[Biojava-l] How STRAP can contribute to BJ3

[Andreas Prlic]

Hi Christoph,

In principle there are the following ways to support BioJava:

* You can help and  answer support emails on the mailing lists.

* You can provide and/or maintain documentation in the biojava wiki.

* You can submit bug fixes by email or to the mailing lists

* You can contribute to the source code.

Regarding your question how BioJava can help Strap, I am not sure how
much biojava code is already used by the software and there seems to
be some overlap in functionality. I tried to have a look at the Strap
code, but I could find a link to the source.  The project page says
the license is GPL, so just a thought: if you are interested in making
your project more transparent, you might consider hosting it at
sourceforge or google code ...   In case you are interested to learn
more about BioJava, the Cookbook provides an overview of some
frequently used features: http://biojava.org/wiki/BioJava:CookBook

Hope that helps,

Andreas




On Sun, Aug 23, 2009 at 2:06 PM, Dr. Christoph Gille
<christoph.gille at charite.de> wrote:
>
> Hi,
>
> As the developer of STRAP http://3d-alignment.eu I am following with
> interest the discussion on the new Biojava (BJ3) design.
>
> STRAP is a free workbench for proteins similar to Jalview or Cinema.
>
> Here I would like to open a discussion on
>
> "How STRAP could contribute to the Biojava BJ3"
>
> and vice versa
>
> "How Biojava can be used to extend the functionality of STRAP".
>
> While STRAP is heavily used as a stand alone application and is a
> protein/alignment viewer in currently 7 Web-services such as PDBSum
> and Prodom, it has been used as an API/toolbox only by a few people.
> In most of these cases Biojava and STRAP had been used simultaneously
> because the functionalities of both toolkits are complementary.
>
> I start the discussion by explaining the plugin interface of STRAP.
>
> For this purpose I created the Web page
> http://3d-alignment.eu/biojava/PluginsForStrap.html
>
> The page explains how plugins with Biojava are written and deployed on
> Web-pages. It contains two examples which are ready to be clicked on a
> computer with Java-Web-Start.
>
> The basic idea is that by clicking a Web link a communication between
> the Browser and STRAP is started which results in loading a remote Jar
> file together with the most recent Biojava.jar through a customized
> ClassLoader. The plugin can then act in response to other mouse clicks in the Web page.
>
> STRAP contains different graphical dialogs for different types of
> plugins.  E.g. plugins that implement the interface Superimpose3D are
> opened in the superimposition-dialog.  Conversely, plugins that
> implement SecondaryStructure_Predictor are opened in the dialog for
> predicting 3D-structure from sequence. The advantage is that the
> developer of a plugin does not need to provide a GUI and can
> concentrate on the logic of the algorithm.
>
> Here is the Web-form of one of the examples in the above Web-page.
>
> <form  action="http://www-intern.charite.de/bioinf/strap/ce.php"  method="POST" >
>  <input  type="hidden"  name="load"   value="PDB:1ryp_A UNIPROT:PSA2_XENLA "  >
>  <input  type="hidden"  name="script" value="
> plugin  ApplyPairAligner_NeedlemanWunsch_Biojava, http://www.charite.de/bioinf/strap/plugins/needlemanWunschBJ.jar http://www.biojava.org/download/bj17/bin/biojava.jar
>    ">
>  <input  type="SUBMIT"  name="SUBMIT" value="Run Biojava-Needleman-Wunsch" >
> </form>
>
> The important Web-variable is "script". It contains the script command
>
>  script   name-of-plugin-class ,  Jar-files for the plugin.
>
> To use Biojava, the jar-file biojava.jar is contained in the list of jar-files.
>
>
> Cheers
>
> Christoph
>
>
>
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l