Biomolecule Toolkit History of Changes

January 12^th, 2022: Biomolecule Toolkit Docker Image 21.20.0-0.19.2-9baed900d

Bugfixes

• Extended list of allowed HTTP methods for CORS requests

December 20^th, 2021: Biomolecule Toolkit Docker Image 21.19.0-0.19.2-9cffacd4d

Bugfixes

• Upgraded log4j versions to the highest for fix the vulnerability CVE-2021-45105

December 16^th, 2021: Biomolecule Toolkit Docker Image 21.19.0-0.19.1-b3dc9fe7d

Bugfixes

• Upgraded log4j versions to the highest for fix these two vulnerabilities CVE-2021-45046 CVE-2021-44228
• Fix for Monomer Search problem for empty polymerType parameter

November 23^rd, 2021: Biomolecule Toolkit Docker Image 21.18.0-0.19.0-76c588d0c

Improvements

• New configuration option (environment variable: CORS_ALLOWEDORIGINS) to adjust CORS-related behavior

July 9^th, 2021: Biomolecule Toolkit Docker Image 21.11.0-0.17.1-0aed42dd6

Bugfixes

• Molar mass calculation failed if a monomer abbreviation contained dash '-' in the HELM string
• Mol to HELM conversion of RNAs decomposed 3' modified linker into natural phosphate and chemical fragment

July 1^st, 2021: Biomolecule Toolkit Docker Image 21.11.0-0.17.0-a7b27f3f2

Bugfixes

• Cis and trans isomerism changed during the HELM to MOL conversion
• Molar mass calculation produced unspecified error when the database was not initialized
• Adding or updating monomers with natural analogue X (peptide) or N (RNA) failed in the Library Manager

Changes

• Service for pairwise sequence alignment is removed

June 1^st, 2021: Biomolecule Toolkit Docker Image 21.9.0-0.16.0-84e62764c

Improvements

• HELM strings with explicit backbone linkages are handled during conversion

January 29^th, 2021: Biomolecule Toolkit Docker Image 21.1.0-0.15.0-b82e4f6a3

Improvements

• Standardizer is integrated as an optionally licensed module

• Molar mass and exact molar mass calculations are available for non-stored macromolecules. The new service calculates "average" or "exact" molar mass from HELM inputs.

October 19^th, 2020: Biomolecule Toolkit Docker Image 20.19.0-0.14.0-d419516db

Improvements

• Exact molar mass calculation for macromolecules is added to the Biomolecule Toolkit.

• Average isotopic mass (molar mass) of a macromolecule can be calculated based on the atomic weights defined in the elements.txt

• Option for expanding all monomers is added to the HELM to MOL conversion.

• Option for expanding branching amino acids is added to the HELM to MOL conversion.

• Option for expanding unnatural amino acids is added to the HELM to MOL conversion.

• Registered monomer attributes are selectable in the monomer's additional data section when the remote library is selected in the Library Manager.

• Monomers without attachment points can be submitted from the Library Manager interface to the monomer library.

• Improved error message on supported monomer R attachment points in the Library Manager.

• User warnings are displayed in the Library Manager's Marvin JS pop-up when a monomer structure does not have an R-group and/or a defined R-group is removed.

• Parallel registration of macromolecules is enabled.
  

Changes

• Leaving group average isotopic mass (molar mass) is calculated based on the atomic weights defined in the elements.txt

• Molar mass calculation based on Mw monomer attribute can be applied on BLOB monomers only.

• Option for contracting natural amino acids is removed from the HELM to MOL conversion.
  

August 10^th, 2020: Biomolecule Toolkit Docker Image 20.16.0-0.13.1-4f26aeaf​

Bugfixes

• Updating Monomer grouping options failed when BMT was configured to use Oracle database with Japanese character set.
  

Changes

• New settings to configure location of Oracle JDBC driver

Oracle JDBC drivers are no longer shipping with Biomolecule Toolkit. It is the responsibility of the customer to obtain the Oracle JDBC driver and add it to the BMT classpath.

July 24^th, 2020: Biomolecule Toolkit Docker Image 20.16.0-0.13.0-54f619e70

Improvements

• MOL to HELM conversion produces in-line smiles RNA sugars in the HELM string from unknown sugars between known linkers and nucleobases
  

Bugfixes

• HELM to MOL conversion removed the stereo-information of unknown monomers.
  

July 6^th, 2020: Biomolecule Toolkit Docker Image 20.15.0-0.12.0-a5de31878

Improvements

• New endpoints are introduced in the Biomolecule Toolkit's admin-controller:

  • List all monomer grouping options
  • Update monomer grouping options

• Options can be set for monomer grouping performed in BioEddie based on monomer properties (text, number)

• The recommended way to configure chemical structure format conversion is to leverage the newly added Biomolecule Toolkit API endpoint /api/molecules/convert instead of JChem Web Services /rest-v0/util/calculate/molExport endpoint.

• Error messages related to chemical structure conversion are more general instead of pointing at JChem Web Services as a potential root cause

• The Library Manager shows notifications upon monomer modifications if the monomer of interest has changed on server side
  

May 18^th, 2020: Biomolecule Toolkit Docker Image 20.12.0-0.11.0-abdc3378e

Improvements

• Explicit hydrogens, that are belonging to unused attachment points where H is leaving group, can be removed during exporting to MOL format (default setting)

• Multiple errors in Monomer controller are collected and returned when monomer validation fails
  

April 6^th, 2020: Biomolecule Toolkit Docker Image 20.10.0-0.10.0- 1fff86c7

Improvements

• The Library Manager is integrated to the Biomolecule Toolkit

• HELM to MOL conversion produces better quality head-to-tail cyclic peptide structures with contracted groups

• Option for generating peptides with contracted, 1-letter coded natural amino acids during HELM to MOL conversion is added and it is set to default
  

March 17^th, 2020: Biomolecule Toolkit Docker Image 20.8.0-0.9.0- a594ab3d

Improvements

• Now Biomolecule Toolkit can produce MOL files with Al, Br and Cx tags in the SAP blocks of amino acids
  

Bugfixes

• Registration of a monomer with unknown attribute produced undefined error message

• Monomer registration and update failed if only the Biomolecule Toolkit is upgraded to a newer version

• Improved error message upon attempting to convert wildcard 'X' in peptides, and wildcard 'N' in nucleotides to a molfile
  

February 7^th, 2020: Biomolecule Toolkit Docker Image 20.4.0-0.8.2- 800c77d7

Improvements

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

January 17^th, 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 20^th, 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 2^nd, 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 7^th, 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

• 4^th attachment point support is now supported
  

Bugfixes

• Upper case and lowercase letters caused errors in searches
  

April 2^nd, 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 29^th, 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 1^st, 2019: Biomolecule Toolkit Docker Image 19.6.0-0.6.2-977fa56d

Bugfixes

• Oracle 11 support was not available.
  

March 1^st, 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 1^st, 2019: Biomolecule Toolkit 19.6.0

Improvements

• Security improvement, database endpoints are disabled by default.
  

February 26^th, 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 19^th, 2019: Biomolecule Toolkit Docker Image 19.4.0-0.6.0-dfee79db

First release of Biomolecule Toolkit Docker Image.

October 11^st, 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

Comprehensive API changes will happen in the next releases

July 31^st, 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 17^th, 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 8^th, 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 5^th, 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 16^th, 2017: Biomolecule Toolkit 17.28.0

Fixes security issues for bioreg web client.

November 2^nd, 2017: Biomolecule Toolkit 17.22.1

Fixes for build package.

October 18^th, 2017: Biomolecule Toolkit 17.22.0

First release of Biomolecule Toolkit.