I had previously sent this, but was not part of the mailing list, so I can only assume it got lost in a spam loop.
I was interested in applying for the All-Java Multiple Sequence Alignment Google Summer of Code project. I wanted to create a project plan but had some questions about the package as it stands now. 1. What exactly has changed with the transition to BioJava 3? From what I've read on the BioJava 3 proposal page, it seems like that the changes are to the organization of the code. Additionally there are some new standards to follow. Java 6 usage is desired, but I am unsure of what of the new features could be used in modifying pairwise sequence alignments. 2. Is the Neighbor Joining Algorithm really the best for this? Are other multiple alignments implementations desired? I have implemented the neighbor joining algorithm very inefficiently in python, it was not particularly difficult. This step seems like it will not take very long. Additionally, parallelism, I have no experience with parallelism in Java and will only have some experience with it in C, will that be an issue? 3. Is there a specific paper with the exact algorithm that should be implemented here? General: Will use cases be provided? Will test data be provided? These would both be useful in coding the test cases which seem to be coded first. Additionally, I have access to my current windows machine as well as as Linux machine for testing, but no Mac. While in theory with java, if it works on one, then it works on another, and especially with if it works on Linux, it should be fine on Mac, should I be worried about strange peculiarities? Thanks, Singer Ma Harvey Mudd College 2011 _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
