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A Quick Guide to Organizing Computational Biology Projects

Figure 1

Directory structure for a sample project.

Directory names are in large typeface, and filenames are in smaller typeface. Only a subset of the files are shown here. Note that the dates are formatted <year>-<month>-<day> so that they can be sorted in chronological order. The source code src/ms-analysis.c is compiled to create bin/ms-analysis and is documented in doc/ms-analysis.html. The README files in the data directories specify who downloaded the data files from what URL on what date. The driver script results/2009-01-15/runall automatically generates the three subdirectories split1, split2, and split3, corresponding to three cross-validation splits. The bin/parse-sqt.py script is called by both of the runall driver scripts.

Figure 1

doi: https://doi.org/10.1371/journal.pcbi.1000424.g001