Visualize it:  biochemistry games for building skills and making scientific contributions

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Presented at: 

Sequencing Finishing and Analysis in the Future, Santa Fe NM, May. 2018 ​Association for Biomolecular Resource Facilities (ABRF), Myrtle Beach, SC Apr. 2018

Abstract: 

Todd M. Smith, Sandra G. Porter, Digital World Biology, LLC, Seattle, WA

The wide application of DNA sequencing has made it possible to identify numerous missense mutations.  While it is possible to assign functional consequence to small numbers of changes, understanding why a given change has impact in ways that the can broadly understand is much harder.  This level of translation requires either an in-depth understanding of biochemistry or access to a knowledgebase containing this kind of information. Thus far, neither exist. If we can teach students how to predict the effects of mutations, they could participate in building that knowledgebase to increase the number and quality of variant annotations, and also improve how clinicians, patients, and the biotech community understand the molecular basis of genetic change.

Achieving the above goal requires three innovations. First, we need to develop students’ skills so that they can make informed and realistic predictions about how a mutation can affect protein function. This kind of understanding requires that students know their amino acids, amino acid functional groups, and chemical interactions between amino acids. Second, data structures that link genomic data, stored in many databases, to protein sequences and structures are needed. Third, new software that allows one to view several layers of information in a common interface is needed to enable hypotheses and annotations. This interface must allow for commenting and be able to save data in structured ways to build the database.

Digital World Biology is investigating solutions to enable student (and citizen scientist) annotation through the development of games to improve student’s foundational knowledge about amino acid and protein biochemistry.  The Company’s Molecule World structure viewing app is being extended to support visualization and annotation support. And, the necessary data structures are being prototyped to enable database development. Preliminary progress and ideas will be presented for comment. Expect to play some games and learn some biochemistry. 

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