[Biojava-l] BioJava in education

[Andreas Prlic]

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 <simon.rayner.cn at gmail.com> 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 <cfriedline at vcu.edu> 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
>>> > _______________________________________________
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>>> > http://lists.open-bio.org/mailman/listinfo/biojava-l
>>>
>>>
>>>
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>>
>>
>>
>> --
>> 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  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>



-- 
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Dr. Andreas Prlic
Senior Scientist, RCSB PDB Protein Data Bank
University of California, San Diego
(+1) 858.246.0526
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