ReproZip Packing Experiments for Sharing and Publication Fernando Chirigati, Juliana Freire | NYU-Poly Dennis Shasha | NYU.

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Presentation transcript:

ReproZip Packing Experiments for Sharing and Publication Fernando Chirigati, Juliana Freire | NYU-Poly Dennis Shasha | NYU

Motivation Published articles are not made reproducible Computational reproducibility may be difficult to achieve Some current solutions require the user to adopt a system o GenePattern [1], Madagascar [2], Scientific Workflow Systems [3] Other solutions rely on capturing information about the computational environment o Virtual Machines o CDE [4] Author How to encapsulate my experiment? Too many dependencies… Too many files to keep track… Sigh. Reviewers Collaborators How to compile this program? How to execute it? How to explore it? Sigh. ReproZip: Packing Experiments for Sharing and Publication Fernando Chirigati – NYU-Poly

ReproZip ReproZip is a packaging solution o It makes it easier for authors to pack experiments and for reviewers to verify computational results It creates reproducible packages from existing experiments on computational environment E o No need to port experiments to other system o Leverages provenance of computational results It unpacks an experiment on computational environment E’ It generates a workflow specification that encapsulates the execution of the experiment o Eases the verification process o Allows users to explore the experiment, while keeping track of provenance ReproZip: Packing Experiments for Sharing and Publication Fernando Chirigati – NYU-Poly

Overview packing (on environment E) files + binaries + workflow Reproducible Package Workflow Provenance Tree Experiment unpacking (on environment E’) Reproducible Package Experiment Extraction files + binaries + workflow verification and exploration ReproZip: Packing Experiments for Sharing and Publication Fernando Chirigati – NYU-Poly

References 1.GenePattern. 2.Madagascar. 3.S. B. Davidson and J. Freire. Provenance and scientific workflows: challenges and opportunities. In SIGMOD, pages , P. Guo. CDE: A Tool for Creating Portable Experimental Software Packages. Computing in Science and Engineering, 14(4):32-35, SystemTap. 6.MongoDB.

Thank You! Fernando Chirigati