geWorkbench (genomics Workbench) is a Java-based open-source platform for integrated genomics. Using a component architecture it allows individually developed plug-ins to be configured into complex bioinformatic applications. At present there are more than 70 available plug-ins supporting the visualization and analysis of gene expression and sequence data. Example use cases include:
- loading data from local or remote data sources.
- visualizing gene expression, molecular interaction networks, protein sequence and protein structure data in a variety of ways.
- providing access to client- and server-side computational analysis tools such as t-test analysis, hierarchical clustering, self organizing maps, regulatory neworks reconstruction, BLAST searches, pattern/motif discovery, etc.
- validating computational hypothesis through the integration of gene and pathway annotation information from curated sources as well as through Gene Ontology enrichment analysis.
genSpace is a suite of collaboration plugins to geWorkbench aimed to support knowledge sharing among computational biologists based on popular social networking motifs. genSpace logs all user activities to a backend server, and data mines this information to recommends tools and workflows (sequences of analysis and visualization tools) in “people like you” style. It also supports Facebook-like friends (direct collaborators) and networks (colleagues from same lab, institution or community), presence facilities including available/away/offline and live activity feed, and a shared research notebook that documents the details of all analyses. The introduction of genSpace web services can be found here.
This research is in collaboration with the Center for the Multiscale Analysis of Genomic and Cellular Networks (MAGNet) on the Columbia University Health Sciences campus, which is funded by NIH and NCI.
Prof. Gail Kaiser, kaiser [at] cs.columbia.edu
Fang-Hsiang (Mike) Su, mikefhsu [at] cs.columbia.edu
Former project students
Papers, Presentations, etc.
C2B2 retreat poster and slides, May 2013
C2B2 retreat poster and slides, May 2012
DEIT 2011 paper and slides – “Towards using Cached Data Mining for Large Scale Recommender Systems”
RSSE 2010 paper and poster – “The weHelp Reference Architecture for Community-Driven Recommender Systems”
C2B2 retreat posters (1 and 2), April 2010
SSE 2010 paper and workshop presentation – “weHelp: A Reference Architecture for Social Recommender Systems”
C2B2 retreat presentation and poster, March 2009
SoSEA 2008 paper and workshop presentation – “genSpace: Exploring Social Networking Metaphors for Knowledge Sharing and Scientific Collaborative Work”
C2B2 retreat presentation and poster, April 2008
geWorkbench repository (login required)
Contact: Fang-hsiang (Mike) Su
Available student project positions:
We are not currently actively seeking new students for this project.