Grand Unification of Physics and Informatics for Genomics: GUPIs for Genomics

Thomas Bishop (LaTech, Ruston)

Mar 17. 2020, 14:30 -- 15:10

Genomics is a physics based material science and an informatics based  biological science. Historically, these two scientific approaches developed independent of one another.The experimental techniques, computational tools and theoretical methods differ significantly between the two scientific approaches. Genomicists are thus often forced to choose one approach or the other. Here we describe a framework and demonstration a web application for unifying physical and informatics data obtained
from theory, experiment and/or computation. The framework is based on representations of DNA or chromatin as oriented space curves. The representations include an internal coordinate reference frame using generalized base pair step parameters and a laboratory reference frame representation in Cartesian coordinations.  Transformations between representations requires a differentiation or integration. Peicewise application of the transformations provides a mechanism for multiscale modeling that spans from continuum to mesoscales. Numerical implementations are sufficiently fast and accurate to support all atom or coarse grained models of chromatin folding from base pairs to whole chromosomes as an interactive web application that unifies physical and informatics data in a genome  dashboard format. Like an automobile dashboard, genome dashboards provide displays and controllers for manipulating data that is inherently both multidimensional and multiscale and for navigating complex landscapes. Genome navigators can develop and test new hypotheses or engage autopilots for unsupervised learning and validation tests.

 

Further Information
Where:
ESI Boltzmann Lecture Hall
Associated Event:
Chromatin Modeling: Integrating Mathematics, Physics, and Computation for Advances in Biology and Medicine (Thematic Programme)
Organizer(s):
Christos Likos (U Vienna)
Stephanie Portillo (NYU, New York)
Tamar Schlick (NYU, New York)