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UserGuide

UserGuide

Here we describe how WellReader's tasks are organized and how one can use the application. If you want to have a look at one module in particular, simply follow the links.

Available components

Upon launching WellReader, the Main Window is shown. It is a visual representation of the microplate and gives access to all analysis functions. The menus and the toolbar allow the user to carry out actions on the data. By clicking on any of the active wells the data are visualized.

Menus list the actions accessible from the main window, mainly actions to load and save your work, specify parameters, and analyze the data. The toolbar contains shortcuts to the most common actions, like loading, saving and setting parameters.

By clicking on one of the active wells, the relevant buttons are enabled on the bottom right side of the window. The buttons give access to the different modules of WellReader, each concerned with a particular analysis task:

Outlier detection module: allows to select outliers in the experimental data
Background correction module: corrects primary data using a defined background
Fit module: adjusts fitting parameters to compute spline curves that smooth and interpolate the data
Promoter activity module: computes reporter concentrations and promoter activities
Concentration module: computes reporter and host protein concentrations
Comparison module: allows to compare expression profiles from multiple wells

Analysis process

Analyzing reporter gene data is not a linear task, so WellReader does not operate in a linear way either. Although there are some clearly defined major steps, analysis often requires to go back and forth between the analysis tasks. The main actions can be grouped into the following categories:

Importing data
Preprocessing data for analysis
Computing promoter activities and concentrations

The first step is carried out only once on the entire microplate. On the contrary, the other two steps may be repeated for each analyzed well.

Importing data

The first step in WellReader consists of importing data produced by the microplate reader. Accordingly, the user needs to specify the properties of each well, and explicitly define wells used for background correction.

A closer look at the data import is provided here.

Preprocessing data for analysis

As mentioned above, this is the most time consuming step. It consists in applying corrections to the primary data in order to compute meaningful promoter activities and concentrations, such as the (automated or manual) detection of outliers and the correction of the data for background levels. Moreover, the data are smoothed and interpolated by means of spline curves. Notice that changes in the treatment of data in one well may require modifications in other wells, notably when the changes concern background wells.

Computing promoter activities and concentrations

The computation of promoter activities and concentrations, as well as the comparison of the results obtained for different wells, are the final steps in the analysis. They can be meaningfully carried out only after the primary data have been appropriately imported and preprocessed in the previous steps.