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April 2nd, 2019: Biomolecule Toolkit Docker Image 19.8.0-0.6.3-999fab6e

See the changes in the Biomolecule Toolkit 19.8.0 improvements and bugfixes. 

March 29th, 2019: Biomolecule Toolkit 19.8.0


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

  • Sequence converter was not working with cyclic flag.

March 1st, 2019: Biomolecule Toolkit Docker Image 19.6.0-0.6.2-977fa56d


  • Oracle 11 support was not available.

March 1st, 2019: Biomolecule Toolkit Docker Image 19.6.0-0.6.1-7a656806

See the changes in the Biomolecule Toolkit 19.4.0 improvements and bugfixes.

March 1st, 2019: Biomolecule Toolkit 19.6.0


  • Security improvement, database endpoints are disabled by default.

February 26th, 2019: Biomolecule Toolkit 19.4.0


  • 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


  • 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

February 19th, 2019: Biomolecule Toolkit Docker Image 19.4.0-0.6.0-dfee79db

First release of Biomolecule Toolkit Docker Image.

October 11st, 2018: Biomolecule Toolkit 18.24.0


  • 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

Comprehensive API changes will happen in the next releases

July 31st, 2018: Biomolecule Toolkit 18.16.0


  • “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.


  • 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.

July 17th, 2018: Biomolecule Toolkit 18.4.0


HELM2 format has become the primary format in Biomolecule Toolkit.


  • 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.

February 8th, 2018: Biomolecule Toolkit 18.3.0


  • 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.


Macromolecule resolvation with bridge connections failed previously.

January 5th, 2018: Biomolecule Toolkit 17.29.0


  • New default monomer library.
  • Oracle property template file has been changed.
  • Isoelectric point calculation API.
  • Prepare macromolecule domain handling on database level


  • There were Oracle specific issues.

November 16th, 2017: Biomolecule Toolkit 17.28.0

Fixes security issues for bioreg web client.

November 2nd, 2017: Biomolecule Toolkit 17.22.1

Fixes for build package.

October 18th, 2017: Biomolecule Toolkit 17.22.0

First release of Biomolecule Toolkit.