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Softzymics has adopted Igor Pro 6, the leading technical computing program for Macintosh and Windows, to create a dedicated enzyme kinetics program–VisualEnzymics. Igor Pro 6 is a full powered technical computing environment with built-in nonlinear regression, 2D and 3D graphs of unlimited complexity, data tables, notebooks, layouts, drawing layer, customizable panels, and programmability.

Igor Pro 6 uses the metaphor of an experiment to combine these elements into a single file. VisualEnzymics is a standard Igor Pro 6 experiment file where all the enzyme kinetic equations and graphs are programmed for your convenience. All you have to do is enter your data and select your analysis.

Igor Pro 6 offers an impressive suite of capabilities that can handle the most demanding scientific data analysis problems, from complex graphing and image handling to multidimensional global fitting. VisualEnzymics utilizes many of these capabilities for analyzing enzyme kinetic data, and because VisualEnzymics was developed in Igor Pro 6, there is no limit to the future development of VisualEnzymics.

Tour some of the outstanding capabilities of Igor Pro 6 . . .


Igor Pro 6 Programming

Igor Pro 6 offers an integrated development environment that gives you the ability to create a custom interface in any experiment file. Any type of analysis that uses Igor Pro's built-in mathematical or graphing capabilities can be reduced to code, compiled, and saved for use by other scientists. Procedures can be written in Igor Pro's structured programming language, or, new  analysis panels an be created by adding control objects to a blank control panel. Igor Pro 6 automatically generates procedure code when panels and graph windows are closed. The code then can be viewed and modified in Igor Pro's Procedure Window. Igor Pro's extensive 2,489 page online manual documents all the commands, operations, mathematical functions, statistical functions, and control operations needed to build a complete interface.

For highly specialized computational needs, Igor Pro 6 can be linked to external code files created in C++. Igor Pro 6 also offers a special toolkit for instrument hardware control though  I/O boards.

Igor Pro 6 functionality and interface are identical on Macs and PCs. Experiment files are interchangeable and can be moved to any computer running Igor Pro 6.

Igor Pro 6 Nonlinear Regression

Igor Pro 6 offers built-in nonlinear regression to user defined equations. The number of parameters and independent variables is virtually unlimited. Regression analysis automatically calculates the model curve, curve fit residuals, model confidence and predictions bands, and adds these to graphs of experimental data. Regression analysis also calculates the error estimates and confidence limits of the model parameters. Model parameters can be fixed or floated, models can be fit to subsets of the data, and various weighting factors can be added to the fitting process. User defined fitting functions can be arbitrarily complex, involving conditionals, loops, convolutions, or differential equations. Global analysis can be used to fit multiple data sets to one or more equations with linked parameters. Multi-dimensional data can be fit in up to four dimensions. Igor Pro 6 uses the Levenberg-Marquardt algorithm with least squares optimization, or can be set to optimize absolute differences for robust fitting.  For data with error in both the dependent and independent variables, Igor Pro 6 offers orthogonal distance regression. Also, fitting functions can be minimized by simulated annealing to find global minima.

Igor Pro 6 meets the most demanding needs for data analysis.


Igor Pro 6 Graphing

Igor Pro 6's internal data structures are highly optimized for mathematical analysis and display of 2D and 3D matrix type data. In 2D space, Igor offers highly customizable X-Y plots, contour plots, image plots, and category plots, and in 3D space offers 3D scatter plots, volume plots, isosurfaces, voxelgrams, object plots, and volume slices. Igor provides the user with complete control over all plot elements so that plots can be customized in unlimited ways. Graphs also have a drawing layer where custom shapes and objects can be drawn and added to graphs. Any type of imported image also may be added to graphs.  Graph annotations include symbol tags, text boxes, and dynamic tags that change with data values. Graphs can be fine-tuned to meet the standards of any type of scientific publication. Multiple graphs can be combined in layout pages or can be exported to presentation programs and manuscripts. Graphs can be embedded in other graphs or in notebooks or in panels. Special commands can be used to slide graph contents in the graph window, or rotate live 3D volumes. Graph elements are fully programmable. Graphs display data changes instantaneously as users execute math calculations on data or manually change data points. Combine unlimited numbers of curves and axes on a graph, and create unlimited numbers of graphs in an experiment file.

Igor Pro 6 Layouts

Igor Pro 6 offers layout pages for creating combined images that can be exported to presentation programs and word processors. Layouts consist of a graphics layer and a drawing layer. The graphics layer can contain graphs, text, and tables. The drawing layer can contain objects created with a panel of drawing tools that includes lines and shapes with full control of colors, lines, and fills. Objects in the drawing layer can be grouped, aligned, distributed, and layered on top of other objects. Precision placement can be achieved with grid coordinates that are displayed in real time as objects are moved in the layout. Layouts can be tinted to highlight results. Images from other programs can be pasted into the graphics or drawing layer. The entire layout can be exported as an Enhanced Metafile, Bitmap, or PNG image. Layouts can be used as a template to illustrate the combined results from an experiment. When a new experiment has been performed, add the new data to a table, and the table and graph in the layout automatically update. Layouts can be saved in a macro format to recreate all the customized features of the layout. Macros can be modified and used in any Igor Pro 6 experiment to create similar layouts. Macro code can be linked to user created control panels to organize and manage layouts from a central control panel.


Igor Pro 6 Tables

Igor Pro 6 uses tables to manage all experimental data. The basic unit of data in Igor Pro 6 is a waveform, or wave. A wave can be a single number or a list of numbers. Waves can be created in one, two, three, and four dimensions, where each dimension corresponds to columns, layers, and chunks of data. The numbers in a wave are displayed in tables as a column of numbers. The numbers can be edited in the table, or can be modified as a result of mathematical functions that perform calculations on wave data. All graphs that display wave data are instantly updated as the waves are changed. Tables can be formatted in all available colors, fonts, and type sizes. Popup menus in tables can be used to format wave data as integers, scientific numbers, date and time, or hexadecimal numbers. Popup menus also can be used to add and delete data, browse waves, redimension waves, and rename waves. Tables can be inserted as sub-windows into panels and graphs, or added to layouts are table objects. Tables can be saved in macro format to recreate tables with custom formatting. Table macros can be transferred to other Igor Pro 6 experiments to create similar table formatting.

Igor Pro 6 Notebooks

Igor Pro 6 offers a special document editor that is implemented as a Notebook window. Each experiment can have one or more Notebooks to describe the work done in the experiment. A Notebook window is similar to a word processor in that it provides the user a way to write and format text in a document window. However, the document window also can contain graphs and tables from the experiment, or any type of image that can be copied and pasted from other programs into Igor Pro 6. Images pasted into Notebooks can be converted to PNG format for high quality display on monitors and in print. Embedded objects can be updated to reflect current data in the Igor experiment. Special link commands in the Notebook text allow computational functions to be executed by clicking on the text. Notebook files can be saved as part of Igor Pro 6 experiments, or can be saved as separate files in TXT, HTM, or RTF formats. Notebooks also can be programmed in Igor Pro's compiled language. This gives the user the ability to format computational results in procedure code and generate formatted text as output from calculations. Notebooks also can be time stamped to document experiments. In addition, Notebooks can be used to create Help files to explain the purpose of an experiment and how the experiment analyzes the data. Specially created Help files are searchable in Igor Pro's Help window.


Igor Pro 6 Panels

Igor Pro 6 offers custom control panels to speed development of unique applications for distribution to other scientists. Blank control panels can be added to any experiment and then programmed by adding various types of standard controls. The available controls in Igor Pro 6 include buttons, checkboxes, popup menus, value displays, set variable displays, tab groups, title boxes, group boxes, sliders, and list boxes. Each type of built-in control has its own associated data structure and event status. Control objects can be defined in control dialog windows, or can be programmed in code. When panel windows are closed, Igor Pro 6 automatically generates all the necessary code to recreate the panel.  Panels also can contain graphs, tables, and images. Highly functionalized control panels can be created to accept user input for complex calculations or to control the display of graphs and data. Igor Pro 6 comes with numerous example experiments to illustrate the use of control panels and individual controls.

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