Revision 26 - (view) (annotate) - [select for diffs]
Modified Fri May 14 22:36:12 2010 UTC (9 years, 9 months ago) by clausted
File length: 2695 byte(s)
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Added mass-transport limitation model simple1to1_mtl.

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Modified Wed Apr 28 01:00:17 2010 UTC (9 years, 9 months ago) by clausted
File length: 2656 byte(s)
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Added copyinterval() to cal_module.  This cuts out a slice of SPR data between two timepoints and puts it in a new ba object.  

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Modified Tue Apr 27 07:18:13 2010 UTC (9 years, 9 months ago) by clausted
File length: 2585 byte(s)
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The new module osprai_one provides access to the important functions in all of the other modules.  Documentation has been started with osprai_one.html.

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Modified Mon Apr 26 21:59:45 2010 UTC (9 years, 9 months ago) by clausted
File length: 2701 byte(s)
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Added clma(), a constrained LMA fitting function.  We can now set a lower and upper bound for fitting.  Be sure that the initial estimate is between, not at, the bounds.  It transforms the parameters using x1 = ((b-a)*tanh(x0)+b+a)/2 for the interval (a,b).  

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Modified Fri Apr 23 01:45:38 2010 UTC (9 years, 10 months ago) by clausted
File length: 2702 byte(s)
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Introduction of the fit_module.  This provides ordinary Levenberg-Marquart curvefitting.  The user can choose which model parameters are fixed and which are allowed to float.  Next, we can add a constrained version.

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Modified Wed Apr 14 00:40:11 2010 UTC (9 years, 10 months ago) by clausted
File length: 1320 byte(s)
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Added features to select time points for measuring binding responses and to output that data to a file or scatterplot.  Added the background subtraction feature to cal_module.  Also a few bug fixes. --CGL

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Modified Tue Apr 13 01:33:13 2010 UTC (9 years, 10 months ago) by clausted
File length: 865 byte(s)
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Addition of cal_module to provide a calibration tool and related features.  Added the time2val function to the ba class.  It has a bug now, but it will be useful for the calibration tool.

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Modified Mon Apr 12 22:59:57 2010 UTC (9 years, 10 months ago) by clausted
File length: 760 byte(s)
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Introduce vu_module.py for viewing ba objects.  This GUI uses Tk and has buttons to allow users to move through the sensorgrams six-at-a-time.  The traces can be dotted or continuous lines or both.  Specify two ba objects and the first will be dotted while the second will be continuous.  This could be useful for comparing real and simulated data. --CGL 

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Modified Sat Apr 10 00:21:02 2010 UTC (9 years, 10 months ago) by clausted
File length: 595 byte(s)
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Add readbiosensor() and writebiosensor() capabilities to io_module.  

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Added Fri Apr 9 17:11:42 2010 UTC (9 years, 10 months ago) by clausted
File length: 525 byte(s)

Initial addition of ba_class, an alternative to SPRdataclass.  This class, ba or Biosensor Array, has one internal structure rather than different internal structures depending on whether SPRit or Biacore or other data was imported.  This makes the code smaller and more readable.  It provides default values, usually 0 or null text, that make it easier to import and export different file formats.  We also add io_module to provide import and export features.  We also add test.py as a convenience for testing and demonstration.