David Koes edited section_Discussion_begin_figure_centering__.tex  about 8 years ago

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}  \end{figure*}  We have cataloged \textbf{X} open-source packages for molecular modeling that provide a wide range of capabilities. As shown in Figure~\ref{licenses}, the most popular license (\textbf{X\%}) is some variant of the copyleft GNU Public License, which ensures that derivative works remain open source. Interestingly \textbf{X\%} \begin{figure}  \centering   \includegraphics[width=.5\linewidth]{../citedist}  \caption{\label{cites} Distribution  of the citations as reported by Google Scholar generated on average every year by those software  packages catalog have a corresponding, with  citeable publication which suggests that much of the software originates from academia. publications.}  \end{figure}  A substantial portion of the packages cataloged are under active development and see significant usage, as shown in Figure~\ref{pies}. We rated \textbf{X\%} of the packages as `A' level development, meaning major features or releases were made within the last 18 months, and \textbf{X\%} see substantial usage (rank 1).   We have cataloged \textbf{X} open-source packages for molecular modeling that provide a wide range of capabilities. As shown in Figure~\ref{licenses}, the most popular license (\textbf{X\%}) is some variant of the copyleft GNU Public License, which ensures that derivative works remain open source. Interestingly \textbf{X\%} of the packages catalog have a corresponding, citeable publication which suggests that much of the software originates from academia. The distribution of average citations generated a year (as reported by Google Scholar) for the citeable publications is shown in Figure~\ref{cites}. The majority of publications generate fewer than 10 citations a year, but about 10\% generate more than 50 a year.  A substantial portion of the packages cataloged are under active development and see significant usage, as shown in Figure~\ref{pies}. We rated \textbf{X\%} of the packages as `A' level development, meaning major features or releases were made within the last 18 months, and \textbf{X\%} see substantial usage (rank 1).  There a number of projects (\textbf{X\%}) where development has apparently ceased (no changes within the last 18 months). Note our methodology for identifying packages eliminates complete abondonware, so this is an underestimate. However, anecdotally although we did find instances where an open source package was referenced in a paper but was no longer available, we did not find this to be a common occurance. Most packages, even those that have remained unchanced for a decade, see some usage. In fact, a number of packages (\textbf{X}), still see significant usage despite having received no development for the past 18 months. This underlies the importance of releasing source code through a third-party site such as SourceForge or GitHub as it ensures the continued existence of a project. A major advantage of open source is that in cases where a popular project is not being actively developed (e.g. AutoDock Vina) new projects can fork the source code and continue development (e.g. smina).