Metadata-Version: 2.1
Name: kfwx
Version: 0.0.7
Summary: A data analysis toolkit for the KFW lab (MacOS X)
Home-page: https://github.com/tiffkwin/KFW
Author: Tiffany Nguyen
License: UNKNOWN
Description: # KFWX Data Analysis Toolkit
        
        > This is a toolkit for **MacOS X** that automatically analyzes data for assays.
        
        1. Installing KFWX
        2. Tools Available
        3. Using the Data Analysis Tools (Tools 1-3)
        4. Using the Merge Tools (Tools 4-6)
        5. Understanding the Output
        
        ## Installing KFWX
        1. Ensure that Python 2.7 is installed. Python 2.7 ***should*** already be installed with MacOS X.
            * Open your Terminal and run the command `python --version`.
            * If the response is `Python 2.7.XX` then you have the correct version of Python installed. Otherwise, you should follow the installation instructions at https://docs.python-guide.org/starting/install/osx/#install-osx.
        2. Make sure that pip is installed.
            * Run the command `pip --version`. 
            * If the response is `pip XX.X from ... (python 2.7)` then you have the correct version of pip installed. Otherwise, you should follow the installation instructions at https://ehmatthes.github.io/pcc/chapter_12/installing_pip.html#pip-on-os-x.
        3. Install kfwx from the Python Package Index with pip.
            * Type the command `pip install kfwx`.
        4. You must have also some other Python modules installed.
            * matplotlib
            * pandas
            * seaborn
            * xlrd
            * openpyxl
            Use the command `pip install matplolib pandas seaborn xlrd openpyxl`. This may take a few minutes to finish.
        
        ## Tools Available
        1. Membrane Potential
        2. NADH Redox
        3. H2O2
        4. Membrane Potential Merge
        5. NADH Redox Merge
        6. H2O2 Merge
        
        ## Using the Data Analysis Tools (Tools 1-3)
        1. Place the raw data files (.txt) to be analyzed in a folder.
        2. Open the command line
        3. Navigate to the folder 
            * e.g. if folder path is users/data_analysis, then type the command `cd users/data_analysis`
        4. Type command `python -m kfwx` to run the toolkit and then follow the instructions provided
        
        ## Using the Merge Tools (Tools 4-6)
        1. Place the excel files (.xlsx) to be merged in a folder.
        2. Open the command line
        3. Navigate to the folder 
            * e.g. if folder path is users/data_analysis, then type the command `cd users/data_analysis`
        4. Type command `python -m kfwx` to run the toolkit and then follow the instructions provided
        
        ## Understanding the Output
        This section explains in detail the significance of the results of the data analysis.
        
        ### Membrane Potential
        1. **Metadata Sheet** - This sheet hosts information about the experiment itself
            * ID - The experimental ID.
            * Standard Curve - A true or false value indicating whether or not the standard curve calculation was used.
            * Slope - The slope value entered by the researcher to be used in calculations.
            * Y-Intercept - The y-intercept value entered by the researcher to be used in calculations.
            * Substrates - A column containing the list of substrates used in the experiment.
            * Additions - A column containing the list of additions used in the experiment.
            * Date - The date the analysis was run in the form YYYY-MM-DD.
        2. **Raw Data** - The raw data taken from the lab tools.
            * The data is in the form  X | Y | X |...
        3. **Averaged Raw Data** - The average membrane potential for 3-minute (i.e., 180 seconds) increments in each data set. Each data set is annotated with the buffer conditions of the assay at that time.
        4. **Corrected Raw Data** - The same data as the Average Raw Data sheet, but with an additional correction calculation which divides each average membrane potential by the the average membrane potential for Ala.
        5. **Standard Curve Data** - The results of the standard curve calculation on the raw data.
            * The data is in the form  X | Y | X |...
        6. **Averaged Standard Curve** - The results of the standard curve calculation on the averaged data.
        
        ### NADH Redox
        1. **Metadata Sheet** - This sheet hosts information about the experiment itself.
            * ID - The experimental ID.
            * Substrates - A column containing the list of substrates used in the experiment.
            * Additions - A column containing the list of additions used in the experiment.
            * Date - The date the analysis was run in the form YYYY-MM-DD.
        2. **Raw Data** - The raw data taken from the lab tools. 
            * The data is in the form  X | Y | X |...
        3. **Stripped Data** - Contains only the columns that correspond to the NADH data points. 
            * The data is in the form  X | Y | X |...
        4. **Reduced Data** - The same data as the Stripped Data sheet, but with an additional reduction calculation.
            * `y_new = (y_old-min)/(max-min)*100`
        5. **Averaged Reduced Data** - The averages of the reduced data for 3-minute (i.e., 180 seconds) increments in each data set. Each data set is annotated with the buffer conditions of the assay at that time.
        
        ### H2O2
        1. **Metadata Sheet** - This sheet hosts information about the experiment itself
            * ID - The experimental ID.
            * Standard Curve - A true or false value indicating whether or not the standard curve calculation was used.
            * Slope - The slope value entered by the researcher to be used in calculations.
            * Y-Intercept - The y-intercept value entered by the researcher to be used in calculations.
            * Substrates - A column containing the list of substrates used in the experiment.
            * Additions - A column containing the list of additions used in the experiment.
            * Mitochondria - The amount of mitochondria use (in milligrams).
            * Date - The date the analysis was run in the form YYYY-MM-DD.
        2. **Raw Data** - The raw data taken from the lab tools.
            * The data is in the form  X | Y | X |...
        3. **Slopes Data** - The slope for 3-minute (i.e., 180 seconds) increments in each data set. Each data set is annotated with the buffer conditions of the assay at that time.
        4. **Corrected Slopes** - The same data as the Slopes sheet, but with an additional correction calculation which divides each slope value by the mg of mitochondria used.
        5. **Standard Curve** - The results of the standard curve calculation on the Raw Data.
        6. **Standard Curve Slopes** - The results of the standard curve calculation on the Slopes Data.
        7. **Corrected Standard Curve Slopes** - The results of the correction calculation on the Standard Curve Slopes data.
        
        ### Membrane Potential Merge
        Combines data from all of the Averaged Standard Curve sheets in the Membrane Potential data analysis Excel files. Each row corresponds to a substrate. The Mean and SEM is calculated for each row.
        
        ### NADH Redox Merge
        Combines data from all of the Averaged Reduced Data sheets in the NADH Redox data analysis Excel files. Each row corresponds to a substrate. The Mean and SEM is calculated for each row.
        
        ### H2O2 Merge
        Combines data from all of the Corrected Standard Curve Slopes sheets in the H2O2 data analysis Excel files. Each row corresponds to a substrate. The Mean and SEM is calculated for each row.
        
        
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 2.7
Classifier: License :: OSI Approved :: Apache Software License
Classifier: Operating System :: MacOS :: MacOS X
Description-Content-Type: text/markdown
