Using Reveal Chromatography: general topics

This section of the user manual is meant to introduce users to some of the basic components of Reveal Chromatography. The following topics are reviewed here:

Overview of the user interface

The user interface of Reveal Chromatography has five components called panes:

User interface of Reveal Chromatography

The central pane

The central pane is the area where details about the elements involved in studies and experiments can be viewed. It is also the area where chromatograms, simulation grids, parameter optimizations, and other analysis tools will be displayed. The central pane has a tab-based view, making it easy to switch back and forth between multiple open displays of chromatograms and experimental or simulated data.

Tab-based viewing

To view additional objects as central pane tabs, users can double-click on these elements in The User Data browser or The Study Data browser.

Within the central pane, users can view multiple elements at once by adding more panes to the central pane area. To do this, right-click in the gray area at the top of the central pane, next to the tab list, and select where the new element will be displayed:

Creating a new central pane area

A new, empty tab area will appear next to the active one:

Empty pane

Users can then open any number of elements to be viewed in the central pane, and drag and drop their tabs into the pane of their choosing:

Viewing multiple tabs at once

Note that this central pane splitting can be done any number of times, to further subdivide the central pane, for example, to create a three area central pane. This can be useful for a variety of tasks, such as viewing the details of the transport and binding models while simultaneously viewing the simulation chromatograms:

General Reveal app view

The User Data browser

The User Data browser displays study-independent parameters and is where the user defines the properties of the components of the system to be studied. These include the properties of products, columns, resins, systems, and chemicals.

Some of the folders in the browser come pre-populated with a few common elements. Users can view the existing elements in each category by double-clicking on a folder or clicking its arrow. Users can create custom new elements for their specific need by right-clicking on a folder and selecting Create New.... (More about this process can be found in the Contributing a new product section of this user manual.)

Creating new elements in the User Data

To save changes made to the User Data, go to File > Save User Data or click on the disk icon located in the application’s toolbar:

Saving the User Data

The Study Data browser

To complement the User Data browser, the Study Data browser contains study-dependent data elements, simulation tools, and analysis tools. These data elements include study-specific buffers, purification method descriptions, binding model(s), and transport model(s), as well as experiments and simulations made from these elements.

Note that transport and binding models can be stored in both browsers. Though they are typically developed in a specific study, they may be saved in the User Data, for sharing across studies, or with collaborators. This is done by copying and pasting these elements from one browser to the other.

Copying and pasting data elements

Many browser elements may be copied and pasted into other locations by right-clicking on the element, selecting Copy, and then right-clicking on the destination folder where the user wishes to paste the element and selecting Paste.

Copying new elements

Pasting new elements into Study Data browser

This can be useful to save, for example, a simulation from a simulation grid or an optimization step into the study simulations so as to retain it for future use. See the Saving your work section for more details about when that is needed.

The performance parameters pane

The performance parameters pane will become relevant after running a simulation. This pane will display the results of the simulation(s) on the following metrics:

  1. Start collect time
  2. Stop collect time
  3. Pool volume
  4. Yield
  5. Pool concentration
  6. Pool product component purities

The job manager pane

The Job Manager Pane provides a view into the workload that has been submitted to Reveal’s CADET job manager. It allows to see the state of the job engine (Running... or Idle), how many run are submitted and left to run, how long it will take for the pending jobs to finish and how many runs have been executed already. The status of already run jobs can be explored in the Job Results table, to see how quickly the job was executed, and if it was successful:

Job manager dock panes

Customizing the interface

There are many ways to customize Reveal Chromatography’s user interface.

The side panes (data browsers, performance pane) can be “undocked” (to become a window that is separate from the main Reveal Chromatography interface). To do so, simply double-click in the top region of the pane or drag the pane out of the main window:

Undock dock panes

Double-click on an un-docked header to dock the window back into the main interface.

Users can create a tabbed view of the data browsers by undocking a pane, and then laying it on top of another pane.

Creating a tabbed view of data browsers

The size of any of the panes may be adjusted at any time by selecting and dragging the border of the pane. Finally, each pane can be closed by clicking the X in its upper right-hand corner. If closed, a pane can be re-opened by selecting it in the View menu:

Adjusting view of the user interface

Customizing the application: the preference panel

More can be done to customize Reveal Chromatography to fit the user’s needs using the preference panel in the Tools > Preferences... menu. The panel looks like the following:

Adjusting view of the user interface

It contains three parts to control three types of preferences:

  1. The application preferences allow users to control where application files are stored.
  2. The User Interface preferences allow users to control how the application looks and feels: window dimensions, confirmation on close, ...
  3. The solver preferences allow users to control the CADET behavior: which CADET executable, where to store CADET files, whether to clean them up on close, the number of CPUs to run CADET, ...

Accessing documentation

To access documentation for the specific version being used, navigate to Help > Open documentation.... There, users can access the full documentation for the version they are running, even if the machine running the software isn’t connected to the internet.

For connected users, the most recent and updated documentation can always be found at .

Updating the Reveal application

To reduce the burden of updating the Reveal Chromatography to the newest version, a new Application Updater tool is available in the Help menu. This allows to update the application in a couple of minutes instead of hours. To see if there is an update available for your version, select Help > Check for updates...:

Adjusting view of the user interface

When updates are available, users will be able select the Download button to download the update locally. It will automatically install at the next

Adjusting view of the user interface

Reporting an issue/submitting feedback

Reveal Chromatography is a software that is under active development. As such, it is possible that users may encounter issues or wish to propose improvements to the software. Users are encouraged to report any issues and feedback to the Reveal team. To do so, navigate to Help > Submit feedback....

Opening a new issue report

A new window will open that contains detailed instructions for reporting any issues effectively. This window will automatically display the software version and build number to be reported, as well as the location of the log file to send to the Reveal team:

Instructions for issue reporting

To reproduce the issue, the project file and/or the User Data may also be needed to provide a prompt resolution of the issue, and will be requested in follow up conversations.