Bioinformatician / Developer at UPPMAX HPC Center, Uppsala University. Interested in Semantic Web, Bioinformatics and Computational Systems Biology, Java, Python, Go, Prolog, Domain Driven Design, Model Driven Development, MediaWiki and Drupal.

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[SOLVED] How to set java.library.path for an Eclipse/Bioclipse plugin?

EDIT: Se solution at the bottom of the page

I'm trying to set the java.library.path system setting for my Bioclipse manager/Eclipse plugin.

Normally, if running java from command line, this variable should be set like so (According to what I've googled up):

java -Djava.library.path=/usr/local/lib/pl-5.7.15/lib/i686-linux/JavaClassName

so I have tried to add the line

-Djava.library.path="/usr/local/lib/pl-5.7.15/lib/i686-linux/"

to the arguments in "Run" > "Run configurations" for my plugin's product file, under the "arguments" tab.

Proposed plan of attack for BioclipseWiki

Being completely new to development for Bioclipse, I'm trying to dig into the developer-centric information available, primarily on the Bioclipse Wiki. Thinking that the feedback from a newcomer might be of some value, I'll below share my reflections and ideas for the wiki.

MediaWiki as platform

I think it has been a wise choice to use MediaWiki as a backend. since it is today becoming a de facto standard, both for huge community-driven knowledge bases with millions of users, as well as in the industry.

Plugin development for Bioclipse - from scratch

I switched laptop recently, so I needed to set up my development environment for Bioclipse 2.2 plugin development from scratch. Since the instructions for how to do this are spread over a couple of blogs and the wiki, I used the occasion to create an integrated howto, for my own documentation as well as for anyone interested.

[SOLVED] "Could not find library -lXpm" when building The SWI-Prolog XPCE package

When trying to build swi-prolog packages from source, the xpce package complains:

Keeping track of installed files when building from source, in Ubuntu

I ran into the trouble that I needed to clean up some software built from source, that did not have the "make uninstall" option, what a mess!

Just found a solution though: paco. Paco keeps track of installed files if you run "make install" through it. Later you can easily remove the installed packages.

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On the two main approaches for knowledge handling on the Semantic Web

Egon pointed me to an interesting blog post on RIF and OWL. The post highlights a situation very relevant for my project: The apparent existence of two main approaches in the field of "knowledge representation and reasoning" (maybe it should be called simply handling?) on the Semantic Web.

Java/Prolog interface (SWI Prolog JPL) up running!

Install notes for SWI Prolog JPL on Ubuntu Jaunty (9.04)

JPL is a bi-directional Java/Prolog interface for SWI-Prolog, which I hope to be able to use for integrating Blipkit into Bioclipse, so I'm happy to have got it up running tonight. Below are some notes from the installation procedure.

NOTE: These are still rather incomplete notes about how to get this to work.

Reading tip: Quick overview of Prolog and it's role in Semantic Web

I Just read this paper on using thea for OWL (Web Ontology Language) reasoning from within Prolog.

Thea - reading OWL2 directly from Prolog

Talking about BLIPKIT, the Thea library - for reading OWL2 ontologies directly from within SWI-Prolog - seems relevant for this project, as a complement to BLIPKIT. It's written (partly) by the author of BLIPKIT.

Some features I noted:

  • SWRL support (SWRL - Semantic Web Rule Language . is a proposed W3C standard for exchange between rule languages on the web)
  • Bridge to the java OWL API
  • translation of ontologies to Description Logic programs

Description Logic vs Prolog

Pellet, the reasoning system already integrated in Bioclipse, is based on so called "Description Logics".