i've been trying to use biojava as a segment of an advanced bioinformatics course for masters students but these are students who are studying virology with a specific interest in bioinformatics. Nevertheless, some students take to it very easily but, for me, it seems the major drawback with biojava is it is a lot more disjointed compared to bioperl,. By this i mean, it's not always easy to find the classes you need, or if the class is available, it was broken during a previous release, or simply wasn't included in the latest version. I think biojava is the way to go for training and a course development project might be the way to get a more cohesive documentation set.
On Fri, Nov 4, 2011 at 9:50 PM, Chris Friedline <[email protected]> wrote: > >> Andreas, >> >> I had to come to it on my own. Seems the focus at this university is on >> Perl only and there's a serious (IMO) disconnect with our CS department. >> Java (or some other OO language) is only a minor requirement for >> bioinformatics undergrads/graduate students. However, I'd love to see this >> change and/or be involved in the development of a course to do just that. >> We've been kicking around developing some intersession modules around >> dealing with genetic data sets using Java/BioJava, but doing actual >> research continues to stand in our way. >> >> On a side note, have you seen the Java Evolutionary Biology Library? >> Would be excellent to combine forces of these development efforts since >> JEBL is well-vetted (e.g., FigTree, BEAST, Geneious), though that's purely >> from a selfish user perspective. ;-) >> >> Chris >> >> On Nov 4, 2011, at 2:21 AM, Andreas Prlic wrote: >> >> > Hi, >> > >> > Is anybody using BioJava in teaching, or has been introduced to >> > BioJava as part of a course? >> > >> > Andreas >> > _______________________________________________ >> > Biojava-l mailing list - [email protected] >> > http://lists.open-bio.org/mailman/listinfo/biojava-l >> >> >> >> _______________________________________________ >> Biojava-l mailing list - [email protected] >> http://lists.open-bio.org/mailman/listinfo/biojava-l >> > > > > -- > Simon Rayner > > State Key Laboratory of Virology > Wuhan Institute of Virology > Chinese Academy of Sciences > Wuhan, Hubei 430071 > P.R.China > > +86 (27) 87199895 (office) > +86 18627113001 (cell) > > -- Simon Rayner State Key Laboratory of Virology Wuhan Institute of Virology Chinese Academy of Sciences Wuhan, Hubei 430071 P.R.China +86 (27) 87199895 (office) +86 18627113001 (cell) _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
