Issues

• GPU offload via TornadoVM: 570× faster all-pairs alignment, 18× faster ASA, identical results

  biojava/biojava#1158 · Filter by author mikepapadim opened on Sep 30, 2026

• AtomContactSet uses Pair<Atom> which is directed (atom1 -> atom2)

  biojava/biojava#1153 · Filter by author aalhossary opened on Sep 3, 2026
  2

• Other download sites open their own connections and do not follow redirects

  biojava/biojava#1152 · Filter by author aalhossary opened on Aug 30, 2026

• Unit tests in biojava-structure depend on data.rcsb.org, and it 502s often enough to cost re-runs

  biojava/biojava#1146 · Filter by author aalhossary opened on Aug 27, 2026

• UniProt XML module code contribution

  biojava/biojava#1112 · Filter by author heuermh opened on Mar 19, 2025
  1

• Unable to find entrez (e -utilities) NCBI

  biojava/biojava#1090 · Filter by author kshitijgarg2609 opened on Apr 12, 2024

• Quality: Sonar RSPEC-1940 "Boolean checks should not be inverted"

  biojava/biojava#1074 · Filter by author jlerbsc opened on Dec 12, 2023

• Suggestion: Sonar S2129 Constructors should not be used to instantiate "String", "BigInteger", "BigDecimal" and primitive-wrapper classes

  biojava/biojava#1066 · Filter by author jlerbsc opened on Jun 25, 2023
  2

• Suggestion: Sonar S1130 "throws" declarations should not be superfluous

  biojava/biojava#1061 · Filter by author jlerbsc opened on May 10, 2023
  4

• Test Smell: it is not a good test practice to use the loop in the test

  biojava/biojava#1038 · Filter by author TestSmell opened on Aug 17, 2022
  5

  

• NCBIQBlastService.sendAlignmentRequest | Always throws ArrayIndexOutOfBoundsException

  biojava/biojava#1033 · Filter by author FC123321 opened on Jun 30, 2022
  1

• Harmonize Profile and LightweightProfile

  biojava/biojava#1018 · Filter by author sbliven opened on Jan 27, 2022 · 6.1.0

• o.b.n.core.sequence.CDSSequence doesn't reverse-complement correctly

  bug
  biojava/biojava#1016 · Filter by author richarda23 opened on Jan 4, 2022

• Maintenance of ontology module

  biojava/biojava#1013 · Filter by author richarda23 opened on Jan 4, 2022
  1

• Add standard documented way how to reduce structure to a subset of chains

  biojava/biojava#1003 · Filter by author rdk opened on Dec 9, 2021
  2

• Support of D-AminoAcids

  enhancementnew feature
  biojava/biojava#993 · Filter by author aalhossary opened on Nov 7, 2021
  7

• Q. Inquiry for the Alignment Render in the BioJava.

  question
  biojava/biojava#983 · Filter by author RoshanShrestha123 opened on Oct 20, 2021
  6

• biojava-modfinder requires external resources that are no longer freely available

  bug
  biojava/biojava#975 · Filter by author josemduarte opened on Sep 30, 2021
  1

• Improve test coverage - currently 49.5% in bio-java core

  biojava/biojava#944 · Filter by author richarda23 opened on Jul 23, 2021
  6

• GenBankWriter does not use information in the original header

  biojava/biojava#942 · Filter by author jamesmorris opened on Jul 12, 2021
  3

• EMBL file parser is not parsing features

  enhancementhelp wanted
  biojava/biojava#923 · Filter by author MaxGreil opened on Mar 10, 2021
  2

• toConciseAlignmentString is non-deterministic

  biojava/biojava#907 · Filter by author sbliven opened on Dec 7, 2020

• Automate production of CITATION.cff file

  task
  biojava/biojava#846 · Filter by author sbliven opened on Aug 20, 2019
  6

• MultipleAlignmentJmol modifies state, causing NullPointerException

  bug
  biojava/biojava#817 · Filter by author sbliven opened on Dec 31, 2018
  4

• CE-Symm assumes models come from BA

  bug
  biojava/biojava#808 · Filter by author sbliven opened on Oct 25, 2018
  4