Concept

BIOISIS is an open access database dedicated to the study of macromolecules by small angle X-ray and neutron scattering (SAXS and SANS). The project is supported by the Department of Energy Office of Science Integrated Diffraction Analysis Technologies, the National Cancer Institute Structural Cell Biology of DNA Repair Machines and the National Institute of General Medical Sciences project MINOS (Macromolecular INsights Optimized by Scattering).

BIOISIS aims to become the complete source for the deposition, distribution and maintenance of SAXS and SANS data and technologies.

Design

BIOISIS was built with the the Ruby on Rails framework (Rails 6.1) and the PostGres relational database. Its chief designer and architect is Robert P. Rambo, Ph. D., of the Lawrence Berkeley National Laboratory and Diamond Light Source. The need for a SAS database for biological sciences was pursued by John Tainer, Ph.D., of the Scripps Research Institute in La Jolla, CA., and Greg Hura, Ph.D., of the Lawrence Berkeley National Lab in Berkeley, CA.

The database is designed around the concept of an “experiment” that is a container for a set of datasets holding SAS data.



If we consider the fact that the structure of a macromolecule in solution is condition specific, then the data and models from a refined SAXS experiment will reflect a condition specific conformational state. Since SAXS experiments at synchrotron sources are highly efficient, a typical data collection at a synchrotron may sample several different experimental conditions, thus yielding measurements of different conformational states. This was an important realization incorporated into the design of BIOISIS.

In contrast, those structures obtained from X-ray crystallography often measure a single conformational state due to both the nature of crystallography and the use of cryogenic temperatures during the experiment. Deposits in BioISIS can be organized by conditions where several SAXS measurements (data files) can be organized into a dataset collection.


In addition to Ruby on Rails and PostgreSQL, BIOISIS utilizes the following opensource programs: