January 22, 2024
Import File Parser
We're excited to announce a significant update to the CDD Vault Import Data wizard. This update introduces a flexible parser to accommodate a wider range of data file formats beyond the traditional tabular ("long and skinny") layout. Now, you can easily import data files organized in various formats, including those resembling a Plate layout.
When importing a data file that is not the traditional tabular format, select the “Preview file” option from the new “Parser type” menu.
Each worksheet/tab of your data file will now be displayed, and you can walk through each one indicating how the data should be assigned for import.
An extra tab is added, named “Preview Import Data”, to show the user just how the data file will be parsed during the import process.
Once a custom parser is defined, save it for future use. Saved parsers will appear in the drop down list of “Paser types” so the user can select it and move directly to step 2 of the Import Data workflow.
Please reach out to support@collaborativedrug.com if additional assignments are needed to properly transform your file.
Control Layout API
A new control_layouts API endpoint can be used to retrieve, create and delete control layouts. This is especially useful when a given protocol has multiple default control layouts or when a random control layout is used on every plate.
Some simple examples include retrieving details of a single control layout by specifying the internal control layout ID:
GET /api/v1/vaults/<vault_id>/control_layouts/<id>
Or retrieving details on all available control layouts:
GET /api/v1/vaults/<vault_id>/control_layouts
In addition to the standard set of query parameters, the GET control_layouts API call also includes:
- plates
- protocols
- runs
This knowledgebase article provides the full documentation for this new API endpoint.
Associating Samples to Readout Rows & Plate Wells
Now that the creation of Samples in CDD Vault is available, users may now associate unique Sample IDs to rows of Protocol readout data and Plate-Wells. When importing data into a Run of Protocol, a unique Sample ID can be used to associate the data to the desired Molecule-Batch. Please note, the Sample name will be added to the display in a future release so it can be seen whenever viewing readout data.
Deplete Samples
Depleting Samples is now possible via the Import Data wizard. Simply create a csv/XLSX file with a column that identifies the Samples (like a unique Sample ID) and a Depletion column with a value of “True” or “1”. Then map this Depletion column to a new, special field (named “Depleted”) listed in the Sample/Inventory Fields section.
Helpful hint: Samples can be depleted via the API as well. Simply pass the parameter: {"depleted": true} when updating (PUT) a specific sample.
This blog is authored by members of the CDD Vault community. CDD Vault is a hosted drug discovery informatics platform that securely manages both private and external biological and chemical data. It provides core functionality including chemical registration, data visualization, inventory, and electronic lab notebook capabilities.