Oliver Rübel


Personal Information
Current Research
Cooperation Partners
Research Vignettes
Recent Publications


Personal Information


Current Research:

In my ongoing research I am working on the development of PointCloudXplore, a tool for visual analysis of 3D gene expression data. Within the scope of the Berkeley Drosophila Transcription Network Project (BDTNP) experimental and computational methods are developed at the Lawrence Berkeley National Laboratory (LBNL) to systematically characterize and dissect the complex expression patterns and regulatory interactions already present in Drosophila Melanogaster prior to gastrulation. In direct cooperation with biologist from the Life Sciences Division at LBNL as well as with the Institute for Data Analysis and Visualization (IDAV) at UC-Davis and the Visualization Group at LBNL we are working on development of tools for visualization and analysis of genetic data. This close cooperation between all these highly qualified institutes enables us to develop visualization tools that facilitate genetic research and which are used by biologists in there ongoing work. The direct cooperation with genetic scientists allows us not only to validate our work at all stages of development but a group of highly qualified aspired users is directly involved in the development of the final tools. The cooperation with IDAV and the Visualization Group at LBNL allows us to develop and communicate new ideas with a group of highly qualified computer scientist which enables us to develop high quality visualization tools.

Analysis and knowledge discovery from large, complex, multi-variate laser wakefield particle accelerator (LWFA) simulation data is a challenging task. One main feature researchers are interested in are beams of high-energy particles formed during the coarse of LWFA simulations. To enable efficient and accurate analysis of these particle beams, dedicated mechanisms for selection and detection of particle beams are needed. Furthermore, to support analysis of selected particle bunches of interest effective visualization methods are required. Since 2007 I have been working in close cooperation with the LOASIS program at LBNL on the development of methods for the analysis of extremely large laser wakefield particle acceleration (LWFA) data. In collaboration with LOASIS, the SciDAC SDM center (LBNL) and researchers from different institutions within VACET, we developed method for fast visual exploration of these highly complex datasets.  I have also been working extensively on the development of methods for automatic detection and analysis of particle beams in LWFA simulation data. 

Cooperation Partners:

  1. IRTG - International Research Training Group: Visualization of Large and Unstructured Data Sets; Applications in Geospatial Planning, Modeling, and Engineering. --  Collegiate since December 2005.
  2. Visualization Group at Lawrence Berkeley National Laboratory (LBNL) -- Student Assistant from July.05-October.05 and July.06 - Now
  3. SciDAC Visualization and Analytics Center for Enabling Technologies (VACET), member since 2007-present
  4. Genomics Division at Lawrence Berkeley National Laboratory (LBNL)  -- March.05 - October.05 and July.06 - Now 
  5. The Biomigaing Group, Life Sciences Division, at Lawrence Berkeley National Laboratory (LBNL), -- Visiting Researcher from March.05 - October.05 and July.06 - present
  6. Institute for Data Analysis and Visualization (IDAV) at the University of California Davis -- Visiting Researcher from March.05 - October.05 and July.06 - present 
  7. LOASIS-program at Lawrence Berkeley National Laboratory (LBNL),  2007-present
  8. SciDAC SDM Center at Lawrence Berkeley National Laboratory (LBNL), 2007-present

Research Vignettes:


     

PointCloudXplore: Visualization and Analysis of 3D Gene Expression Data. (More information)

Analysis of Laser Wakefield Particle Acceleration Data.  (More information)





High-performance Interactive Data Exploration of Extremely Large Data. (More information)
Automatic Beam Path Analysis of Laser Wakefield Particle Acceleration Data. (More information)


Recent Publications:

O. Rübel C.G.R. Geddes, E. Cormier-Michel, K. Wu, Prabhat, G.H. Weber, D.M. Ushizima, P.Messmer, H. Hagen, B. Hamann, and E.W. Bethel, "Automatic Beam Path Analysis of Laser Wakefield Particle Acceleration Data", in IOP Computational Science & Discovery, 2009 (to appear)

Rübel, O., Prabhat, Wu K., Childs H., Meredith J. Geddes C.G.R., Cormier-Michel E., Ahern S. Weber G.H., Messmer P., Hagen H., Hamann B. and Bethel E.W., High Performance Multivariate Visual Data Exploration for Extremely Large Data, SuperComputing 2008 (SC08), Austin TX, November 15-21, 2008 (pdf) (BibTeX)

Rübel, O., Weber G.H., Huang M.-Y., Bethel E.W., Biggin M.D., Fowlkes C.C., Luengo Hendriks C.L., Keraenen S.V.E., Eisen M.B., Kowles D.W., Malik J., Hagen H. and Hamann B., Integrating Data Clustering and Visualization for the Analysis of 3D Gene Expression Data, to appear in IEEE/ACM Transactions on Computational Biology and Bioinformatics (preprint pdf)(BibTeX)

List of Publications