Biomolecule Toolkit History of Changes

January 17th, 2020: Biomolecule Toolkit Docker Image 20.1.0-0.8.1-62d50e33

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

December 20th, 2019: Biomolecule Toolkit Docker Image 19.27.0-0.8.0-6e217040

Bugfixes

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

December 2nd, 2019: Biomolecule Toolkit Docker Image 19.25.0-0.8.0-ee57fa39

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

November 7th, 2019: Biomolecule Toolkit Docker Image 19.22.0-0.7.0-898dfcbd

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

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

Bugfixes

• 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

Bugfixes

• 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

Improvements

• Security improvement, database endpoints are disabled by default.

February 26th, 2019: Biomolecule Toolkit 19.4.0

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

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

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

July 31st, 2018: Biomolecule Toolkit 18.16.0

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.

July 17th, 2018: Biomolecule Toolkit 18.4.0

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.

February 8th, 2018: Biomolecule Toolkit 18.3.0

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.

January 5th, 2018: Biomolecule Toolkit 17.29.0

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.

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.