[Biojava-l] Updating to latest BioJava 3.0.7 - experiences in project LaJolla

Andreas Prlic andreas at sdsc.edu
Wed Feb 12 23:36:52 UTC 2014

Hi Raphael,

Glad to hear the upgrade worked well for you!

In principle biojava-trunk does compile most of the time. (see
http://ccpublic.rcsb.org/cruisecontrol/buildresults/biojava ). However, I
just re-built it and you are right, something is wrong. Seems we are
getting rather inconsistent responses from a Uniprot web service request.
If this does not resolve itself soon, I'll contact Uniprot to take a look.
I suspect one of their servers is down...

Thanks and best wishes,


On Wed, Feb 12, 2014 at 7:17 AM, Raphael André Bauer <
raphael.andre.bauer at gmail.com> wrote:

> Hi,
> five years ago I finished my PhD thesis. One part of the thesis was an
> algorithm called "LaJolla". It was able to compute structural
> alignments of RNAs (which was pretty new at that time) and proteins
> (which was not new). LaJolla was written in Java 1.6 and used BioJava
> 1.6 (and some other now outdated stuff). Biojava wasn't even available
> from Maven at that time, which made building the thing a bit
> cumbersome. LaJolla uses BioJava internally to parse PDB files and in
> the calculation of the shift and rotation matrices for the structural
> alignment.
> Now I had some time to upgrade LaJolla. Moved it from svn /
> sourceforge to github and especially made it build again with latest
> stuff like Maven 3.11, BioJava 3.0.7. I Also released version 2.2 -
> ready to use on the command line.
> The experience of upgrading LaJolla from Biojava 1.6 to BioJava 3.0.7
> was really smooth. There were some changes I had to make, but it took
> not to long how to figure out how stuff in 3.0.7 works. LaJolla builds
> smoothly and even has its own CI server. Now LaJolla no longer is a
> dead project from a code perspective.
> That means many things. But it especially means that the BioJava
> community did a really great job on running the project over the last
> couple of years. Thanks for that and keep up the awesome work!
> Because I am no longer working in academia I am not sure were the
> project goes to. But as it's now on github it's a lot easier to
> collaborate. If you have ideas let me know :) Pull requests are always
> welcome! (http://github.com/raphaelbauer/lajolla).
> Cheers,
> Raphael
> (ps. I was not able to build BioJava master on my machine - which
> makes sense, because CI also says the build is failing. But that's
> hopefully just temporary.)
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