Biomolecule Toolkit History of Changes

    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

    {primary} 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.