Chris Mueller

Synthetic Programming High-performance code generation from Python. BLAST on IBM's Cell BE.

Chem/Bioinformatics Direct comparisons of full genomes. Fast algorithms for proteins clustering. Visual techniques for interpreting the results. Chemical similarity matrix visualization. AltiVec-enhanced molecular fingerprint comparison.

Computational Biology Multi-scale Software frameworks for tissue simulation using the Cellular Potts Model. Collaborative research with the Biocomplexity Institute at IU and the Laboratory for Computational Life Sciences at Notre Dame.

Data Mining and Graph Algorithms Data mining and analysis projects. Using sparse matrix algorithms to mine large graphs. Visualizing large graphs and data sets. Support Vector Machine poster. MDS vs. FastMap cage match.

Generic Programming and Software Libraries Towards a programming paradigm that enables high-performance without sacrificing productivity and accessibility. Generic Programming in Java without Generics.

High Performance Computing High Performance Python. HPC on Apple hardware.

Visualization Large format and high-resolution visualization. Large data visualization. Links to visualization tools.

Classes and Academics PhD related information. List of classes taken. How to get a PhD in under 4 years.

Fun Stuff Projects not necessarily related to research, but worth sharing. Automatic musical transcription. Weather radar scaping app. iSight rear-view mirror.

• 8/16/2006 — CorePy talk at SciPy2007
• 7/10/2007 — Performance Analysis talk for UITS
• 6/30/2007 — Officially Graduated
• 6/18/2007 — CorePy/Cell B.E. talk at STI Cell Workshop
• 5/25/2007 — Passed thesis defense
• 4/10/2007 — Software arch talk at IMAG Model Sharing Workshop
• 3/22/2007 — Third place finish: Elevator Pitch Competition at the Indiana Entrepreneur Bootcamp
• 3/21/2007 — First place finish: IU Compuater Science and Informatics Graduate Research Poster Session
• 3/13/2007 — Seminar at Virgina Tech Bioinformatics Institute
• 2/10/2007 — Agile HPC talk at RIDMS-2
• 11/14/2006 — Cell BE/BLAST talk at SC06
• 11/2/2006 — Paper presentation at LCPC2006
• 10/25/2006 — Attended the UT-Cell Workshop in Knoxville, TN.
• 10/23/2006 — Paper presentation at DLS'06
• 9/8/2006 — Thesis proposal accepted
• 8/17/2006 — Synthetic Programming talk at SciPy2006

• Runtime Synthesis of High-Performance Code from Scripting Languages C. Mueller, et. al. Dynamic Language Symposium 2006
• Distributed Force-Directed Graph Layout and Visualization C. Mueller, et. al. EGPVG'06, May 2006.
• Solving the advection-diffusion equations in biological contexts using the cellular Potts model D. Dan, et. al. Physical Review E 72, 041909 (2005).
• High-Performance Direct Pairwise Comparison of Large Genomic Sequences C. Mueller, et. al. Accepted to IEEE Transactions on Parallel and Distributed Systems, Special Issue - High-Performance Computational Biology (2006).
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• Databases and SQL OSL Lab Lunch Talk, November 2, 2005
• Developing Reliable Complex Software Systems in a Research Environment I-Light 2005, September 21, 2005
• Data Clustering Overview Oral Quals, September 9, 2005 (Info-graphic)
• The Ecology and Biodiversity of Libraries Dagstuhl Workshop on Software Libraries, March 9, 2005 (supplemental poster)
• Support Vector Machines B659: Web Mining, March 3, 2005 (Info-graphic)
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