Biology, physics and interactive computing researchers are collaborating to design and build a system that creates a standard process in acquiring and analyzing network data in the biological sciences while creating flexibility for end-users through a new software interface.
The Institute for Data and High Performance Computing is funding the seed project to enable the researchers to develop a proof-of-concept for the database system to store, analyze and describe data collected from 2D and 3D imaging of biological network structures. Researchers say the system will have the potential to fill a need for expanded data management requirements for large-scale biological data on sponsored research.
The current project will focus on two distinct biological systems for the initial datasets - plant roots and ant colonies in soil.
“These two systems share common methodological challenges and technological means of observation,” says Joshua Weitz, principal investigator and associate professor in the School of Biology. “Both plant roots and ant colonies are complex 3D networks that develop below ground and both can be observed using imaging technology in artificial and real soils.”
Weitz and co-PI Daniel Goldman, associate professor in the School of Physics, are actively researching the structure, function and dynamics of plant roots and ant colonies, respectively. They have identified that both systems lack a framework for acquiring, organizing, analyzing, visualizing and disseminating image data and identified spatial networks.
The development of an integrated database application to analyze the spatial networks in biology, which relates to an organism’s environment, is expected to enhance the pace of discovery and the reproducibility of results when the system is deployed. The researchers say that the two selected biological systems will ensure that the integrated system is truly cross-cutting in its ability to handle heterogeneous data from various sources and in various data representations.
The Georgia Tech project will facilitate key steps toward a common framework for the integrated analysis of spatial networks in biology. Weitz’s group collaborates with plant biologists to characterize root system structures of crop plants grown in “artificial soil” and of crop plants grown in natural environments. Goldman’s group will look at how the physical interaction of insects with their building materials influences nest structure.
Co-PI Alexander Bucksch, postdoctoral scientist in the School of Interactive Computing, will apply his experience on the project in analysis of large-scale networks in the plant sciences. Abhiram Das, Ph.D. candidate in Bioinformatics, is being funded through the IDH seed grant and is involved with the database development. The database application eventually will be available for other research problems.