Thanks Simon, v. interesting. Can you provide some more details? What kind of tasks were you requiring the students to perform? I agree, a project to prepare course material would be great.
Andreas On Fri, Nov 4, 2011 at 4:18 PM, simon rayner <[email protected]> wrote: > 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 > -- ----------------------------------------------------------------------- Dr. Andreas Prlic Senior Scientist, RCSB PDB Protein Data Bank University of California, San Diego (+1) 858.246.0526 ----------------------------------------------------------------------- _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
