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 LaJolla was written in Java 1.6 and used BioJava 1.6 (and some other now outdated stuff).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.) _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
