{"id":12170,"date":"2019-03-22T18:43:22","date_gmt":"2019-03-22T18:43:22","guid":{"rendered":"http:\/\/www.appservgrid.com\/paw92\/?p=12170"},"modified":"2019-03-22T18:43:22","modified_gmt":"2019-03-22T18:43:22","slug":"how-to-choose-the-best-open-source-software","status":"publish","type":"post","link":"https:\/\/www.appservgrid.com\/paw92\/index.php\/2019\/03\/22\/how-to-choose-the-best-open-source-software\/","title":{"rendered":"How to Choose the Best Open Source Software"},"content":{"rendered":"

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After reading the O\u2019Reilly book \u201cFoundations for Architecting Data Solutions<\/strong><\/a>\u201d, by Ted Malaska and Jonathan Seidman, I reflected on how I chose\u00a0software\/tools\/solutions\u00a0<\/strong>in the past and how I should choose them going forward.<\/p>\n

As a bioinformatician you need to be able to quickly discern whether a publication\/tool is really a major advancement or just marginally better. I\u2019m not just talking about the newest single-cell RNA-seq technique or\u00a0another file format<\/a>, but for every\u00a0problem\u00a0<\/strong>case you have. Whether that be data visualization tools,\u00a0presentation tools<\/a>, distributed storage systems\u00a0etc.<\/em><\/p>\n

It\u2019s not just about how useful the tool may be, it also depends on the quality of the documentation, how simple it is to install, where it sits in the open-source life cycle,\u00a0etc.<\/em><\/p>\n

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Xkcd is funny but competing standards aren\u2019t. Don\u2019t believe me? Just look at how many\u00a0pipeline tools<\/a>\u00a0exist!<\/p>\n

When faced with so many options how can one choose the solutions that fit their need?<\/p><\/blockquote>\n

Why open\u00a0source?<\/h3>\n

I\u2019ve worked with a few licensed software solutions in the past; for example,\u00a0BLAST2GO<\/a>\u00a0(plug: use dammit from Camille Scott instead!<\/a>),\u00a0Matlab<\/a>, and an image stitching software called\u00a0Autopano Giga<\/a>\u00a0(now defunct). One of my greatest frustrations was learning these tools only to later change roles and no longer have them available. As a consultant for the Department of Fisheries and Oceans the prohibitive cost of a Matlab was what pushed me over the edge into learning another high-level programming language\u200a\u2014\u200aR. FWIW:<\/p>\n

\u201c[Matlab] They obfuscate their source code in many cases, meaning bugs are much\u00a0harder to spot<\/a>\u00a0and impossible to\u00a0edit ourselves without risking court action<\/a>. Moreover, using Matlab for science results in\u00a0paywalling our code<\/a>. We are by definition making our computational science closed.\u201d\u200a\u2014\u200aexcerpt from\u00a0I Hate Matlab: How an IDE, a Language, and a Mentality Harm<\/strong><\/a><\/p><\/blockquote>\n

Most companies eschew third party solutions or build their product as a hybrid of proprietary and open-source to keep their costs lower. For example, Amazon Web Services (AWS) offers it\u2019s Simple Storage Service (Amazon S3) for a fee but is built upon open source software like Apache Hadoop. I\u2019m not saying\u00a0not\u00a0<\/em>to use AWS (or any other cloud provider) because sometimes you are constrained to\u00a0having\u00a0<\/em>to; I actually used AWS for a project (transcriptome assembly of a coral species<\/a>) with Docker. Currently I\u2019m working with sensitive information that must be kept on-site, under lock-and-key, so alternative solutions are used.<\/p>\n

Most of the newer big data platforms, and successful open-source projects began as internal projects at companies or universities for the first couple years before going through an external incubation phase. For example:<\/p>\n