UltraScan data analysis
The UltraScan platform (Demeler 2008) provides an ideal open source environment for further development of the Open AUC Project. It is based on platform independent and portable development tools and open source programming languages (Qt, qwt, qwtplot3d, GNU C/C++, Perl, PHP, HTML, MySQL). UltraScan has been placed under Subversion (http://subversion.tigris.org) version control, providing support for multi-user development and branching. A Trac bug tracking system and WiKi (http://trac.edgewall.org) is used to manage development goals and user feedback via a ticketing system (http://wiki.bcf.uthscsa.edu/ultrascan/). UltraScan has been successfully ported to Windows (Windows 2000, NT4, XP, Vista), Linux/X11 (all hardware platforms), Macintosh OS-X and Darwin/X11 (Intel and G3/G4), Sun Solaris (7–10), SGI Irix (6.4 and higher), Open-, Net-, and Free-BSD, as well as other X11-based Unix versions.
UltraScan itself consists of an extensible C++ class library and a Qt-based multi-threaded graphical user interface (GUI) with independent binaries linking to the UltraScan class library. This system has proven to be the best arrangement to guarantee optimal memory management and robustness. Should multiple modules be running and one of them encounters a fatal error, all other open modules are unaffected and will continue to function normally. The library offers classes for many popular data analysis methods such as van Holde–Weischet (Demeler and van Holde 2004), dc/dt (Stafford 1992), second moment (van Holde 1985; Demeler 2005), c(s) (Schuck 2000), nonlinear and linear least squares optimization (Demeler and Saber 1998), modeling of ASTFEM solutions of the Lamm equation (Cao and Demeler 2005, 2008) by two-dimensional spectrum analysis (Brookes et al. 2006, 2009), by genetic algorithm optimization (Brookes and Demeler 2006, 2007), and by Monte Carlo analysis (Demeler and Brookes 2008).
We propose a binary data standard for all experimental AUC data that replaces the currently used inefficient ASCII storage. An intrinsic absorbance spectrum can be derived by globally fitting wavelength scans taken at multiple concentrations. The spectra can be used as basis functions in the spectral decomposition fitting of spectra from mixtures (Demeler 2005). UltraScan further offers a complete data editing environment for absorbance, intensity, fluorescence, Rayleigh interference, and multiwavelength absorbance velocity and equilibrium data, and contains a module for import of legacy data and for conversion of binary formatted experimental data back to the legacy ASCII format. Intensity data can be converted to pseudo-absorbance data and corrected for time invariant noise contributions with the two-dimensional spectrum analysis.
A toolkit for visualization provides comprehensive two-dimensional and three-dimensional visualization capabilities. A reporting mechanism dynamically generates HTML reports from an experiment for all analyses performed by the user. Hydrodynamic correction routines automatically adjust hydrodynamic data for standard conditions by calculating buffer densities and viscosities from user-supplied composition, as well as estimating partial specific volumes from protein sequence data.
A wide range of simulation modules assist the user in the design of experiments and modeling of experimental results. Multi-speed velocity and equilibrium experiments can be simulated with arbitrary precision, and for arbitrary models involving reversible self- and hetero-associating reactions. Kinetic rate constants can be defined to simulate the reaction kinetics. A new bead modeling program, US-SOMO (based on SOlution MOdeler, Rai et al. 2005), facilitates rigid body modeling of NMR and X-ray crystallography structures (described below).