Re: Help on Project Biojava

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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=3Dis%3Aopen+is%3Aissue+label%3=
A%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 <[email protected]> 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 o=
f
> a feature and since we are Java beginners we are trying to find one simpl=
e
> feature that can be improved. We are thinking about putting an informatio=
n
> 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
> Jos=C3=A9 Alves
> Margarida Viterbo
>
> Em 21.11.2016 11:10, Spencer Bliven escreveu:
>
>> =E2=80=A2 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])
>>
>> =E2=80=A2 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.
>>
>> =E2=80=A2 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.
>>
>> =E2=80=A2 Repositories (data centric) (For accessing & manipulating shar=
ed
>>> data by multiple subsystems)
>>>
>>
>> One of the core goals of Biojava is to provide access to popular
>> webservices (e.g. NCBI, EMBL, PDB).
>>
>> =E2=80=A2 Client-server and N-tier systems (For accessing shared data an=
d
>>> 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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<div dir=3D"ltr">I think Jmol commands are already sufficiently documented =
at=C2=A0<a href=3D"http://chemapps.stolaf.edu/jmol/docs/">http://chemapps.s=
tolaf.edu/jmol/docs/</a>. I would suggest something more specific to BioJav=
a.<div><br></div><div>I usually point to our <a href=3D"https://github.com/=
biojava/biojava/issues?q=3Dis%3Aopen+is%3Aissue+label%3A%22Ideas+for+Studen=
t+Projects%22">Ideas for Student Projects</a>=C2=A0list for new contributor=
s, although they do require some bioinformatics knowledge. If you are looki=
ng for something less technical,=C2=A0<a href=3D"https://github.com/biojava=
/biojava/issues/438">438</a>=C2=A0might be reasonable. We also could use so=
me documentation improvements at either the <a href=3D"https://github.com/b=
iojava/biojava.github.io">website</a>=C2=A0or <a href=3D"https://github.com=
/biojava/biojava-tutorial">tutorial</a>, if any parts of your project would=
 be helpful for a broader audience.<br></div><div><br></div><div>-Spencer</=
div></div><div class=3D"gmail_extra"><br><div class=3D"gmail_quote">On Mon,=
 Dec 5, 2016 at 12:44 PM, bio12058 <span dir=3D"ltr">&lt;<a href=3D"mailto:=
[email protected]" target=3D"_blank">[email protected]</a>&gt;</span> wrote=
:<br><blockquote class=3D"gmail_quote" style=3D"margin:0 0 0 .8ex;border-le=
ft:1px #ccc solid;padding-left:1ex">Hello,<br>
<br>
Thank you so much for your reply! Meanwhile, we did a pull request about a =
bug that we tried to solve.<br>
<br>
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 G=
UI. What do you think?<br>
<br>
Best regards and thank you for your attention,<br>
<br>
Sofia Silveira<br>
Cristina Martins<br>
Jos=C3=A9 Alves<br>
Margarida Viterbo<span class=3D""><br>
<br>
Em 21.11.2016 11:10, Spencer Bliven escreveu:<br>
</span><blockquote class=3D"gmail_quote" style=3D"margin:0 0 0 .8ex;border-=
left:1px #ccc solid;padding-left:1ex"><span class=3D""><blockquote class=3D=
"gmail_quote" style=3D"margin:0 0 0 .8ex;border-left:1px #ccc solid;padding=
-left:1ex">
=E2=80=A2 Mode-view-controller (MVC) (For interactive processing)<br>
</blockquote>
<br>
Biojava focuses mostly on providing models. However, the<br>
biojava-structure-gui package has some visualization tools using<br>
Swing. As a library, it&#39;s important for BioJava to have strong<br>
encapsulation between the MVC components, since downstream users might<br>
be using a different visualization package. There are a few places<br>
where MVC encapsulation is poor, but these are important issues to fix<br><=
/span>
(e.g. #396 [1])<span class=3D""><br>
<br>
<blockquote class=3D"gmail_quote" style=3D"margin:0 0 0 .8ex;border-left:1p=
x #ccc solid;padding-left:1ex">
=E2=80=A2 Pipes and filters (or data flow) (For batch processing) - I<br>
think you follow this one!<br>
</blockquote>
<br>
BioJava 4 provided this through IO streams for parsers and writers.<br>
With the move to Java 8, many of the newer APIs in BioJava 5 will<br>
support java.util.stream, which provides filtering and parallelization<br>
explicitly. BioJava is also compatible with Apache Spark, which<br>
enables scaling map/reduce style processing across clusters.<br>
<br>
<blockquote class=3D"gmail_quote" style=3D"margin:0 0 0 .8ex;border-left:1p=
x #ccc solid;padding-left:1ex">
=E2=80=A2 Layered architecture (For complex systems with functionalities<br=
>
at different levels of abstraction)<br>
</blockquote>
<br>
Supported to some extent by the modular architecture of BioJava.<br>
BioJava is designed to function as a library, so you could view it as<br>
a data modelling layer embedded in some larger application by<br>
downstream users.<br>
<br>
<blockquote class=3D"gmail_quote" style=3D"margin:0 0 0 .8ex;border-left:1p=
x #ccc solid;padding-left:1ex">
=E2=80=A2 Repositories (data centric) (For accessing &amp; manipulating sha=
red<br>
data by multiple subsystems)<br>
</blockquote>
<br>
One of the core goals of Biojava is to provide access to popular<br>
webservices (e.g. NCBI, EMBL, PDB).<br>
<br>
<blockquote class=3D"gmail_quote" style=3D"margin:0 0 0 .8ex;border-left:1p=
x #ccc solid;padding-left:1ex">
=E2=80=A2 Client-server and N-tier systems (For accessing shared data and<b=
r>
resources from multiple locations)<br>
</blockquote>
<br>
This is more provided by downstream systems. For instance, the RCSB<br>
has used a client-server setup for large-scale structural alignments.<br>
The clients perform alignments using biojava, and then report results<br>
back to a central server for aggregation (Prlic et al (2010)<br></span>
Bioinformatics. 26(23): 2983-2985 [2]).<br>
<br>
-Spencer<br>
<br>
Links:<br>
------<br>
[1] <a href=3D"https://github.com/biojava/biojava/issues/396" rel=3D"norefe=
rrer" target=3D"_blank">https://github.com/biojava/bio<wbr>java/issues/396<=
/a><br>
[2] <a href=3D"https://doi.org/10.1093/bioinformatics/btq572" rel=3D"norefe=
rrer" target=3D"_blank">https://doi.org/10.1093/bioinf<wbr>ormatics/btq572<=
/a><br>
</blockquote>
<br>
</blockquote></div><br></div>

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