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Fighting Galactic Misconceptions (FGB): Misconception 1

Is Galaxy only useful for genome scientists? Absolutely Not!

This is the first post in a series explaining why major misconceptions about Galaxy are, well, misconceptions. Galaxy does a lot of things and contains many components, making it difficult to quickly comprehend everything that it can do. It also evolves rapidly. As a result, there is a number of misconceptions about what it is and what can (or cannot) be done with it. To spread the ultimate knowledge across the Universe, we are starting the “Fighting Galactic Misconceptions (FGBs)” series. You might note that the word "Misconceptions" is abbreviated as "B" because misconceptions are generally Bullsh*t (yes, we were definitely inspired by a certain effort). This series identifies the most common misconceptions and explains why they are, simply put, BULLSH*T!

FGB1 : Galaxy is only useful for genome scientists ... But, all scientists have genomes, right?

While most scientists have genomes, Galaxy is most definitely NOT only useful to scientists who study them. Let’s do a little deconvolution. Who is a Genome Scientist anyway? It is an individual who believes that a magical input dataset, massaged by a bunch of tools holds answers to all mysteries of life in all its shapes and forms (here we pause to express our deep respect to protein researches as they have to deal with significantly higher number of alphanumeric characters). To establish if this belief has any merit a Genome Scientist uses an unwieldy array of tools (here the term “tool” is used to signify a useful software product; Note that not all software products are useful: remember Clippy?) to sequentially change formats of the files into a final “tab-delimited state”. This final tab-delimited state is occasionally used to generate informative graphs (see here for a review) but usually it is not necessary: typically the message is soooo clear that it is immediately published by certain highly respected publishers in nature and/or science fields.

Are these day-to-day sufferings of a genome scientist so very different from the hardship experienced by, say, a climate researcher, a particle physicist, a natural language processing specialist or any other scientist dealing with any data? Nope! You start with the data, feed it to some command line tool(s), study outputs, defend a Ph.D. dissertation, and repeat this all over again at the next career iteration.

Galaxy has nothing specific to genomics or, for that matter, to biological discipline. It can integrate ANY command line tool, ingest and process ANY type of data, and it can be used WITH or WITHOUT the graphical user interface. So if you integrate tools designed for processing of climate data and configure appropriate datatypes, you get a Climate Galaxy. Similarly you can get a Machine Learning Galaxy, a Computational Chemistry Galaxy, an Imaging Galaxy, a Proteomic Galaxy or any other Galaxy you need. So the notion that the Galaxy is only useful for genomic scientists is ... bullsh*t.