Release Notes
Here's what's new in the Tuesday, April 15th, 2025 release of the CAPYBARA Web App:
Removal of Archive Tab
The Archive tab has been removed from the Navbar and all pilot samples have been moved back into the main Files directory.
QC Failures
Cases that have failed QC will now show a black "X" badge on the case card. Cases that have failed QC can be filtered for in the directory screen.
Navigating Cases
A new set of green navigation arrows have been added to the Results screen. These arrows navigate between cases within the same tab (Active, Ready to be Resolved, Resolved).
Editing Case Data
Editing case data has become more streamlined. Clicking the Edit Case button now takes you directly to Edit Mode of the Tissue Upload page. The Missing Information! badge on case cards are now clickable and will take you to the page where the missing information is.
Patients With No Case Alert
If a patient has been created but no case has been created for it, a red alert will show up on all pages of the website prompting the user to create a case for it. The alert lists all patients that have no cases.
Removal of Archive Tab
The Archive tab has been removed from the Navbar and all pilot samples have been moved back into the main Files directory.
QC Failures
Cases that have failed QC will now show a black "X" badge on the case card. Cases that have failed QC can be filtered for in the directory screen.
Navigating Cases
A new set of green navigation arrows have been added to the Results screen. These arrows navigate between cases within the same tab (Active, Ready to be Resolved, Resolved).
Editing Case Data
Editing case data has become more streamlined. Clicking the Edit Case button now takes you directly to Edit Mode of the Tissue Upload page. The Missing Information! badge on case cards are now clickable and will take you to the page where the missing information is.
Patients With No Case Alert
If a patient has been created but no case has been created for it, a red alert will show up on all pages of the website prompting the user to create a case for it. The alert lists all patients that have no cases.
Here's what's new in the Thursday, March 13th, 2025 release of the CAPYBARA Web App:
Email Notifications
Users now receive email notifications when one or more case that they created had RNA-seq data uploaded to it in the past 24 hours and is ready to be resolved. The email contains links to all of these cases.
Email Notifications
Users now receive email notifications when one or more case that they created had RNA-seq data uploaded to it in the past 24 hours and is ready to be resolved. The email contains links to all of these cases.
Here's what's new in the Wednesday, February 12th, 2025 release of the CAPYBARA Web App:
OTTER v2
Version 2 of the OTTER classifier has been released and all GAPP samples, including the 12 pilot samples, have been re-classified against v2 of the atlas. v1 classifications are still available to view by switching the model version in the RNA-seq Upload page.
OTTER v2
Version 2 of the OTTER classifier has been released and all GAPP samples, including the 12 pilot samples, have been re-classified against v2 of the atlas. v1 classifications are still available to view by switching the model version in the RNA-seq Upload page.
Here's what's new in the Monday, January 20th, 2025 release of the CAPYBARA Web App:
Search All Directories
A new search bar has been added to the top of the screen which searches all directories.
Edit Patient Shortcut
A new Edit Patient button has been added to the Results page for convenience.
Bug Fixes and Performance Improvements
The website loads faster and has improved performance.
Search All Directories
A new search bar has been added to the top of the screen which searches all directories.
Edit Patient Shortcut
A new Edit Patient button has been added to the Results page for convenience.
Bug Fixes and Performance Improvements
The website loads faster and has improved performance.
Here's what's new in the Thursday, December 19th, 2024 release of the CAPYBARA Web App:
Downloads Page
A new Downloads tab has been added to the navigation bar. Download a customised .csv file by selecting the cases and columns you want to include in it.
Cases Shortcut
All patient files now have buttons for each of their cases that reveal case details without having to navigate to the cases screen. A New Specimen button has also been added to the patient file itself to create a new patient specimen straight from the directory screen.
Online/Offline Status Indicators
The bottom left-hand corner of all screens now shows receptor online/offline status indicators. This will be useful in preventing staggered case IDs.
Leave Page Confirmation
If patient or case data is in the middle of being filled out and the Save button has not been clicked yet, the browser will now show a confirmation pop-up to leave the page without saving or to go back and save.
Performance Improvements
The CAPYBARA Web App now loads faster and has improved performance.
Downloads Page
A new Downloads tab has been added to the navigation bar. Download a customised .csv file by selecting the cases and columns you want to include in it.
Cases Shortcut
All patient files now have buttons for each of their cases that reveal case details without having to navigate to the cases screen. A New Specimen button has also been added to the patient file itself to create a new patient specimen straight from the directory screen.
Online/Offline Status Indicators
The bottom left-hand corner of all screens now shows receptor online/offline status indicators. This will be useful in preventing staggered case IDs.
Leave Page Confirmation
If patient or case data is in the middle of being filled out and the Save button has not been clicked yet, the browser will now show a confirmation pop-up to leave the page without saving or to go back and save.
Performance Improvements
The CAPYBARA Web App now loads faster and has improved performance.
Here's what's new in the Monday, December 9th, 2024 release of the CAPYBARA Web App:
Organisation of Patient Files
Three new tabs have been added to the directory screen for further organisation of patient files. A new Unresolved concordance option has been added to facilitate the addition of this feature:
If a case has a concordance selected, the case will be moved to the Resolved tab and the date and time of the concordance selection will be recorded. The turnover time is also calculated by taking the difference between the case creation and case closing times. This change does not apply to the first 12 PT samples.
OTTER Classification
OTTER now lists out all possible classifications for a particular case along with the final class name, if applicable. The path to the final class name has also been added.
Generate Report
Generate a .pdf report for any case by clicking the three dots next to the Edit Case button, then clicking Generate Report. **PDF Design is a work in progress
Filters
Added Patient Created By, Case Created By, and Final Diagnosis filters to the directory screen.
Email Verification
New users must now verify their email address before they can access the CAPYBARA Web App. An email will be sent to the user's email address with a verification link.
Organisation of Patient Files
Three new tabs have been added to the directory screen for further organisation of patient files. A new Unresolved concordance option has been added to facilitate the addition of this feature:
- Active - Stores patient files with at least one case that has no RNA-seq data uploaded
- Ready to be Resolved - Stores patient files with at least one case that has RNA-seq data uploaded but has an Unresolved concordance
- Resolved - Stores patient files where all cases have had a concordance selected
If a case has a concordance selected, the case will be moved to the Resolved tab and the date and time of the concordance selection will be recorded. The turnover time is also calculated by taking the difference between the case creation and case closing times. This change does not apply to the first 12 PT samples.
OTTER Classification
OTTER now lists out all possible classifications for a particular case along with the final class name, if applicable. The path to the final class name has also been added.
Generate Report
Generate a .pdf report for any case by clicking the three dots next to the Edit Case button, then clicking Generate Report. **PDF Design is a work in progress
Filters
Added Patient Created By, Case Created By, and Final Diagnosis filters to the directory screen.
Email Verification
New users must now verify their email address before they can access the CAPYBARA Web App. An email will be sent to the user's email address with a verification link.
Here's what's new in the Tuesday, November 19th, 2024 release of the CAPYBARA Web App:
Fusions
Added the ability to upload fusions.tsv files. Fusions now show up on the final results screen in a tabular format.
Download CSV
Download a .csv file for any case by clicking the three dots next to the Edit Case button, then clicking Download CSV.
Histology Slide Scale Bar
When viewing a histology slide using the Slide Viewer, a dynamic scale bar appears in the bottom left corner of the slide.
Fusions
Added the ability to upload fusions.tsv files. Fusions now show up on the final results screen in a tabular format.
Download CSV
Download a .csv file for any case by clicking the three dots next to the Edit Case button, then clicking Download CSV.
Histology Slide Scale Bar
When viewing a histology slide using the Slide Viewer, a dynamic scale bar appears in the bottom left corner of the slide.