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

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].