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

[Raphael André Bauer]

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1.6 (and some other now outdated stuff).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.)