AUC Data Acquisition and Control Software
AU-AOS and FDS
The Analytical Ultracentrifuge Advanced Operating system (AU-AOS) is the control software for the Analytical Ultracentrifuge Fluorescence detection system (AU-FDS). The AU-FDS accessory for the Beckman XL-A / XL-I instruments compliments the existing detectors. Fluorescence excitation is at 488 nm, and light emission in the wavelength range of 505 to 565 nm are detected. These characteristics make the AU-FDS suitable for use with extrinsic dyes (fluorescein, Alexa488, Oregon Green) and with Green Fluorescent Protein. The resulting optical system has excellent sensitivity (100 pM fluorescein) and discrimination. The FDS works as an add-on to existing Beckman analytical ultracentrifuges, old or new. The original Beckman instrument operation is not affected. The AU-FDS utilizes confocal optics to track the location of fluorophores. High-speed electronics measure the entire rotor rotation, allowing all samples to be measured simultaneously.
For more information on either the AU-AOS or the AU-FDS: http://www.avivbiomedical.com/aufds.php
AUC Analysis Software
SEDANAL is software package for sedimentation velocity or equilibrium data analysis that can handle any arbitrary reaction scheme with up to 28 components and/or 28 species related by up to 27 chemical reactions. Both isodesmic and isoenthalpic indefinite self-associations may be fit. A Model Editor program is used to maintain a small database of models that are used by the main SEDANAL fitting program. Two other programs have been included within SEDANAL: 1) DCDT, for the model independent analysis of sedimentation velocity data and, 2) BIOSPIN, for the model independent analysis of sedimentation equilibrium data. SEDANAL is distributed for free.
For more information: http://www.rasmb.bbri.org/sedanal.html
UltraScan is a comprehensive data analysis software package for hydrodynamic data from analytical ultracentrifugation experiments. The software features an integrated data editing and analysis environment. UltraScan provides the highest possible resolution for sedimentation velocity experiments using high-performance computing modules for 2-dimensional spectrum analysis, genetic algorithm, and for Monte Carlo analysis. A database is integrated for data management, and the UltraScan LIMS system provides web-based access to the database and supercomputing functionality. Supercomputing resources are provided through a NSF Teragrid Science Gateway. UltraScan and the LIMS are distributed free of charge for research use.
For more information: http://ultrascan.uthscsa.edu/index.php
Sednterp is a general purpose tool for the interpretation of sedimentation equilibrium and sedimentation velocity data. It collects many diverse functions into a single program. Sednterp is useful both for computing molecular structural estimates from experimental data and for interpolating physical parameters of common buffers used in sedimentation experiments. An extensive help file describes both how to use the program, and provides an extensive review of how the results are calculated. The newest version of Sednterp allows new data tables, new calculations and new graphs to be added as modules that may distributed to other users. Sednterp is free, and may be downloaded from: http://www.rasmb.bbri.org/software/windows/sednterp-philo/
For the analysis of sedimentation velocity, dynamic light scattering, and sedimentation equilibrium data. It has a variety of models for the analysis with discrete species and size-distributions, including ls-g*(s), c(s), c(M), and c(s, ff0), and their specialized variants. It has extensive set of rigorous statistical tools, including regularization and Bayesian analysis that allow tailoring the analysis to the specfic prior knowledge available about the studied macromolecules. A large number of calculator and tool-box functions are available for experimental planning and data analysis. High-quality plotting interfaces are available through MATLAB and GUSSI.
SEDFIT User Group (~ 400 members as of 2011): https://list.nih.gov/cgi-bin/wa.exe?SUBED1=SEDFIT-L&A=1
Information on annual Workshops at NIH and overseas locations: https://sedfitsedphat.nibib.nih.gov/workshop/default.aspx
A platform for multi-method and global analysis of interacting systems by a variety of biophysical solution methods, including analytical ultracentrifugation, isothermal titration microcalorimetry, fluorescence and other spectroscopy, dynamic light scattering, and surface binding with biosensors. Different reaction schemes for self-associations, two components, and three component interacting systems are available, many expressed in various forms to efficiently express cooperativity factors. For sedimentation velocity, a variety of generalizations of c(s) are available, among others multi-signal sedimentation velocity, and density contrast sedimentation velocity. For interacting system in sedimentation velocity, SEDPHAT offers fast Lamm equation solutions, effective particle models, and multiple experimental planning tools. Sedimentation equilibrium analyses can be performed with multi-speed, multi-signal, and soft mass conservation approaches. ITC analyses are implemented for global analysis of binary or ternary titrations in multiple orientations, with a variety of interaction models, including temperature-dependent, ligand-linked, and protonation-linked binding. Advanced statistical analysis and fitting tools are implemented.
SEDPHAT Users group: https://list.nih.gov/cgi-bin/wa.exe?A0=SEDPHAT-L