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This is a [known issue]() and seems to be intrinsic to the workload we're using. We should investigate whether another workload would be more interesting.
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Examine biojava and determine whether it is a suitable workload for inclusion in the suite.
https://github.com/biojava/biojava
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Cannot resolve GenbankReaderHelper - library issues with biojava? Current workaround is commenting out lines 132-145 in _**org.cidarlab.data.genbank.GenbankImporter**_
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BioJava has an OBO parser:
https://github.com/biojava/biojava/blob/biojava-4.1.0/biojava-ontology/src/main/java/org/biojava/nbio/ontology/obo/OboFileParser.java
Is it fit for purpose?
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In general, integration of the TOPS code with other java protein data models (Jmol, BioJava, ...). This issue on BioJava suggests drawing TOPS (or other topology diagrams) from BioJava:
https://githu…
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The pdb-to-uniprot alignments we get for some entries don't seem right, e.g.
1ozv.A, the n-terminus looks like this:
```
1 …
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## DM_INVALID_MIN_MAX
1. We hasn't supported number like "1D" yet.
jmh: org/openjdk/jmh/profile/LinuxPerfNormProfiler.java
```java
multiplier = Math.max(1D, Math.min(0D, multiplie…
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As a thought exercise (I'm not suggesting we actually implement these suggestions at this time), how might Disq be extended to provide distributed `RDD`s for models from libraries other than htsjdk?
…
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The goal of the **BioJava Cookbook** is to introduce users to the applications and demonstrate the possibilities that the **BioJava** library offers using a set of examples.
The **BioJava Cookbook*…
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During performance evaluation, I've noticed that `biojava` has a very odd result for the number of retired instructions for the mutator. Every plan in the current MMTk (so `GenImmix`, `Immix`, `MarkCo…