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\subsection*{Advantages and Disadvantages of Open Source}  The value of open source software in cheminformatics and molecular modelling modeling  is somewhat controversial. Unsurprisingly, those affiliated with commercial scientific software argue that traditional commercial development, with its associated support and continuous  development, provides a superior value \cite{Krylov_2015}, while open source advocates feel the benefits outweigh the burdens \cite{Gezelter_2015,Jacob_2016}. Our goal is not to revisit these arguments. Instead, we assert that open source scientific software is a \textit{de facto} part of the scientific community community,  and so in this review we catalog those open source packages that fall within the domain of cheminformatics and molecular modeling. There are a few aspects of the open source software debate that we find particularly relevant. First, opponents are right to point out that free software is not free - users of open source software generally take on a much greater burden in supporting the software than with commercial software. This is one reason why it is important, when possible, to seek open source software that is under active development and supported by a broad community. Therefore, in this review we attempt to quantify the current level of development and usage of each package as an indirect measure of quality and usability. Second, the primary advantage of open source software is the ability to redistribute code without restriction. This inherently enables reproducibility and lets scientists ``stand on the shoulders of giants'' instead of reinventing the wheel. Consequently, in this review we limit ourselves to a survey of true open source software and exclude source-available software that may place restrictions on the publication of reproducible research results.