Hi,

I found you project while searching the internet for a free OS alternative to Vector NTI (VNTI)
http://www.invitrogen.com/site/us/en/home/LINNEA-Online-Guides/LINNEA-Co....

As you are probably aware of Invitrogen (owner of VNTI) has recently discontinued its free-license program for academic usage of VNTI after more than 3 years. You now need to pay more than 1000 GBP if you want to continue using that program.
Despite the disappointment about this tactics I always believed in free standards and I think scientific data should always be free.

A little bit less expensive software, doing similar things that VNTI, is geneious. Its worth mentioning as regarding to the BioJava homepage, it's based on Biojava. If you look closely at the program many functions really do look 1:1 like Biojava GUI, but of course I'm not an expert... but still I wondered how difficult it would be to implement some basic plasmid / protein managment into Bioclipse...

The thing I imagine would be necessary:
a) Plasmid viewer as in here: http://www.geneious.com/assets/img/aboutGeneious/4.0/plasmid_map.png
b) Selectable Sequence (DNA and Protein) viewer with markups for Enzymes, features and more (Biojava obvoiusly does something similar already: http://biojava.org/wiki/BioJava:CookBook:Interfaces:ProteinPeptideFeatur... )
c) A way of cloning pieces together...
d) Import of Genbank and FastA files...

There are of courese plenty other things VNTI can do, but these basic features would be a good start. Other things (Alignments etc) could probably easy implemented as plugins.?

What do you think about that? Does it fit in the Bioclipse project?

Regards,
Jan Gebauer