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Copying.txt 1 (9 years ago) by clausted: Initial import of Osprai project
License.txt 1 (9 years ago) by clausted: Initial import of Osprai project
SPRdataclass.py 1 (9 years ago) by clausted: Initial import of Osprai project
ba_class.py 28 (9 years 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!
cal_module.py 24 (9 years 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.
converter-manual.html 2 (9 years ago) by clausted: Initial check-in of the html manual for converter.py.
converter.py 25 (9 years 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.
curvefitting.py 25 (9 years 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.
dat_example.obj 25 (9 years 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.
example-biosensor.txt 10 (9 years ago) by clausted: Add example-biosensor.txt as a convenience for testing.
example-clamp.txt 4 (9 years ago) by clausted: Example input data files for testing purposes.
example-clamp2.txt 8 (9 years ago) by clausted: Add four example SPR data files to help in testing code. --CGL
example-icm.txt 8 (9 years ago) by clausted: Add four example SPR data files to help in testing code. --CGL
example-key.tsv 8 (9 years ago) by clausted: Add four example SPR data files to help in testing code. --CGL
example-sprit.txt 8 (9 years ago) by clausted: Add four example SPR data files to help in testing code. --CGL
example-z03-cal.txt 4 (9 years ago) by clausted: Example input data files for testing purposes.
example-zkey.tsv 4 (9 years ago) by clausted: Example input data files for testing purposes.
fit_module.py 28 (9 years 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!
io_module.py 14 (9 years 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
mdl_module.py 26 (9 years ago) by clausted: Added mass-transport limitation model simple1to1_mtl.
model_example.obj 25 (9 years 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.
modelbasic.py 25 (9 years 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.
modelbasic_varyC.py 25 (9 years 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.
modelclass.py 25 (9 years 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.
modelclass1.py 1 (9 years ago) by clausted: Initial import of Osprai project
modelcompeting_varyC.py 25 (9 years 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.
modelparallel.py 25 (9 years 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.
modelparallel_varyC.py 25 (9 years 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.
modeltwostate.py 25 (9 years 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.
modeltwostate_varyC.py 25 (9 years 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.
osprai_one.html 24 (9 years 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.
osprai_one.py 27 (9 years 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.
test.py 28 (9 years 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!
vu_module.py 16 (9 years ago) by clausted: Fix bug in "Next" button script.
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