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Select one of the tabs below to learn more about each page and their available features

The Four Modules

*All graphs can be downloaded as a .svg file*
  • Module 1
    • Used to make plots of different types based on data uploaded by the user
      • Create scatter + line plots for 2-column or xy datasets
      • Create scatter box plots (aka swamp plots) or violin plots for 1-column datasets
  • Analysis Modules:
    (These make scatter + line plots using 2-column or xy datasets)
    • Module 2
      • Used to fit a non-linear model to direct binding data
    • Module 3
      • Used to fit a non-linear model to competition binding data
    • Module 4
      • Used to determine the time at which a polymerization reaction is 50% complete, and the rate of polymerization at this point
      • Has 3 different analysis modes available on the "Results" page
    • Example Graph for Modules 2 and 3
    Example Graph for Module 4

Available Features

  1. Data Format Radio Buttons
    (Only applicable to Module 1)
    • Two-column data consists of xy pairs
      A two-column dataset is used to make scatter and line plots, where:
      • the x values determine point position on the horizontal axis
      • the y values determine point position on the vertical axis
    • Single-column data consists of x values only
      A single-column dataset may be used to create either:
      • A scatter box plot, where:
        • the x values determine point position on the vertical axis
        • the name of the dataset determines horizontal position
      • A violin plot, which:
        • visualizes the peaks and distribution of the x values
  2. Upload New File
    • Accepts .csv and .txt files
    • Overwrites existing content in the textarea with the uploaded datasets given that the format of file content is valid
    • Uploading a file with valid data format does not require the user to click on 'Update Changes'
  3. Upload File To Append
    • Also accepts .csv and .txt files
    • Appends uploaded datasets to existing data within the textarea
    • Uploading a file with valid data format does not require the user to click on 'Update Changes'
  4. Example Data Dropdown
    • Provides various examples of valid data that are available to use according to the selected module
  5. Flip x & y Checkbox
    • Given two-column datasets, this flips the x and y values for each dataset in the text area
      NOTE: The 'Update Changes' button must be clicked after flipping the xy pairs
  6. Update Changes
    • Must be clicked only after making direct changes to the textarea or flipping the xy pairs on two-column datasets
  7. Delete Selected Button
    • Deletes selected data sets on the 'Data Sets' table and updates the content of the textarea accordingly
  8. Analyze Data Button
    • Navigates the user to the "Results" page given that valid data sets have been input or provided

Required Data Format

For Uploaded Files and Textarea Content
  • For .csv files,
    • All data set names must be on the first row
    • Numeric x values must be directly beneath the dataset name
    • Numeric y values (if present) must be immediately to the right of the x values
    Figure 1: single-column datasets
    Figure 2: two-column datasets
  • For .txt files,
    • Start with the data set name and follow with rows that each correspond to numeric value/s
      • For two-column datasets, separate the x and y values on each row with either a space or a tab
    • Separate each data set with a new line before each data set name
    *NOTE* Content of the textarea must follow the same required data format for .txt files
    Figure 3: single-column datasets
    Figure 4: two-column datasets

Graph Customization

Scatter + Line Plots
  • 'Customize Graph' Table
    'Customize Graph' table for Module 4
    'Customize Graph' table for Modules 1, 2, and 3
    • Reference Line
      (Applicable only to Module 4)
      • Determines which dataset's min and max actin lines to use and plot on the graph after performing actin analysis
    • Plot
      • Toggles the display of line and scatter points for a dataset on the graph
    • Line Style
      (only becomes available after clicking 'Fit Dataset' atop the 'Input Module Parameters' table)
      • Includes the following options:
        • Line color
        • Line type, e.g. solid/dash
        • Line width
    • Marker Style
      • Includes the following options:
        • Marker color
        • Marker shape
        • Marker width
  • Figure Labels and Axis Settings Form
    • Configure graph and axes titles
    • Toggle log scale on each axis
    • Change interval and range of each axis
  • Graph Resize Grabber
    (Also available for violin plots under Module 1)
    • Dynamically resizes graph with a click and drag
    • Found on the bottom right of the graph space

Graph Customization

Scatter Box & Violin Plots
  • Figure Labels Form
    • Configure graph and axes titles
  • Other Customization Options
    *NOTES*
    • Custom options in orange are for violin plots only
    • Custom options in blue are for swamp or scatter box plots only
    • Base Custom Options
      • Plot
        • Toggles the display of the dataset as either a bar or a violin on the graph
      • Marker Color
      • Marker Width
      • Bar/Violin Color
      • Mean
        • Toggles the display of a mean line for the violin that represents a dataset
      • Markers
        • Toggles the display of markers on the violin that represents a dataset
    • Axes
      • Y Axis Scale
        • Toggle linear or log scale for y axis
      • Min Y
        • Set minimum for y axis
      • Max Y
        • Set maximum for y axis
      • Bar Width
        • Offers three preset sizes: Thin, Medium, Wide
        • Dynamically resize width of bars on the graph and shift them accordingly on the x axis
    • Tick Marks
      • Tick Size
        • Sets the length of the ticks on both axes
      • Tick Spacing
        (available for both swamp or scatter box plots and violin plots)
        • Sets the interval between each tick on the y axis
    • Error Bars
      • Error Bar
        • Toggles the appearance of an error bar for each plotted bar on the graph based on the error method selected
      • Method
        • Determines the error method to use and show as an error bar for each plotted bar on the graph
      • Color
        • Sets the color of each error bar
      • Caps
        • Attaches a cap on both ends of each error bar
      • Cap Size
        • Sets the length of each cap
      • Cap Width
        • Sets the width or thickness of each cap

Data Analysis

Modules 2, 3, and 4
  • 'Input Module Parameters' Table
    'Input Module Parameters' table for Module 4
    • 'Analysis Mode' dropdown is only available for Module 4
      • Provides different preset/recommended Window2 values according to selected actin analysis mode
        • Window2 determines which area of concentrated points on the plotted line to highlight on the graph
    • Includes fields for each parameter to perform data analysis according to the selected module
      • List of required parameters differ according to the selected module
    • 'Fit Dataset' button performs data analysis using the values provided for each parameter
      • Successful execution of data analysis does the following:
        • For Modules 2 and 3
          • Graph the fit lines
        • For Module 4
          • Highlight concentration of points according to selected analysis mode and Window2 value
          • Graph the min and max intensity lines based on which dataset's reference line has been selected
  • Computation Result Console
    Console output for Module 3
    Console output for Module 4
    • Found below the 'Save Session' form on the "Results" page
    • Outputs the results of the computation in human-readable format after clicking 'Fit Dataset'

Session/Task Retrieval Feature

  • Create New Task From Current Session
    Form for saving current session as a task that can be retrieved
    Expected message for successful creation of new task
    • To save current session as a retrievable task/session:
      • Provide a valid session name, no more than 50 characters
      • Provide a valid email address
      • Click 'Save Session As' button
    • Retrievable task/session enables users to:
      • Save their graph customization selections
      • Save the parameters that they provided for any of the analysis modules
    • The Session Name will be appended with 'by prefix-of-email'
      • For example,
        given session name 'Mod 1 test' and email address bobby@example.com,
        the full session name will be 'Mod 1 test by bobby'
    • Upon creation, saved task/session will be given a 7-day expiration date
      • If needed, the expiration date can be extended
        (see below for more details)
  • Retrieve and Save Changes to An Existing Task/Session
    Expected email with task retrieval link
    Header on "Results" page for a saved session
    • Given successful task/session creation, an email will be sent to the address provided containing the task retrieval link
      • Clicking on the link will navigate the user to the "Results" page for that task/session
    • Selecting 'Save Session' will output a popup message to confirm the overwrite of previously saved information with current data
      • An option will also be given to extend the task/session for another 7 days
        (e.g. the new expiration date will be 7 days from the time of the user's selection of this option)