New User Interface: the UI was revisited to optimize space usage and improve the user experience. The new design is more compact (e.g. grouping ownership & life cycle fields under collapsible sections) and offers a better overview of the data. In particular, the Experiment page was redesigned.
Study Contributors: the Study now offers to add contributors with their contribution roles (eg submitter, investigator, ...). This information is now used when exporting Studies to MAGE-TAB format.
Study Experimental Factors and Required Annotatiosn: the Study now offers to set which annotation types are required for items and flag those that represent studies' experimental factors. For example, one can set that Sample items must have a Developmental Stage annotation. This information is now used when exporting Studies to MAGE-TAB format. Later, it will be used to guide users and validate studies.
AVITI sniffer (CLI): new AvitiRunSniffer was added to the CLI to easily register AVITI assay data from a standard directory generated by the AVITI sequencer. Use like labid register assays -n AvitiRunSniffer -t sequencing -i /dropbox_path/20240815_AV233002_Galouzis-24s001111/ -s <study_UUID>
Shipment Filtering on items' list page: a Shipments column was added for shippable items (e.g. TREC Specimens, Samples, etc.) to easily list all items associated with a shipment from the item list view
TREC Specimen support:
Addition of new properties (e.g. date and time of collection) and a Derived From allowing to link TREC specimen in a parent-child relationship to reflect e.g. aliquoting.
Addition of new annotation type to support BioSample annotations, 20K TREC Specimens annotated with BioSample annotations (more to come soon)
Improved support of single cell sequencing by adding new Read Layout ... annotation types to describe cDNA, UMI, Cell Barcode, and Sample Index slots in reads. All these annotations expect values like read/offset/length where read one of read1, read2, readn, index1, index2, offset is the offset in the read where the slot starts (use 0 for no offset), and length is the length of the slot (number of bases). For example read1/0/16 describes the first 16 bases of read1.
Experiment summary is now a text field (was limited to 255 chars)