[Biojava-dev] biojava3-core release candidate

[PATERSON Trevor]

Hi Andreas et al.

Thanks for putting the candidate 3.0-alpha1 release on your maven repository.

We can pull the artifact down down and use it fine - the only snafoo was that the parent pom is a SNAPSHOT and our local mirror archive is configured to ignore snapshots - so I had to pull it down directly.

Do you plan on deploying source jars alongside the release artifacts, and perhaps javadoc jars? Source jars matching the release artifact would be extremely useful...

There is still something (?missing?) in the biojava and github subversion trees that breaks subversion checkouts for us - so I use the github zip download for source code - and obviously that may not match the artifact release version.

The BioJava DNAsequence functionality that we rely on in our Ensembl Java API (jensembl) demo code works fine - now that access to the ProxySequenceReader is allowed. So I will update our sourceforge project to use the biojava3-core-3.0-alpha1 dependency.

We have used our jensembl demo to write a Java plug-in for the Savant genome browser - which allows it to pull in chromosomes and annotations from recent releases of ensembl and ensemblgenomes. The sequence can also be uploaded and displayed in the browser - using the BioJava functionality.

We plan on writing this work up - to show the potential for an Ensembl Java API, allowing integration of Ensembl datasources with Java visualisation applications - and obviously integration with BioJava will be another big plus. If we can manage to get funding to continue this work we will implement far more functionality in the demo API, and would doubtless use many more BioJava features.

Savant LINK: compbio.cs.toronto.edu/savant/index.html
jensembl LINKS: jensembl.sourceforge.net  sourceforge.net/projects/jensembl

Thanks for all the good work done by the whole biojava3 team.

Trevor

 

Trevor Paterson PhD
new email trevor.paterson at roslin.ed.ac.uk 

Bioinformatics 
The Roslin Institute
The Royal (Dick) School of Veterinary Studies
University of Edinburgh
Scotland EH25 9PS
phone +44 (0)131 5274197

bioinformatics.roslin.ed.ac.uk

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