Science Gateways

XSEDE creates Science Gateways, customized portals granting members access to HPC applications, workflows, shared data and other services. XSEDE Gateways unite communities of like-minded members, whether united by discipline or other criteria. Please visit the XSEDE website for more on the following topics:

High-Resolution Modeling of Hydrodynamic Experiments with UltraScan

PI
Borries Demeler
Field of Science
Biophysics
Relevant Link(s)
Portal Homepage
Additional Contact(s)
Borries Demeler Emre Brookes Gary Gorbet

Description: This XSEDE portal provides access to the high performance computing back-end of UltraScan (http://www.ultrascan.uthscsa.edu) which is used to analyze analytical ultracentrifugation experiments by high-resolution methods. Users can request an individual database to analyze sedimentation velocity data from their instruments. Training workshop and seminars are available on a continuing basis. Contact demeler@biochem.uthscsa.edu for more information.

The objective of the research addressed by this portal is the hydrodynamic study of biological macromolecules and synthetic polymers by high-resolution modeling of analytical ultracentrifugation (AUC) experiments. Such experiments provide insight into the properties of biological macromolecules, and permit the investigation of structure-function relationships of biological systems implicated in many diseases, including cancer. Biological macromolecules with medical relevance as well as nanoparticles, polymers and colloids can be analyzed using novel high-resolution analysis methods that rely on high-performance computing. The Center for Analytical Ultracentrifugation of Macromolecular Assemblies at the University of Texas Health Science Center at San Antonio (UTHSCSA) has implemented a web-based front end to this portal to provide the necessary computational infrastructure for data analysis. This portal also functions to provide users of the UltraScan data analysis software access to XSEDE resources. UltraScan is a package for the analysis of analytical ultracentrifugation experiments (http://www.ultrascan.uthscsa.edu) using high-performance computational resource from XSEDE to support high-resolution analysis of experimental data. Users can fit their experiments using a 2-dimensional spectrum analysis, genetic algorithm optimization, and Monte Carlo analysis to obtain superior detail and also to process systematic noise components in the data. The XSEDE portal functions in conjunction with the UltraScan software and the UltraScan Laboratory Information Management System (USLIMS) hosted at UTHSCSA (Dept. of Biochemistry, Bioinformatics Core Facility). The USLIMS is based on a MySQL database with storage resources where users can store their experimental data and ancillary data required for analysis.