IPRO 313

1

IPRO 313 Development and
Documentation of INSANE, a Computational
Environment for the Analysis of Small Angle X-Ray
Scattering (SAXS) Data at BIOCAT
Illinois Institute of Technology, 3101 S.
Dearborn, Chicago, Illinois 60616
Documentation
Statement of Purpose
Experimental Setup
Software

The documentation was developed with the software
simultaneously. The documentation, initially,
was meant to serve as a guide for the programmers
writing the software. It was meant to serve as a
reference for them while they gained an
understanding of what functions the software is
supposed to perform. As the software developed,
the documentations role changed from that of a
guide for developers to that of a manual for end
users. In its final form the document will
serve as a reference for all users who wish to
implement the software in their research. As
such, it must incorporate the needs of all
individuals who will be using the software. This
includes both novice users and very experienced
users. The documentation will need to provide
for users with these varying needs. This brings
up the question of, How can we meet the needs of
both users in one document? Our answer was to
create a web-based document that has both
introductory information about SAXS and how to
use the INSANE software, as well as, more
advanced information about the algorithms and the
actual tasks being performed by the software. It
is our hope that this information will provide
users with all of the information necessary to
fully realize the potential of the INSANE
software package.
This project seeks to develop a user-friendly,
computational environment for rapid and
sophisticated analysis of small angle x-ray
scattering (SAXS) data at the BIOCAT beamline at
Argonne National Lab. As such, we have employed
the talents of two types of individuals. We have
a cadre of computer science and computer
engineers who are performing the actual software
engineering and we also have a team of biophysics
students who are attempting to create and
maintain an evolving documentation that will
benefit all end users of the software.
Camera
sample
X-ray
CCD
Beam stop
Scattered x-rays
Sample Image
Experimental Set-up at BIOCAT Experiments are
set up in a similar manner to the diagram. After
obtaining images with both short and long cameras
to obtain scatters of up to 15 degrees, the data
is analyzed using one of several data analysis
programs. It is at this point that the INSANE
software is implemented.
INSANE Software Package
Background Information
Small angle x-ray scattering (SAXS) allows for
low-resolution structural determination of
macromolecules in solution. Obtaining solution
structures is of great importance in biology
because many biologically important molecules are
unable to be crystallized, thus, they are not
available to the most common method for
structural determination, x-ray crystallography.
This method is also essential for comparisons
between crystalline and solution forms. When
structures are determined in solution physiologic
conditions can be emulated and the structures
obtained in these studies are very likely to be
homologous with the biologically active form of
the molecule. The problem associated with
obtaining solution scattering information is not
found in the acquisition of data, but in the
analysis. Software analysis programs vary widely
in the field due, in part, because of the needs
of the individuals doing the research vary but
also because there is no one program that allows
a user to easily analyze data. The INSANE
software package will read datafiles from the
Advanced Photon Source in the SMV format and
display the image, subtract the buffer images,
mask the data, and automatically find the center
of the scattering data as well as report the
diameter of the ring, statistics, and present a
one dimensional graph summarizing the data. The
Python programming language will be used for the
graphic user interface (GUI) because of its
availability on all platorms (Windows, Macintosh,
Unix and Linux) and compatibility with PGPlot
libraries. Processor intensive operations will be
coded in C and Python wrapper functions will be
written to integrate these into the GUI.This
software will streamline the tedious process of
analyzing SAXS images by hand and will keep the
data free of errors incurred from human
mistakes.  
Future
Acknowledgements
We would like to thank Dr. Tom Irving, Dr. Nick
Menhart, and Ahmed Mirza for demonstrating
various aspects of SAXS theory as well as
reviewing the documentation. We would also like
to thank Jaby Jacob for providing a demonstration
of IGOR-Pro.