Improvements

• Speed of SVG generation is increased for sequential (10-fold) and parallel (15-fold) conversions

Bugfixes

• MOL to HELM conversion of oligonucleotides with a chemical modification on 3' prime broke the phosphate-sugar backbone

• HELM to MOL conversion of phosphate linkers was not handled correctly

Bugfixes

• Inline chemistry image generation for BioEddie did not include SVG content

Improvements

• Single residue placeholder 'X' in peptide query sequences and single residue placeholder 'N' in nucleotide query sequences. Placeholder '*' to define any number of unknown monomers (0, 1... n) in peptide and nucleotide query sequences

• Import of sequences containing unnatural monomers with separators

Bugfixes

• HELM to MOL conversion failed for RNAs when 5'-linkers or sugars without nucleobases are present.

• MOL to HELM conversion of cyclic structures created invalid HELM strings by swapping R1 and R2 attachment points

Improvements

• Multi-letter monomer abbreviations with '.' separators in query sequences

• Derivatives search filter is added to search filters

• 4th attachment point support is now supported

Bugfixes

• Upper case and lowercase letters caused errors in searches

Bugfixes

• Updating more than one BLOBs failed with duplication check error.

• Sequence converter was not working with cyclic flag.

Bugfixes

• Oracle 11 support was not available.

Improvements

• Security improvement, database endpoints are disabled by default.

Improvements

• Error and result code improvements

• Distance based similarity filter is added to search filters

• MOL to HELM conversion reduces the number of generated CHEMs that are attached to a e.g. CHEM monomer if their heavy atom number is below four

• New parameter for sequence conversion for cyclic sequences

Bugfixes

• Macromolecule by helm lookup (POST /rest/macromolecules/helm) failed when sending a HELM which did not match any registered macromolecules

• New attachment point creation (POST /rest/admin/attachmentPointTypes) failed in Oracle

• The entityType property of AttributeOption appeared in Swagger two times under different names: entityType and macromoleculeTypeName

• Multiple sugars differing only in stereo information were not recognised correctly

• Canonicalization of cyclic RNA sequences resulted in incorrect attachment point information

• HELM to MOL conversion failed for RNAs which had a connection at the terminal P linker

• New macromolecule type registration failed

Improvements

• New Rest endpoint for health check: /health

• Data migration from older versions handled automatically

API changes

See the detailed description in apichanges_18_24_0.html

Improvements

• “No structure” registration.

  • New options for entity types to control the rules of structureless macromolecules. The entity type has MUST_CONTAIN, CAN_CONTAIN and MUST_NOT_CONTAIN options.

  • Structureless rules validation on entity registration.

• Lot registration.

  • Lot level registration without structure but with lot level attributes.

  • Attribute data validation on lot level.

  • LOT ID generation based on parent ID. (CID)

  • New page for Lot registration in the Biomolecule registration client.

• Flexible ID generation for entity types.

  • Default settings for generating corporate ID for macromolecules

  • Admin service to create new ID generating rules by entity types.

• Data type validation for attributes.

• More flexible additional data definition on macromolecule and component level.

• Registering biomolecules with domains.

Bugfixes

• Response code of get macromolecules by helm service (/rest/macromolecules/helm) was incorrect when the result set was empty.

• Macromolecule annotations were not appeared in the output HELM string.

• Retrieving macromolecules was slow for 100 monomers components.

Improvements

HELM2 format has become the primary format in Biomolecule Toolkit.

Bugfixes

• Cyclic HELM conversion to sequence format failed.

• Search with entity type filter in biotoolkit demo page caused error.

• Synchronization problem was present in aromatic MonomerCount service.

Improvements

• Two new endpoints for macromolecule property calculation:

  • Pairwise SequenceAlignment calculation

  • Aromatic MonomerCount calculation

• IsoelectricPoint web service input type has changed, it has fored to text/plain.

• HELM2 formatted macromolecule registration is available.

Bugfixes

Macromolecule resolvation with bridge connections failed previously.

Improvements

• New default monomer library.

• Oracle property template file has been changed.

• Isoelectric point calculation API.

• Prepare macromolecule domain handling on database level

Bugfixes

• There were Oracle specific issues.