OpenWorm is an attempt to build a biophysical simulation of the model organism C. elegans via assimilation of published data from a range of sources. Publication of biological data is often weakly structured and has no standardised format making assimilation challenging. Currently PyOpenWorm acts as a quick data access layer for researchers to query C. elegans anatomy and physiology. It currently incorporates data from the primary literature, WormAtlas and WormBase. This project would aim to expand the data available for model validation and for query in PyOpenWorm. Expanding the data available would aid hypothesis generation in the C.elegans research community, by allowing fast access to past observations and by facilitating the generation of more robust models through model validation tests such as SciUnit. However, ultimately it could also be a poster child to inspire an increase in standardisation and statistical accountability in the publication of biological research as a whole. As an additional project, we will start work to create "Standard Worm" which will enable researchers to compare variability in experimental worms to a standard reference space.

Organization

Student

Emily Thomas

Mentors

  • Stephen Larson
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2019