Bioinformatician / Developer at UPPMAX HPC Center, Uppsala University. Interested in Semantic Web, Bioinformatics and Computational Systems Biology, Java, Python, Domain Driven Design, Model Driven Development, MediaWiki and Drupal.
This blog is currently mostly filled with documentation of two past projects:
-- Samuel Lampa - firstname.lastname@example.org
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):
so I have tried to add the line
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.
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.
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.
When trying to build swi-prolog packages from source, the xpce package complains:
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.
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.
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:
Pellet, the reasoning system already integrated in Bioclipse, is based on so called "Description Logics".