Keywords:

DATA, DOMAIN, MEASUREMENT, BIOPHYSICAL, DISCOVERY, ANALYSIS, SCIENCE, BOX, GENOME,

Genomic Sciences

Digest:
...Biophysical Perspective Biophysics and the Genomic Sciences David C. Schwartz1,*
1Department of Chemistry, Laboratory of Genetics, Laboratory for Molecular and
Computational Genomics, University of Wisconsin-Madison, Madison Wisconsin ABSTRACT
It is now rare to find biological, or genetic investigations that do not rely on
the tools, data, and thinking drawn from the genomic sciences....
...In this perspective, I describe a path of how biophysical thinking greatly
contributed to this revolution in ways that parallel advancements in computer
science through discussion of several key inventions, described as ''foundational
devices.'' These discussions also point at the future of how biophysics and the
genomic sciences may become more finely integrated for empowering new measurement
paradigms for biological investigations....
...Considering genomic sciences as being the creation of or the analysis of large
data sets for biological or genetic investigation (a personal and loose
definition), it is evident that biophysical thinking has provided the cauldron for
a remarkable level of invention and innovation in the genomic sciences....
...Although a major factor differentiating biophysics from the genomic sciences is
the size and type of data sets, it was biophysical thinking that enfranchised
genomicists to make discoveries using large data sets through advancements in
molecular measurement and manipulation....
...The focus of this Biophysical Perspective is to follow a path of how biophysics
enabled such large-scale measurements (data sets) and how these genomic data sets
are now opening new directions for biophysical investigations....
...At that point in time, the genomic sciences and biophysics become one....
...An investigator may develop a hypothesis (idea) to be tested or validated
through physical measurements and analysis....
...Notably, these domains and their respective parts are portrayed here as
supporting highthroughput measurements, which become usable data sets for analysis
in ways that portend discovery or large-scale hypothesis generation and
validation....
...Given the scope of this undertaking, local measurement pipelines and analyses
were established at the participant sites, with high-level data integration and
analysis centralized at a data analysis center, complemented by a data coordination
center providing community access portals....
...Accordingly, we can envision separate versions of the discovery parts box
depicted in Fig....
...In other words, ENCODE did not centralize the ''physical'' domain (red box) of
the discovery schema so that a single, fully integrated workflow could perform all
of the necessary measurement processes; rather, it leveraged the intrinsic
advantages of data fungibility and portability for integrative analyses performed
across participants' findings and data sets....
...FIGURE 1 Dissecting the discovery science parts box: Experiments comprise five
interdependent domains indicated by colored boxes....
...Measurement outcomes are processed, creating data sets compiled within
databases....