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Revision 32 - Directory Listing
Modified Fri Jul 23 01:23:44 2010 UTC (9 years, 2 months ago) by clausted
Add a new directory to contain Osprai documentation files.  Help files consist of html and css.
Revision 31 - Directory Listing
Modified Tue Jul 13 09:51:41 2010 UTC (9 years, 3 months ago) by ywan
Removal of a temporary file used to test svn.
Revision 30 - Directory Listing
Modified Tue Jul 13 09:50:19 2010 UTC (9 years, 3 months ago) by ywan
just for test
Revision 29 - Directory Listing
Modified Thu May 20 01:14:55 2010 UTC (9 years, 4 months ago) by clausted
Add a parameter ('cofa') to the 1to1 models that represents a concentration factor.  This allows for easier analysis of a dilution series.  For example, if two ROIs contain data for the same sample but at a dilutions of 1:2 and 1:4, the set 'conc' value to the molar stock concentration and set the two 'cofa' values to 0.5 and 0.25.
Revision 28 - Directory Listing
Modified Wed May 19 06:06:07 2010 UTC (9 years, 4 months ago) by clausted
Changes to params dictionary.  Valid values for 'fixed' are 'fixed' 'float' or an integer.  True and False are no longer acceptable.  Now mutli-ROI curve fitting seems to work!
Revision 27 - Directory Listing
Modified Wed May 19 01:49:52 2010 UTC (9 years, 4 months ago) by clausted
New LMA function in fit_module allows us to simultaneously fit parameters to the data in several ROIs that share that parameter.  This is not yet fully tested.  More comments have been added to ba_class.  The __all__ variable has been added to osprai_one to assist the automatic documentation.
Revision 26 - Directory Listing
Modified Fri May 14 22:36:12 2010 UTC (9 years, 5 months ago) by clausted
Added mass-transport limitation model simple1to1_mtl.

Revision 25 - Directory Listing
Modified Wed Apr 28 20:22:24 2010 UTC (9 years, 5 months ago) by rjaynes
Add py and obj files to allow modeling of more SPR experiments with converter and curvefitting modules.  This is the work of Yuhang Wan and Rui Hou.

1. In "converter.py": 
      Add the saving and reading function for the sprclass data object.
      Also add function "keyfile_read_fake" to provide default information for SPRit and ICM formats in case of the bug when do background_subtract.
      Fix the bugs in "background_subtract".
      Tested by DAM and ICM formats.
2. In model modules:
      "modelclass.py" is the parent class for all the other model classes that performs the theoretical simulating, loading and saving of the parameter or simulated data. Rui and I also add some other model modules like competing model, twostate model, parallel model, and the time variable concentrated models, where the simulated result is compared with Clamp's simulation to make sure the equations are correct. 
       The basicmodel and basicmodel_varyC class are tested. 
3. In "curvefitting.py":
      Add typical pipeline for operation. The examples are packed with the file. 
      Add function to show the Elapsed time for each fitting.
Revision 24 - Directory Listing
Modified Wed Apr 28 01:00:17 2010 UTC (9 years, 5 months ago) by clausted
Added copyinterval() to cal_module.  This cuts out a slice of SPR data between two timepoints and puts it in a new ba object.  
Revision 23 - Directory Listing
Modified Tue Apr 27 07:18:13 2010 UTC (9 years, 5 months ago) by clausted
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.
Revision 22 - Directory Listing
Modified Tue Apr 27 07:17:58 2010 UTC (9 years, 5 months ago) by clausted
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.
Revision 21 - Directory Listing
Modified Tue Apr 27 07:17:13 2010 UTC (9 years, 5 months ago) by clausted
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.
Revision 20 - Directory Listing
Modified Mon Apr 26 21:59:45 2010 UTC (9 years, 5 months ago) by clausted
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).  
Revision 19 - Directory Listing
Modified Fri Apr 23 01:45:38 2010 UTC (9 years, 5 months ago) by clausted
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.

Revision 18 - Directory Listing
Modified Thu Apr 22 07:36:31 2010 UTC (9 years, 5 months ago) by clausted
Add a simple 1to1 model function.
Revision 17 - Directory Listing
Modified Thu Apr 22 00:22:37 2010 UTC (9 years, 5 months ago) by clausted
Start work on curve fitting.  Added two properties, model and params, to ba.roi in ba_class.  Add mdl_module which will hold functions that model SPR interactions.  
Revision 16 - Directory Listing
Modified Sun Apr 18 05:34:10 2010 UTC (9 years, 6 months ago) by clausted
Fix bug in "Next" button script.
Revision 15 - Directory Listing
Modified Wed Apr 14 07:14:32 2010 UTC (9 years, 6 months ago) by clausted
Bug fix.
Revision 14 - Directory Listing
Modified Wed Apr 14 00:40:11 2010 UTC (9 years, 6 months ago) by clausted
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
Revision 13 - Directory Listing
Modified Tue Apr 13 06:48:56 2010 UTC (9 years, 6 months ago) by clausted
Fixed bugs in cal_module and ba_class where arrays of zeros--empty ROIs--would cause errors.
Revision 12 - Directory Listing
Modified Tue Apr 13 01:33:13 2010 UTC (9 years, 6 months ago) by clausted
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.
Revision 11 - Directory Listing
Modified Mon Apr 12 22:59:57 2010 UTC (9 years, 6 months ago) by clausted
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 
Revision 10 - Directory Listing
Modified Mon Apr 12 18:33:59 2010 UTC (9 years, 6 months ago) by clausted
Add example-biosensor.txt as a convenience for testing.
Revision 9 - Directory Listing
Modified Sat Apr 10 00:21:02 2010 UTC (9 years, 6 months ago) by clausted
Add readbiosensor() and writebiosensor() capabilities to io_module.  
Revision 8 - Directory Listing
Modified Fri Apr 9 17:18:59 2010 UTC (9 years, 6 months ago) by clausted
Add four example SPR data files to help in testing code.  --CGL
Revision 7 - Directory Listing
Modified Fri Apr 9 17:11:42 2010 UTC (9 years, 6 months ago) by clausted
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.
Revision 6 - Directory Listing
Modified Fri Apr 9 16:52:52 2010 UTC (9 years, 6 months ago) by clausted
Added CONSTANTS to represent data file type identification integers.  These should be used throughout the code in the future to make it more readable.  Also added some default injection data to make it possible to convert a SPRit file to a CLAMP file without having an Analyte/injection file.  Also note a changed dictionary key IDcal->ID in one instance. --CGL
Revision 5 - Directory Listing
Modified Wed Apr 7 06:46:26 2010 UTC (9 years, 6 months ago) by clausted
Changes made to allow use with Linux.  Can now read SPRit and output Clamp formats.  Replace == and != with "in" and "not in" string comparisons.  Change IDcal to ID in line 834.  Add function "method_read_fake" to provide default information.  Change WindowsError exception to OSError exception.  Allow user to specify default pathway for saving files by entering null string "".
Revision 4 - Directory Listing
Modified Tue Apr 6 06:38:33 2010 UTC (9 years, 6 months ago) by clausted
Example input data files for testing purposes.
Revision 3 - Directory Listing
Modified Tue Apr 6 05:40:47 2010 UTC (9 years, 6 months ago) by clausted
Functions in converter are renamed to conform to python PEP8 style.  Some uppercase names have been made lowercase.
Revision 2 - Directory Listing
Modified Tue Apr 6 05:35:46 2010 UTC (9 years, 6 months ago) by clausted
Initial check-in of the html manual for converter.py.
Revision 1 - Directory Listing
Added Wed Mar 17 05:34:43 2010 UTC (9 years, 7 months ago) by clausted
Initial import of Osprai project