- Added support for stoechiometry in sequences in Biocorpora MAB. When a sequence contains multiple chains, the ratio between each chain is not limited to 1:1.
- Updated sequence search engine to handle stoechiometry: exact search now requires equal stoechiometry for all sequence chains. Let A and B be two peptide chains. If sequence S1 contains chains A and B, sequence S2 contains 1 A and 2 B and sequence S3 contains 2 A and 2 B, then S1, S2 or S3 do not match each other: S1 and S2 do not have the same ratio, and S1 and S3 do not have the same molecular weight.
- Updated calculation of sequence properties to take stoechiometry in account (MW, Extinction coef. Abs 0.1% and pI).
- Display alignment of sequence with the closest germlines in the Sequence Viewer.
- Improved change tracking in registration module. All the editable fields about a registered entity are traced.
- Change tracking of registered entities has been improved.
- Unmodified fields are not listed in the change tracking report.
- Added more explicit error messages when a required value is missing from a form.
- Reviewed the management of error messages.
- Consolidated all the database query modules into a single service.
- Extended the functionality of the aggregation of multiple data sources in reports. These reports can be used in applications requiring in-context filtering (e.g., compound browser) now.
- Added support for report display plugins.
- Copy document link to clipboard.
- Fixed bug that prevented the content of folders to be displayed when two users access Biocorpora on the same browser.
- Added calculated properties for sequences: MW, Isoelectric point, Extinction coefficient, Theoretical absortion.
- When editing a clone sequence, it is now possible to automatically update the regions in the form before submitting the sequence.
- Improved navigation between standard sequence lists and NGS experiments
- Enable sample processing from the web interface. Raw FASTA or FASQ files must be copied on the server. Then, the processing is fully managed from the web interface: CDR3 identification, clonotype identification, CDR3 search.
- Users can select clonotype identification parameters, such as how many clonotypes are loaded in the view, the minimum number of reads per CDR3 and per clonotype, the number of example full-length sequences to import.
- Sample clonotypes are stored in a file on the server to avoid the need to recalculate clonotypes every time analysis parameters are modified (e.g., increase the number of clonotypes loaded in the view, or search for a CDR3). Not all clonotypes are loaded in the database to optimize performance.
- When a sample is reanalyzed, the result of the full-length sequences that had been previously aligned onto germlines is re-used to decrease analysis time.
- Until version 3.25.7, only the top clonotypes were loaded in the view. It is now possible to add clonotypes containing an arbitrary CDR3 (CDR3 search).
- Fixed the display of CDR3 occurrence in the cross sample analysis. Until version 3.25.7, CDR3 occurrence was loaded only for the CDR3 in the top clonotypes. If a CDR3 was not in the top clonotypes of all the samples, it was displayed as not found in those sample in which it was less represented. CDR3 statistics are now displayed for all the samples, and zero is displayed when the CDR3 was not found in a sample.
- Added interface to load, process and visualize NGS datasets.