SpectraLab SoftwareSpectraLab (SpLab) software package is
a universal tool for advanced data analysis in
(bio)chemical spectroscopy and kinetics. I wrote the core
of SpectraLab in 1988-1991 for an Apple-II computer
running under CP/M DOS. The MS-DOS version of SpectraLab
that incorporates spectral deconvolution and principal
component analysis functions was designed in 1992-1993.
Its general design and basic algorithms are described in (Davydov,
et al, 1995). Please, refer to the above publication
if you use the package in your work. Since then,
SpectraLab went through substantial re-design and,
finally, has been transferred to the Windows
platform.
The current version of the package is written with the use of Win32Forth and DelphiŪ (vers. 7). It runs under Windows XP and higher. The program is designed to manipulate a set of up to 132 spectra (or kinetic traces, or any other kind of two-dimensional data sets) simultaneously. It allows easy manipulations and mathematical operations with traces (add, subtract, divide, take a derivative, etc.). It also has utilities for smoothing, re-sampling (including interpolation), automatic baseline correction, and manual editing. The spectral analysis section of SpectraLab includes a multi-dimensional least-square fitting algorithm, which allows approximating a spectrum with a linear combination of spectral standards (spectral prototypes) and a polynomial function (to compensate for the turbidity component). In combination with a set of prototypical spectra of absorbance of the high-spin, the low-spin, and the P420 states of cytochromes P450 (which are included with the package for several different P450 species), it allows quantitative determination of the concentration of the respective states of the enzyme. The program also includes the Principal Component Analysis (PCA) engine, which is used in the global analysis of the spectral changes in the series of spectra obtained in titrations, kinetic experiments, etc. It allows for automatic correction of the changes in turbidity, the absorbance of the titrant, or fluctuation of the baseline during the experiment. In addition, the program incorporates non-linear least-square fitting routines (based on Marquardt and Nelder-Mead algorithms), which allow fitting of the data sets (including a global fitting of three-dimensional sets) to a number of predefined functions, such as Michaelis-Menten, Hill, or "Tight-Binding" equations, sum of exponents, second-order kinetics, etc. The package thus includes most of the mathematical tools needed in the routine work in biochemical spectroscopy and enzyme kinetics. While the program is menu-driven and self-explanatory, it also includes a powerful, Forth-based scripting language. Script-based control provides powerful means for automated data processing. It also allows the user to define new "words" (commands) that can be added to the SpectraLab vocabulary permanently (i.e., saved between the sessions), thus providing the user an opportunity to tailor the software for various specific applications.
The complete Help System, which includes a comprehensive SpectraLab Users Guide, a description of SpectraLab scripting language, and an introduction to Forth programming (which may be helpful in writing advanced scripts and automatizing data processing with SpectraLab), is now incorporated into the package. The SpectraLab User's guide is also available on this website. If you would like to browse it, you can follow this link:
.
The source code of the Win32Forth part of the package is now available at https://github.com/dmrdavyd/spectralab. The part of the code written in Delphi will follow soon. You can download the distributive of the latest version of SpectraLab through the download form provided at the bottom of this page. Please, fill in your name and e-mail address in this form - it will allow me to alert you about any possible bugs discovered in the program and inform you about the availability of updated versions.
To use the program, you need to create a new empty folder (like C:\SpectraLab or C:\Program Files\SpectraLab) and unpack the entire content of the downloaded ZIP archive into it. It will also create sub-folder \STANDARDS containing a collection of spectral standards used in spectral analysis. It includes the files with the (micromolar) extinction coefficients specific to cytochromes P450 3A4, 2B4, 2B6, P450BM-3, P450cam, P450eryF, and CYP261C1 (P450-SS9). You may also find there the spectral standards of P450 reductases - rat liver NADPH-P450 reductase (CPR) and the flavin domain of P450BM-3 (BMR). The main file of the package is SPLAB-MMX.EXE. You may start the program by double-clicking on it in Windows Explorer. You may also create a link to this file on your desktop.
Please, be aware that some anti-virus programs consider the executables of Win32Forth-written programs as potential malware and may black-list, quarantine, or even delete them. It is a persistent and well-known problem. The developers of Win32Forth software informed anti-virus companies about it repeatedly. It helps, but for a short time - the problem reappears. Be sure that it is a false alarm if you get a virus warning. If your anti-virus program says that there is an "unknown" or "generic" virus in SpectraLab found by "heuristics", you may decisively ignore the warning and add the program to the list of exceptions.
If you have any questions about the program and its use, please send me an e-mail, and I will gladly answer them. In addition, I will appreciate any comments, suggestions, and bug reports.
To download the package,
fill in your name and e-mail address in the form below and
click the "Download" button
The current version of the package is written with the use of Win32Forth and DelphiŪ (vers. 7). It runs under Windows XP and higher. The program is designed to manipulate a set of up to 132 spectra (or kinetic traces, or any other kind of two-dimensional data sets) simultaneously. It allows easy manipulations and mathematical operations with traces (add, subtract, divide, take a derivative, etc.). It also has utilities for smoothing, re-sampling (including interpolation), automatic baseline correction, and manual editing. The spectral analysis section of SpectraLab includes a multi-dimensional least-square fitting algorithm, which allows approximating a spectrum with a linear combination of spectral standards (spectral prototypes) and a polynomial function (to compensate for the turbidity component). In combination with a set of prototypical spectra of absorbance of the high-spin, the low-spin, and the P420 states of cytochromes P450 (which are included with the package for several different P450 species), it allows quantitative determination of the concentration of the respective states of the enzyme. The program also includes the Principal Component Analysis (PCA) engine, which is used in the global analysis of the spectral changes in the series of spectra obtained in titrations, kinetic experiments, etc. It allows for automatic correction of the changes in turbidity, the absorbance of the titrant, or fluctuation of the baseline during the experiment. In addition, the program incorporates non-linear least-square fitting routines (based on Marquardt and Nelder-Mead algorithms), which allow fitting of the data sets (including a global fitting of three-dimensional sets) to a number of predefined functions, such as Michaelis-Menten, Hill, or "Tight-Binding" equations, sum of exponents, second-order kinetics, etc. The package thus includes most of the mathematical tools needed in the routine work in biochemical spectroscopy and enzyme kinetics. While the program is menu-driven and self-explanatory, it also includes a powerful, Forth-based scripting language. Script-based control provides powerful means for automated data processing. It also allows the user to define new "words" (commands) that can be added to the SpectraLab vocabulary permanently (i.e., saved between the sessions), thus providing the user an opportunity to tailor the software for various specific applications.
The complete Help System, which includes a comprehensive SpectraLab Users Guide, a description of SpectraLab scripting language, and an introduction to Forth programming (which may be helpful in writing advanced scripts and automatizing data processing with SpectraLab), is now incorporated into the package. The SpectraLab User's guide is also available on this website. If you would like to browse it, you can follow this link:
The source code of the Win32Forth part of the package is now available at https://github.com/dmrdavyd/spectralab. The part of the code written in Delphi will follow soon. You can download the distributive of the latest version of SpectraLab through the download form provided at the bottom of this page. Please, fill in your name and e-mail address in this form - it will allow me to alert you about any possible bugs discovered in the program and inform you about the availability of updated versions.
To use the program, you need to create a new empty folder (like C:\SpectraLab or C:\Program Files\SpectraLab) and unpack the entire content of the downloaded ZIP archive into it. It will also create sub-folder \STANDARDS containing a collection of spectral standards used in spectral analysis. It includes the files with the (micromolar) extinction coefficients specific to cytochromes P450 3A4, 2B4, 2B6, P450BM-3, P450cam, P450eryF, and CYP261C1 (P450-SS9). You may also find there the spectral standards of P450 reductases - rat liver NADPH-P450 reductase (CPR) and the flavin domain of P450BM-3 (BMR). The main file of the package is SPLAB-MMX.EXE. You may start the program by double-clicking on it in Windows Explorer. You may also create a link to this file on your desktop.
Please, be aware that some anti-virus programs consider the executables of Win32Forth-written programs as potential malware and may black-list, quarantine, or even delete them. It is a persistent and well-known problem. The developers of Win32Forth software informed anti-virus companies about it repeatedly. It helps, but for a short time - the problem reappears. Be sure that it is a false alarm if you get a virus warning. If your anti-virus program says that there is an "unknown" or "generic" virus in SpectraLab found by "heuristics", you may decisively ignore the warning and add the program to the list of exceptions.
If you have any questions about the program and its use, please send me an e-mail, and I will gladly answer them. In addition, I will appreciate any comments, suggestions, and bug reports.
To download the package,
fill in your name and e-mail address in the form below and
click the "Download" button