Discngine assay, version 6.5.0
Release Date: 17/10/2024
General
Improvements
#12255 File upload security
In order to improve the overall security of the Discngine assay platform, the type of files that can be uploaded in all file upload fields has been restricted. This should not affect the usual use of the platform, but if you encounter any issues, please contact Discngine support.
#12258 Text input security
In order to improve the overall security of the Discngine assay platform, some characters are now banned from being used in the input fields. If you have any problems, please contact Discngine support.
Reference Data
New Features
#11890, #11890 Targets can be stored in the application
The information related to targets can now be managed in Reference Data
- These pages contain the ability for an administrator to add, update, and delete the targets, target variants, tissues, and cell lines
- This feature is optional and can be activated by platform administrators if required.
#11693 Locations can be added in Reference Data
Locations are now managed the Reference Data application
- You can add multiple hierarchical sites
- They are used in the Assay Catalog application
Known limitations, updated in the following releases:
- A site cannot be retired.
- Sample is not referring to these locations yet, and is using its own system of locations.
Sample
New Features
#7999 Advanced Search from Plate/Vial
A new advanced search is available, allowing you to search your plates and vials:
- by one or more annotations values
- by filtering them with a list of barcodes
From this list, you can execute multiple actions like displaying lineage, creating jobs, or adding annotations.
#11422 Display the sample lineage for any containers
When looking at a plate or rack details, when selecting a well or a vial, you can now display the lineage of the related samples by clicking the "Sample Lineage" button.
#11435 Retrieve annotations and control layout from registration
Container annotations and control layouts can now be retrieved during the registration process.
This information can still be modified in the container details page, and during some of the jobs' steps.
#10340 New annotations workflow "Container - Bulk Update Annotations Values"
A new workflow named "Container - Bulk Update Annotations Values" is available and replaces the workflow "Container - Update Metadata". This workflow allows the bulk edition of annotations from a list of barcodes (File, Job, List, or Text (one per line)).
The annotations can now be applied on vials and not only on plates.
Please note that a large amount of vocabulary items (~500+) can break the annotation edition at the task requesting step of the annotations workflow "Container - Bulk Update Annotations Values". (#12416) We recommend that you edit annotations through the quick access (right hand panel) from the Browse pages.
Improvements
#11419 Improvement of the barcode administration accessibility
Sample administrators can easily dispose and retire one or multiple containers/racks using the Utilities panel.
Dispose: the barcodes of containers/racks to be changed.
Retire: The container/rack is renamed (with the suffix RETIRED), moved to the garbage and the validation of the containers/rack is run
Users can perform these actions upon request.
#11209 Improve reception from registration
You can now more easily receive your containers by selecting them from the registration summary page.
#10340 Improve interface when applying annotations
The interface to apply annotations from the plates and vials list has been reworked.
The administration of these annotations is now available through Reference Data, as for the other applications
Bugs resolved
#11240 It was possible to register a 384 wells plate as a 96
It was previously possible to register plates with well positions that did not match the selected format. Such plates will now be marked as invalid during registration.
#11838 Request validated even if the rack is empty
Empty racks (without vial or with only empty vials) used to be considered as valid at the requesting step of a job. They are now considered as invalid.
#11278 Requesting step does not warn when a requested item is invalid
For some workflows, at the requesting step, non existing items were considered valid. This is not the case anymore and they are properly marked as invalid.
#12107 The workflow "In-Plate Dilution" doesn't have the correct default volume unit
The default volume unit in the workflow "In-Plate Dilution" now matches the default unit defined in Sample administration (instead of defaulting to mL).
#12081 The survey is blocked when a well is empty
An empty well in a plate will no longer block the parsing of a survey logfile in the Update Inventory from File workflow, even if the survey provides information on the content of this well. In such cases, the information is ignored and the well is still considered empty.
Desupported features
FTP barcode printers
The FTP barcode printers are no longer supported. As such, the default DNG Zebra GX430t printer is removed from the list of available printers.
Workflow "Container - Update Metadata"
The workflow has been deprecated and replaced by "Container - Bulk Update Annotations Values"
Assay
Bugs resolved
#11904 Plate Mapping management in Execution mode led to error
In run mode, at the Plate Mapping step, a control layout and/or a dose layout can be modified in order to apply the correct layout to the analysis. This action used to generate an error. The underlying code has been reworked to fix this issue.
#11881 OML Normalizations breaks when going to the administration
In Assay, it is possible to create normalizations that make use of Oracle Machine Learning (OML) behind the scenes. Viewing and editing such normalizations in the administration used to lead to inconsistencies, errors or misconfigurations. The affected pages have been fixed, and these actions can now be carried out without any issues.
#12086 Hit Selection buttons are hidden when they should not
At the Sample Analysis step, during the hit selection the related action buttons were sometimes hidden. This is now fixed and the buttons are always displayed as long as you have selected at least one hit.
#12089 Switching visualization template causes session state error
In visualization page, after switching template, you can now continue your analysis without refreshing the page first.
#12163 Cross Run not available from campaign page
The "View as Crossruns" button in the campaign page is now working as expected.
Deprecated features
Autopilot
Autopilot mode is deprecated and will be removed in the next release. At the same time, the execution mode will be improved to ease the analysis.
Readout transformations
Readout transformations are deprecated and will be removed in a future release. Normalizations exist to perform the same operations. In order to help you recognize them during this change, they are each prefixed with the term "Readout Transformation".
Desupported features
ROUT automatic analysis
You can no longer use ROUT automatic analysis. If you are interested in this feature, please address a feature request to Discngine support.
Warehouse
Bugs resolved
#12249 Advanced Queuing system indicates unpublish action twice
In some customizations, we use a messaging platform (through Advanced Queuing) to notify other systems about actions related to Warehouse publication. When we unpublish a run from Warehouse, this platform indicated that this action happened twice instead of just once. This is now fixed.
Assay Catalog
A new application has been released, named Assay Catalog. This application allows you to describe and annotate the assays performed in your organization. In a next version, you will be able to store the experimental data linked to this assay.
Register an Assay
An assay can be registered in draft:
- With generic parameters (name, short name, description, owner, site)
- With an optional target (target, tissue, cell line, variant/mutation)
- With a group of attributes or single attributes, coming from an assay template defined in the administration
- With one or more experimental protocols, containing several files/URLs
- With expected conditions and result, coming from Condition/Results types defined in the administration
The list of assays is displayed in the home page, and can be filtered on these attributes.
Publication process
Once the draft is ready, the assay owner can request a publication.
- Each user can find its requests in the "My Submissions" section
- All pending requests will be listed in the "Pending Approvals" section, and must be reviewed and accepted by an authorized user
- Once accepted, the assay is available.
flowchart LR
A(Draft)-- Publication Requested -->B(Published)
B-- Retirement Requested -->C(Retired);
style A fill:#dbdbdb,stroke:#008EB2,stroke-width:2px,color:#008EB2
style B fill:#dbdbdb,stroke:#278701,stroke-width:2px,color:#278701
style C fill:#dbdbdb,stroke:#F44336,stroke-width:2px,color:#F44336
Register an Assay set
An assay set is a group of two assay or more.
- They can have 2 status: Available and Retired
- Assays can be imported in the assay set
- The common attributes are displayed
- The common condition/result types are displayed, and can be changed/replaced from this page
The list of assay sets is visible from the application and can be filtered as usual
Administration
Assay templates and groups
Attributes or group of attributes can be created/edited from the administration
- These groups or attributes can be linked to one or several assay template
- They can be available or retired
An assay template can be created/edited from the administration
- This assay template can contain several groups of attributes and single attributes
- This template can be associated with an assay for the attributes to be filled when an assay is created.
- Assay templates can be available or retired
Condition & Result Types
The condition & result types can be created/edited from the administration
- They can be available or retired
- They can contain several validations
- They can be added to one or several assays or assay sets.
The validations to perform on these conditions or results can be created/edited from the administration
- They can be linked to one or more condition/result type
- They can be available or retired
Template of Condition and Result Types can be created/edited from the administration
- They can contain several conditions and results types
- They can be used to add/replace the condition/result types at once to an assay or assay set
- They can be available or retired
Known bugs
Reference Data
#12419 Slashes in vocabularies raise errors
#12412 When displaying Site details, in specific conditions, the Parent location displays an ID instead of the location name
#12405 On the Well Type page, after creating a new type, the field "Last Updated By" contains "APEX_PUBLIC_USER" instead of your username
#12111 When creating vocabulary items, the code and short name cannot have the same value
Sample
#12416 A large amount of vocabulary items (~500+) can break the annotation edition at the task requesting step of the workflow Container - Bulk Update Annotations Values
#12360 During a reformatting job, if you select Source dilution with multiple copies, the dilution is listed multiple times in the generated worklist
#12267 When a batch is invalidated, the samples that contain this batch are no longer displayed in the container detail pages
#12079 When using the workflow Update Inventory from File, if an input barcode does not exist, the error message displays the output barcode instead of the input one
#11869 Invalid wells are blocking transformation workflows (replication, compression, etc.) when the quantity is insufficient even though they should be ignored
Assay
#12418 Aggregated data in the copy are deleted after copying and reverting a run
#11628 At the Sample Analysis step, the Revalidate All button leads to an error
Assay Catalog
#12444 The same attribute can be added multiple times to a group of attributes, which leads to display errors and inconsistencies.
#12425 When first creating an Assay Template, the description is not saved