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Current computational notebooks, such as Jupyter, are a popular tool for data science and analysis. However, they use a 1D list structure for cells that introduces and exacerbates user issues, such as messiness, tedious navigation, inefficient use of large screen space, performance of non-linear analyses, and presentation of non-linear narratives. To ameliorate these issues, we designed a prototype extension for Jupyter Notebooks that enables 2D organization of computational notebook cells into multiple columns. In this paper, we present two evaluative studies to determine whether such “2D computational notebooks” provide advantages over the current computational notebook structure. From these studies, we found empirical evidence that our multi-olumn 2D computational notebooks provide enhanced efficiency and usability. We also gathered design feedback which may inform future works. Overall, the prototype was positively received, with some users expressing a clear preference for 2D computational notebooks even at this early stage of development.
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PyRosetta Jupyter Notebooks Teach Biomolecular Structure Prediction and Design
ABSTRACT Biomolecular structure drives function, and computational capabilities have progressed such that the prediction and computational design of biomolecular structures is increasingly feasible. Because computational biophysics attracts students from many different backgrounds and with different levels of resources, teaching the subject can be challenging. One strategy to teach diverse learners is with interactive multimedia material that promotes self-paced, active learning. We have created a hands-on education strategy with a set of 16 modules that teach topics in biomolecular structure and design, from fundamentals of conformational sampling and energy evaluation to applications, such as protein docking, antibody design, and RNA structure prediction. Our modules are based on PyRosetta, a Python library that encapsulates all computational modules and methods in the Rosetta software package. The workshop-style modules are implemented as Jupyter Notebooks that can be executed in the Google Colaboratory, allowing learners access with just a Web browser. The digital format of Jupyter Notebooks allows us to embed images, molecular visualization movies, and interactive coding exercises. This multimodal approach may better reach students from different disciplines and experience levels, as well as attract more researchers from smaller labs and cognate backgrounds to leverage PyRosetta in science and engineering research. All materials are freely available at https://github.com/RosettaCommons/PyRosetta.notebooks.
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- Award ID(s):
- 1740549
- PAR ID:
- 10311400
- Author(s) / Creator(s):
- ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; more »
- Date Published:
- Journal Name:
- The Biophysicist
- Volume:
- 2
- Issue:
- 1
- ISSN:
- 2578-6970
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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- Free Publicly Accessible Full Text
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Accepted Manuscript1.0
- Journal Article:
- https://doi.org/10.35459/tbp.2019.000147
