Speed up filtering of large studies using the submit button

Bas Leenknegt

01-05-2023 3 min read

Exploring large studies in cBioportal has become much faster with the new ‘manual submit’ mode. The latest cBioPortal release (v5.3.3) allows the user to select multiple filters without having to wait for intermediate page reloads. In this article, we will explore the benefits of this mode and how to use it effectively.

The Challenge

When exploring a study, users can add filters to the study page. Filters are applied automatically, which is convenient but also requires the user to wait for all the data to be loaded before a new filter can be added. For small studies, reloading is fast, but for larger studies, the loading time increases. When a user already knows which filters they would like to apply, it can become quite cumbersome having to wait for each filter. For those users, it would be nice to remove the waiting time between filters.

AACR GENIE serves as a good example, with over 160,000 samples at the time of publication. A user could add filters to it, as shown in Figure 1. But if you would try to mimic these filters, you will quickly notice it is quite laborious having to select a filter, then having to wait for all the panes to reload before being able to add the next filter.

Figure 1b. When the study size increases, loading time increases. But who wants to wait?

Our solution

Users can now enable the ‘manual submit’ mode in a new settings menu at the top right of the study page. With this 'manual submit' mode, users can add filters without waiting for page reloads. Filters are queued and applied all together in one go when the user clicks the submit button. This reduces the waiting time between filters and allows users to quickly view specific subsets without interruptions.

Figure 2. The manually submit option will queue filters and apply them when the submit button is clicked.

Try it yourself

To use the 'manual submit' mode, click the settings cog at the top right of a study page and select the 'manual submit' radio button. Filters are now marked with a dashed border, indicating that they have not yet been applied. Users can keep adding filters without interruptions until they click the submit button.

Closing remarks

The Hyve provides services to develop, extend and improve features in cBioPortal such as the auto-submit toggle described in this article. Implemented features are released to the community via the cBioPortal repository on GitHub. We hope you like this new feature and that it proves helpful in your work. For inquiries on cBioPortal feature development projects or other services concerning cBioPortal, please contact us.