Freek De Bruijn

Scientific programmer



Manager of projects

ConceptRewrite A frontend built to search, edit and create concepts for ConceptWiki
MassComb Proteomics: tools and wrappers for X! Tandem and mzidentml-parsers.
Pindel Pindel: a pattern growth approach to detect break points of large deletions , medium sized insertions, inversions and other structural variations from paired-end short reads.
SedMat Proteomics: single experiment matching tool.
conceptwiki A universal open access repository of editable concepts. This is part of Open PHACTS.
cw-api-client A generic ConceptWiki API client for Java/Groovy applications
data-mining Automatically recognizing concepts in human-readable text. This project uses Peregrine as text indexer. It searches for known terms in an input text and maps them to concepts in an ontology. If a term could refer to more than one concept then Peregrine tries to disambiguate it.
msCompare Framework for the analysis of label-free LC-MS data for comparative profiling studies
nbiceng Generic code and mailing lists for the BioAssist Engineering Team
proteomics Generic code and mailing lists for researchers and developers working in the BioAssist proteomics task force.
pview-cli This project adds a command line interface (cli) to pview (see
wikidata A web site application that stores knowledge and information using concept triples. Users can both view and edit the contents of the triple store using a wiki-like application.

Member of projects

conerice Configuration files and documentation for bioinformatics servers/services.
fgweb A web-interface that allows to integrate functional genomics data and bioinformatic tool flows with a minimum of time investment in robust web-based software.
foundation Project for the setup of a foundation for the governance of open source software in a bioinformatics context; software that is not used by programmers; software for which the governance requires a community of users (life-scientists, biologists, clinicians, laboratory personnel, etc) as well as a community of programmers (bioinformaticians, informaticians, statisticians, etc)
galaxytools Tools developed by various groups in the BioAssist platforms together with their tool configs for installation in a Galaxy server.
linker A web based user interface ("Knowledge Enhancer") using semantic technology to create a popup in the browser linking terms in the text to concepts in the ConceptWiki and other third party services. Aimed at knowledge discovery.
nbicgalaxy A hosting place for documents, discussions, bug reports on NBIC Galaxy Server
sysadmin General system administration scripts used by the BioAssist Engineering Team