With the advent of Genotyper 3.0, we're excited to mark a first big step towards our vision to build the best agrigenomics LIMS system. In this article, we'll describe several new features that are part of Genotyper 3.0.
New features in Genotyper 3.0
A new design
Navigation & navigating
Along with the release of Metrics, our user interface is updated and a new navigation menu is now available.
Hover over the navigation icon 
in the top left corner to open the navigation menu and choose the module of your interest in the top panel.
From the center panel of the navigation menu you can browse to your other Breed Bio applications, such as Metrics.
In the bottom panel more practical menus are still available:
Team module to add or update your users
Support module to find our company information and a link to our knowledge base and support desk
Tenant switcher, to log in on other Breed Bio laboratory environments you may be a member of
To give you and your team more space to analyze data, the main navigation menu is now hidden by default, and available only when hovering over the navigation icon.
Navigating between applications and within modules is easy: each nested page is part of a breadcrumb that you can trace back to the first page of these modules. For example, within an assay detail, you're always only 1 click removed from everything in that module: both the Analyses Overview and the Analysis Matrix overview of the analysis is visible.
Analysis overview & analysis detail screens
Our analysis overview & analysis detail screen have been gradually improving over time. When adding new features, we did not always think about the correct layouting, spacing and positioning of other elements. With our new design, we've improved the location of some elements - without removing them. This restructuring allows us to offer everyone more space to look at graphs, browse through tables and more.
In the old design, a lot of space would be taken up by elements that are hard to understand. A good example is the spacing between shortfall and the # of shortfall samples, making it hard to read these labels. Alongside a text-size that is too small, finding the right information was sometimes hard for users.
The new design features all of the elements, but brings them together in less space and makes that easier to understand. The table header now features the class colors to help you navigate results easily. Next to that, the overall statistics of your analysis and the state of the analysis are also always available.
In the table, the percentage of all regular datapoints is calculated and sums up to 100%. Shortfall, inconclusive and bad datapoints are only visualized if present on the plate.
Failed control datapoints are visualized as a number compared to the total amount of controls.
The table header shows which warning thresholds are exceeded in the colour of their corresponding severity.
Interpreted Export Mappings
Many of our users would take files from Genotyper, and interpret the results into something external lab customers would be able to understand. In our larger vision, Reports would take care of interpreting allelic discrimination results and translating them to higher level reports.
For now, we've introduced Export Mappings in the Assays Module. Alongside allele names, which will be used as axis labels and in exports, you can now configure Export Mappings to e.g. export "X:Y" or "A:G" results as "HET". In short: each of the 3 classes can now be exported as a custom value.
If both an allele name (set in Assays module) and export mapping are available, the export mapping will have priority in the export file.
The assay details tabs can be reached in 2 ways:
navigate from an opened analysis and click on the assay name on top of the screen (above the assay summary)
Or search for the assay in the Assays module and click on the line item.
Tip:
Export mappings can also easily be exported and imported with the Bulk import and export feature for assays.
Be aware:
This has impact on your export files, so make sure to double check downstream consumers of export files for compatibility.
Assay and plate statuses
As part of an extensive redesign and general spring (summer?) cleaning, we've updated assay and plate statuses to give you more granular control of the status of each assay and plate.
Explicit warning marks
A new warning icon is introduced to use during the analysis of your data, called the "marked for review" flag. Regardless of whether the data has already been viewed, it can be marked for review to make sure you or a colleague knows what needs to be double checked.
Mark 1 PCR plate for review via the '…' icon in the plate table, or mark a selection of PCR plates via the Action dropdown.
The ‘marked for review’ flag has the highest priority in the assay list when sorting by warnings 
Matrix view updates
Visualization of plate and assay information in the matrix view is revised and updated:
A plate that hasn’t been viewed yet has a thick line on its left side which disappears once the plate is viewed.
When new data is added to an assay through a partial import, these plates and/or assays are visualized in green. Viewed data has a thick green line on the left which disappears once the plate is viewed.
Warnings are visualized on assay level and PCR plate level, with priority
Marked for review (highest priority)
Flagged Assay
Severity high
Severity low (lowest priority)
PCR plate status in the matrix view are now also visualized on plate level. If a plate has both warning and a status, the plate status will be visualized prior to the warning.
Failed plate
Plate not submitted
Plate is excluded from history
General improvements
Opening an analysis
We’ve improved how we handle Ctrl + Click (Apple: Cmd + Click) in different parts of Genotyper. Now, when you Ctrl + Click an analysis in the Analysis Overview, it will open in a new window. Similar behaviour is enabled when you Ctrl + Click the assay name in the Analysis Assay detail view.
Next to that, it’s now possible to filter your Analyses Overview based on the Instrument type, visualizing all analyses for a certain instrument type.
Assay flagging
To prevent users from accidentally (un)flagging an assay during their data-analysis, a warning message will pop-up after clicking on the flag-icon.
Selected plates behavior
For a selection of plate(s), the selection is kept in place when scrolling through assays, as long as no samples are selected.
Note that Genotyper will search for plates with the exact same plate name to perform the selection. For master plates this name often is the “PCR plate name + master plate name”.
Merged history grid warning
If the setting ‘History grid merge behaviour’ is set to ‘Merge applicable history grids’, a combination of multiple history grids is visualized if applicable for the plate selection.
In previous versions of Genotyper a large warning pop up would be shown to make the user aware of this combined history grid. We now have minimized this warning to a badge on the history grid icon in the graph.
History grid is not visualized
History grid is visualized
History is a combination of 2 readers and is not visualized
History grid is a combination of 2 readers and is visualized
Chosen read saving behavior
For plates with multiple reads, the save button is now available to save reads when multiple plates are selected.
Next to that, it's now possible to autosave a read through editing data 'in' that read.
A new setting is introduced under General > Analysis settings > Read saving behaviour.
Manual save only: when selecting a different read than the AI choice (for one or multiple plates), this will never be saved automatically.
Manual save and auto-save upon edits: when selecting a different read than the AI chosen one (for one or multiple plates), this will be be saved automatically after changing sample calls on the selected plate(s).
Reason for failing a PCR plate
Genotyper will now ask for a reason when submitting a PCR plate as failed.
The reasons for failure that are available in the drop-down can be updated under Settings > General > Failed plate settings.
Failing a PCR plate is currently only available for data imported via Kraken, but we plan to have this option available for all datafile types soon. Interested? Please let us know!
Statistics becomes Usage
The former Statistics module in Genotyper is renamed to Usage. Usage will only visualize the analyzed datapoints, which are part of your lab’s Genotyper license. The module is available for users with an admin profile.
Bugfixes
For very large analyses with +500.000 datapoints, the export generation could fail due to clogging up of our systems. A solution that handles usage of memory in a more efficient way now ensures that even for very large files the data can be exported without a problem.
Tooltip when hovering over classifications in the graph view now mentions the allele labels and keyboard short-key, instead of the less pleasant [object Object]
In case a user that was deleted attempts to log in they will no longer be stuck on an error page, but receive a clear error message saying ‘No account found with this email’.
It is now possible to change the first and last name of a user, and we also no longer invert them
An existing user can now be updated in that way that the user is not linked to any of the user profiles.
Thank you to everyone for pushing us forward and we're always available via [email protected] for new requests, bugs or other matters.