[Biojava-l] Help on Project Biojava

[Spencer Bliven]

I think Jmol commands are already sufficiently documented at
http://chemapps.stolaf.edu/jmol/docs/. I would suggest something more
specific to BioJava.

I usually point to our Ideas for Student Projects
<https://github.com/biojava/biojava/issues?q=is%3Aopen+is%3Aissue+label%3A%22Ideas+for+Student+Projects%22>
list
for new contributors, although they do require some bioinformatics
knowledge. If you are looking for something less technical, 438
<https://github.com/biojava/biojava/issues/438> might be reasonable. We
also could use some documentation improvements at either the website
<https://github.com/biojava/biojava.github.io> or tutorial
<https://github.com/biojava/biojava-tutorial>, if any parts of your project
would be helpful for a broader audience.

-Spencer

On Mon, Dec 5, 2016 at 12:44 PM, bio12058 <bio12058 at fe.up.pt> wrote:

> Hello,
>
> Thank you so much for your reply! Meanwhile, we did a pull request about a
> bug that we tried to solve.
>
> We have to do a last study on this project. It is about the enhancement of
> a feature and since we are Java beginners we are trying to find one simple
> feature that can be improved. We are thinking about putting an information
> about all the possible Jmol commands that user can write on the structure
> GUI. What do you think?
>
> Best regards and thank you for your attention,
>
> Sofia Silveira
> Cristina Martins
> José Alves
> Margarida Viterbo
>
> Em 21.11.2016 11:10, Spencer Bliven escreveu:
>
>> • Mode-view-controller (MVC) (For interactive processing)
>>>
>>
>> Biojava focuses mostly on providing models. However, the
>> biojava-structure-gui package has some visualization tools using
>> Swing. As a library, it's important for BioJava to have strong
>> encapsulation between the MVC components, since downstream users might
>> be using a different visualization package. There are a few places
>> where MVC encapsulation is poor, but these are important issues to fix
>> (e.g. #396 [1])
>>
>> • Pipes and filters (or data flow) (For batch processing) - I
>>> think you follow this one!
>>>
>>
>> BioJava 4 provided this through IO streams for parsers and writers.
>> With the move to Java 8, many of the newer APIs in BioJava 5 will
>> support java.util.stream, which provides filtering and parallelization
>> explicitly. BioJava is also compatible with Apache Spark, which
>> enables scaling map/reduce style processing across clusters.
>>
>> • Layered architecture (For complex systems with functionalities
>>> at different levels of abstraction)
>>>
>>
>> Supported to some extent by the modular architecture of BioJava.
>> BioJava is designed to function as a library, so you could view it as
>> a data modelling layer embedded in some larger application by
>> downstream users.
>>
>> • Repositories (data centric) (For accessing & manipulating shared
>>> data by multiple subsystems)
>>>
>>
>> One of the core goals of Biojava is to provide access to popular
>> webservices (e.g. NCBI, EMBL, PDB).
>>
>> • Client-server and N-tier systems (For accessing shared data and
>>> resources from multiple locations)
>>>
>>
>> This is more provided by downstream systems. For instance, the RCSB
>> has used a client-server setup for large-scale structural alignments.
>> The clients perform alignments using biojava, and then report results
>> back to a central server for aggregation (Prlic et al (2010)
>> Bioinformatics. 26(23): 2983-2985 [2]).
>>
>> -Spencer
>>
>> Links:
>> ------
>> [1] https://github.com/biojava/biojava/issues/396
>> [2] https://doi.org/10.1093/bioinformatics/btq572
>>
>
>
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