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Reproducible Ad hoc analysis
After some time, Alice has a result she believes is important and will eventually form part of a paper, and she wants to make sure Carl can see exactly what she did. At this point she builds a set of R scripts which process the data though a series of steps. She stores the scrips in a GitHub repository associated with the project. She also uses a few bioinformatics tools from the command line of linux as part of her process. Now, she re-runs the analysis, this time recording what she did using Synapse provenance features to link all the files starting with raw data through all intermediate results and ending with a set of figures, vectors, and other output data. All this can be pushed up to Synapse as before, but now there is a graphical representation of her process available in Synapse that Carl can use to review her work.