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Table 1 A summary of tools and standards for reproducible computational biology

From: Where next for the reproducibility agenda in computational biology?

Area/activity Tools and standards
Umbrella projects for guidelines and standards MIBBI [11], COMBINE [45]
Training GOBLET [34, 35], Software Carpentry [8, 76, 77], Data Carpentry [78]
Data exchange and analysis PSI-MI [12, 13], BioPAX [14, 15]
Model exchange and annotation MIRIAM [43], COMBINE standards [45] e.g. SBML [46]
Simulation experiments MIASE [44], SED-ML [47]
Notebooks Jupyter [57, 58], Mathematica [59], knitr [60], Sweave [61].