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authorBoud Roukema <boud@cosmo.torun.pl>2020-04-19 15:58:51 +0200
committerBoud Roukema <boud@cosmo.torun.pl>2020-04-19 15:58:51 +0200
commite682332669b804bdecaf3eddd2521bcfe0eb7241 (patch)
treeb48e749effb35c4df49a39dbbb0b3222fc969db7
parentd4fb323e74aa5065e9ac84e99ed2d26e09c27156 (diff)
Clickable URLs for the 19 earlier reproducibility solutions
In this commit, the URLs for the 19 "earlier solutions" at the beginning of "3 Principles" are recovered from tex/src/paper-long.tex and put behind the package names as clickable words. To reduce the chance that these are interpreted as references, "Project1 (yyy1), Project2 (yyy1)" is changed to "yyy1: Project1, Project2". We cannot add full references because of the 8000-word space constraint. With a minor word improvement, this commit overall reduces the word count very slightly, by 9, according to pdftotext paper.pdf |wc paper.txt before and after the commit.
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@@ -201,7 +201,7 @@ As a consequence, before starting with the technical details it is important to
The core principle of Maneage is simple: science is defined by its method, not its result.
\citet{buckheit1995} summarize this nicely by noting that modern scientific papers are merely advertisements of a scholarship, the actual scholarship is the coding behind the analysis that ultimately generated the plots/results.
-Various solutions have been proposed for this since the early 1990s, for example RED (1992), Apache Taverna (2003), GenePattern (2004), Galaxy (2010), WINGS (2010), Image Processing On Line journal (IPOL, 2011), Active papers (2011), SHARE (2011), Verifiable Computational Result (2011), SOLE (2012), Sciunit (2015), Binder (2017), Popper (2017), WholeTale (2019), and many more.
+Many solutions have been proposed for this since the early 1990s, including: 1992: \href{https://sep.stanford.edu/doku.php?id=sep:research:reproducible}{RED}; 2003: \href{https://taverna.incubator.apache.org}{Apache Taverna}; 2004: \href{https://www.genepattern.org}{GenePattern}; 2010: \href{https://galaxyproject.org}{Galaxy}, \href{https://wings-workflows.org}{WINGS}; 2011: \href{https://www.ipol.im}{Image Processing On Line journal} (IPOL), \href{https://www.activepapers.org}{Active papers}, \href{https://is.ieis.tue.nl/staff/pvgorp/share}{SHARE}, \href{https://vcr.stanford.edu}{Verifiable Computational Result}; 2012: \href{https://osf.io/ns2m3}{SOLE}; 2015: \href{https://sciunit.run}{Sciunit}; 2017: \href{https://mybinder.org}{Binder}, \href{https://falsifiable.us}{Popper}; 2019: \href{https://wholetale.org}{WholeTale}.
To highlight the uniqueness of Maneage in this plethora of tools, a more elaborate list of principles are required:
\begin{enumerate}[label={\bf P\arabic*}]