: Forensic bioinformatics and reproducible research in high-throughput biology}, + journal = {The Annals of Applied Statistics}, + year = {2009}, + volume = {3}, + pages = {1309}, + doi = {10.1214/09-AOAS291}, +} + + + + + +@ARTICLE{scheidegger08, + author = {Carlos Scheidegger and David Koop and Emanuele Santos and Huy Vo and Steven Callahan and Juliana Freire and Cláudio Silva}, + title = {Tackling the Provenance Challenge one layer at a time}, + journal = {Concurrency Computation: Practice and Experiment}, + year = {2008}, + volume = {20}, + pages = {473}, + doi = {10.1002/cpe.1237}, +} + + + + + +@ARTICLE{moreau08, + author = {Moreau, Luc and Ludäscher, Bertram and Altintas, Ilkay and Barga, Roger S. and Bowers, Shawn and Callahan, Steven and Chin JR., George and Clifford, Ben and Cohen, Shirley and Cohen-Boulakia, Sarah and Davidson, Susan and Deelman, Ewa and Digiampietri, Luciano and Foster, Ian and Freire, Juliana and Frew, James and Futrelle, Joe and Gibson, Tara and Gil, Yolanda and Goble, Carole and Golbeck, Jennifer and Groth, Paul and Holland, David A. and Jiang, Sheng and Kim, Jihie and Koop, David and Krenek, Ales and McPhillips, Timothy and Mehta, Gaurang and Miles, Simon and Metzger, Dominic and Munroe, Steve and Myers, Jim and Plale, Beth and Podhorszki, Norbert and Ratnakar, Varun and Santos, Emanuele and Scheidegger, Carlos and Schuchardt, Karen and Seltzer, Margo and Simmhan, Yogesh L. and Silva, Claudio and Slaughter, Peter and Stephan, Eric and Stevens, Robert and Turi, Daniele and Vo, Huy and Wilde, Mike and Zhao, Jun and Zhao, Yong}, + title = {The First Provenance Challenge}, + journal = {Concurrency Computation: Practice and Experiment}, + year = {2008}, + volume = {20}, + pages = {473}, + doi = {10.1002/cpe.1237}, +} + + + + + +@ARTICLE{witten2007, + author = {Ben Witten and Bill Curry and Jeff Shragge}, + title = {A New Build Environment for SEP}, + journal = {Stanford Exploration Project}, + year = {2007}, + volume = {129}, + pages = {247: \url{http://sepwww.stanford.edu/data/media/public/docs/sep129/ben1.pdf}}, +} + + + + + +@ARTICLE{miller06, + author = {Greg Miller}, + title = {A Scientist's Nightmare: Software Problem Leads to Five Retractions}, + journal = {Science}, + year = {2006}, + volume = {314}, + pages = {1856}, + doi = {10.1126/science.314.5807.1856}, +} + + + + + +@ARTICLE{reich06, + author = {Michael Reich and Ted Liefeld and Joshua Gould and Jim Lerner and Pablo Tamayo and Jill P Mesirov}, + title = {GenePattern 2.0}, + journal = {Nature Genetics}, + year = {2006}, + volume = {38}, + pages = {500}, + doi = {10.1038/ng0506-500}, +} + + + + + +@ARTICLE{ludascher05, + author = {Ludäs\-cher, Bertram and Altintas, Ilkay and Berkley, Chad and Higgins, Dan and Jaeger, Efrat and Jones, Matthew and Lee, Edward A. and Tao, Jing and Zhao, Yang}, + title = {Scientific workflow management and the Kepler system}, + journal = {Concurrency Computation: Practice and Experiment}, + year = {2006}, + volume = {18}, + pages = {1039}, + doi = {10.1002/cpe.994}, +} + + + + + +@ARTICLE{ioannidis05, + author = {John P. A. Ioannidis}, + title = {Why Most Published Research Findings Are False}, + journal = {PLoS Medicine }, + year = {2005}, + volume = {2}, + pages = {e124}, + doi = {10.1371/journal.pmed.0020124}, +} + + + + + +@ARTICLE{bavoil05, + author = {Louis Bavoil and Steven P. Callahan and Patricia J. Crossno and Juliana Freire and Carlos E. Scheidegger and Cláudio T. Silva and Huy T. Vo}, + title = {VisTrails: Enabling Interactive Multiple-View Visualizations}, + journal = {VIS 05. IEEE Visualization}, + year = {2005}, + volume = {}, + pages = {135}, + doi = {10.1109/VISUAL.2005.1532788}, +} + + + + + +@ARTICLE{dolstra04, + author = {{Dolstra}, Eelco and {de Jonge}, Merijn and {Visser}, Eelco}, + title = {Nix: A Safe and Policy-Free System for Software Deployment}, + journal = {Large Installation System Administration Conference}, + year = {2004}, + volume = {18}, + pages = {79. \url{https://www.usenix.org/legacy/events/lisa04/tech/full_papers/dolstra/dolstra.pdf}}, +} + + + + + +@ARTICLE{oinn04, + author = {Oinn, Tom and Addis, Matthew and Ferris, Justin and Marvin, Darren and Senger, Martin and Greenwood, Mark and Carver, Tim and Glover, Kevin and Pocock, Matthew R. and Wipat, Anil and Li, Peter}, + title = {Taverna: a tool for the composition and enactment of bioinformatics workflows}, + journal = {Bioinformatics}, + year = {2004}, + volume = {20}, + pages = {3045}, + doi = {10.1093/bioinformatics/bth361}, +} + + + + + +@ARTICLE{schwab2000, + author = {Matthias Schwab and Martin Karrenbach and Jon F. Claerbout}, + title = {Making scientific computations reproducible}, + journal = {Computing in Science \& Engineering}, + year = {2000}, + volume = {2}, + pages = {61}, + doi = {10.1109/5992.881708}, +} + + + + + +@ARTICLE{buckheit1995, + author = {Jonathan B. Buckheit and David L. Donoho}, + title = {WaveLab and Reproducible Research}, + journal = {Wavelets and Statistics}, + year = {1995}, + volume = {1}, + pages = {55}, + doi = {10.1007/978-1-4612-2544-7\_5}, +} + + + + + +@ARTICLE{claerbout1992, + author = {Jon F. Claerbout and Martin Karrenbach}, + title = {Electronic documents give reproducible research a new meaning}, + journal = {SEG Technical Program Expanded Abstracts}, + year = {1992}, + volume = {1}, + pages = {601}, + doi = {10.1190/1.1822162}, +} + + + + + +@ARTICLE{eker03, + author = {Johan Eker and Jorn W Janneck and Edward A. Lee and Jie Liu and Xiaojun Liu and Jozsef Ludvig and Sonia Sachs and Yuhong Xiong and Stephen Neuendorffer}, + title = {Taming heterogeneity - the Ptolemy approach}, + journal = {Proceedings of the IEEE}, + year = {2003}, + volume = {91}, + pages = {127}, + doi = {10.1109/JPROC.2002.805829}, +} + + + + + +@ARTICLE{stevens03, + author = {Robert Stevens and Kevin Glover and Chris Greenhalgh and Claire Jennings and Simon Pearce and Peter Li and Melena Radenkovic and Anil Wipat}, + title = {Performing in silico Experiments on the Grid: A Users Perspective}, + journal = {Proceedings of UK e-Science All Hands Meeting}, + year = {2003}, + pages = {43}, +} + + + + + +@ARTICLE{knuth84, + author = {Donald Knuth}, + title = {Literate Programming}, + journal = {The Computer Journal}, + year = {1984}, + volume = {27}, + pages = {97}, + doi = {10.1093/comjnl/27.2.97}, +} + + + + + +@ARTICLE{stallman88, + author = {Richard M. Stallman and Roland McGrath and Paul D. Smith}, + title = {GNU Make: a program for directing recompilation}, + journal = {Free Software Foundation}, + year = {1988}, + pages = {ISBN:1-882114-83-3. \url{https://www.gnu.org/s/make/manual/make.pdf}}, +} + + + + + +@ARTICLE{somogyi87, + author = {Zoltan Somogyi}, + title = {Cake: a fifth generation version of make}, + journal = {University of Melbourne}, + year = {1987}, + pages = {1: \url{https://pdfs.semanticscholar.org/3e97/3b5c9af7763d70cdfaabdd1b96b3b75b5483.pdf}}, +} + + + + + +@ARTICLE{feldman79, + author = {Stuart I. Feldman}, + title = {Make -- a program for maintaining computer programs}, + journal = {Journal of Software: Practice and Experience}, + volume = {9}, + pages = {255}, + year = {1979}, + doi = {10.1002/spe.4380090402}, +} + + + + + +@ARTICLE{anscombe73, + author = {{Anscombe}, F.J.}, + title = {Graphs in Statistical Analysis}, + journal = {The American Statistician}, + year = {1973}, + volume = {27}, + pages = {17}, + doi = {10.1080/00031305.1973.10478966}, +} + + + + + +@ARTICLE{roberts69, + author = {{Roberts}, K.V.}, + title = {The publication of scientific fortran programs}, + journal = {Computer Physics Communications}, + year = {1969}, + volume = {1}, + pages = {1}, + doi = {10.1016/0010-4655(69)90011-3}, } |