project index project and user administration
Scientific programmer
BioAssist
NBIC
| 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 compbio.cs.princeton.edu/pview). |
| 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. |
| 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 |