Software Engineering (SE) Core
Overview
The SE Core (Director, Dr. Wayne Hubbell; Staff, Dr. Christian Altenbach) provides custom software and consulting services for computer instrument control and advanced data analysis (including image analysis) where commercial off the shelf solutions don’t exist.
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Dr. Christian Altenbach has 4+ decades of programming experience but has specialized in LabVIEW since 1996. He is a “Certified LabVIEW developer “(CLD) and is recognized by National Instruments as a “LabVIEW Champion” (founding member) and has presented seven times at their annual conference about advanced programming topics.
He has interfaced many instruments for computer control, including a vintage Varian Electron Paramagnetic Resonance (EPR) spectrometer and a high-pressure jump system that includes real-time data analysis. He has hands-on experience with interfacing PCI cards, USB devices, and programming embedded solutions and Field Programmable Gate Arrays (FPGA). Many of his data analysis programs are used by labs worldwide. They include full-featured simulation and fitting of EPR spectra of spin labeled macromolecules and analysis of Double Electron-Electron Resonance (DEER) data of doubly-spin labeled macromolecules in terms of inter-spin distance probability distributions.
In an academic environment, turnkey solutions are rare and ideally students should also learn to write their own programs, a valuable skill for many career paths. Dr. Altenbach can provide introductory LabVIEW courses, organize LabVIEW user groups, and provide personal guidance in program architecture and performance optimization.
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Two Examples of Analysis Software
MultiComponent: Fitting of multicomponent first derivative EPR spectra
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Software features
- Up to four spectral components, each with multiple parameters.
- Flexible parameter assignment. Any parameter can be held fixed or be fittable.
- Parameters (fixed or fittable) can be shared by multiple components if desired.
- Choice of fitting algorithm (Levenberg-Marquardt, Nelder-Mead, Monte Carlo, etc.).
- All fitting algorithms are tunable. Default tuning parameters are optimized.
- Spectral weighting to emphasize or disregard spectral regions.
- Real-time display of fitting progress
- Fitting can be interrupted at any time.
- Reads ASCII, ELEXSYS, EMX data files.
- Significant performance enhancement due to parallelization, caching and algorithm tuning.
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LongDistances: Determination of distance distributions based on magnetic dipole interaction between pairs of spin labels in a macromolecule. The raw data is derived from DEER spectroscopy, a pulsed EPR experiment.
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Software features
- Full interactive control over all aspects of fitting
- Automatic or interactive zero point determination (infinite resolution)
- Automatic or interactive background determination using Tikhonov regularization as criterion.
- Non-negative Tikhonov regularization (default) or plain Tikhonov regularization
- Choice of background models (1D, 2D, 3D, variable-D, linear, quadratic, none.)
- Interactive data preparation (trimming, phase)
- Automatic or interactive phase correction or fitting of phase independent magnitude data.
- Extremely fast algorithms (e.g. calculation of a new kernel matrix in sub-milliseconds).
- Model-free fitting (direct Tikhonov regularization for preview, highly optimized refinement on demand, optional background co-fitting)
- Model based fitting (up to 6 lineshape components with full control over all shape parameters)
- Co-fitting of background.
- Optimization and automatic determination of optimal regularization parameter.
- Optional excitation bandwidth correction (simulation and analysis)
- Error analysis and confidence bounds.
- Data browser with preview feature.
- Built-in simulation feature to generate any imaginable simulated data for algorithm validation.
- Simulation can realistically expose the inherent limitation of the method
- Highly parallel algorithms with full support for multiple CPU cores.
- Rich full-page print output with full documentation of all aspects of the analysis and settings.
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Two Examples of Instrument Control Software and Hardware
Telocin: Varian EPR spectrometer control (Based on embedded hardware).
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Software features
- Scan magnetic field & record EPR signal
- Signal averaging
- Integration, spectra comparison, metrics
- Save & load
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P-jump: Software to control a hydrostatic pressure generator (HUB 440 and HUB 880 from Pressure Biosciences) and provide for a rapid (ms) pressure jump.
Pressure dependent conformational changes in proteins reveal important structural and thermodynamic properties. Pressure jump studies reveal the time course as the protein adapts to the new state.
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Software features
- Control the operation of valves and the pressure generator, read pressures (up to 100,000 psi) and current state of the system
- Record time dependent EPR signal
- Jump from any pressure to any other pressure in about 1ms
- Signal averaging of multiple jumps, including automatic correction for valve jitter
- Instant exponential fitting in real time during acquisition.
- Save & load
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