Jupyter Notebooks are extensively used in research and education. We recently organized a workshop at UC San Diego and invited students, postdocs, research scientists, and faculty to share experiences and identify challenges of using Jupyter notebooks. The workshop covered the use of Jupyter in many disciplines, ranging from Astrophysics, Bioinformatics, Datascience, Genomics, Medicine, to Structural Bioinformatics, as well as classroom use with hundreds of students and publication of reproducible science. Here we present a summary of our findings in the form of guidelines.
We’d like to hear attendees’ experiences and challenges to expand and refine the guidelines. We hope to capture best practices during JupyterCon to help guide both authors of notebooks as well as the evolution of the Jupyter environment to address challenges in reproducible research.
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