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exampledata/ 37 (8 years ago) by clausted: New folder "exampledata" will hold data files used for testing and for tutorial demonstrations.
help/ 35 (8 years ago) by clausted: Updates to the documentation. Mention the online help. Add hyperlinks to SVN clients.
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 36 (8 years ago) by clausted: Add zerotime() and zerovalue() to cal_module for zeroing the initial values of sensorgrams.
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.
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 29 (9 years 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.
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 36 (8 years ago) by clausted: Add zerotime() and zerovalue() to cal_module for zeroing the initial values of sensorgrams.
test.py 29 (9 years 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.
vu_module.py 16 (9 years ago) by clausted: Fix bug in "Next" button script.
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