Chris Mueller

Publications

Thesis

• Synthetic Programming: User-Directed Run-Time Code Synthesis for High Performance Computing
  Christopher Mueller. Ph.D. Thesis. Submitted June 1, 2007

Journals

• High-Performance Direct Pairwise Comparison of Large Genomic Sequences
  Christopher Mueller, Mehmet Dalkilic, and Andrew Lumsdaine. IEEE Transactions on Parallel and Distributed Systems, Special Issue - High-Performance Computational Biology Vol 17, Issue 8, pp. 764-772 (August 2006)
• Solving the advection-diffusion equations in biological contexts using the cellular Potts model
  Debasis Dan, Chris Mueller, Kun Chen, James A. Glazier. Phys. Rev. E 47, 041909 (2005).

Conferences and Workshops (refereed)

• A Comparison of Vertex Ordering Algorithms for Large Graph Visualization
  Christopher Mueller, Benjamin Martin, and Andrew Lumsdaine. APVIS 2007.
  
  
• Interpreting Large Visual Similarity Matrices
  Christopher Mueller, Benjamin Martin, and Andrew Lumsdaine. APVIS 2007.
  
  
• Expression and Loop Libraries for High-Performance Code Synthesis
  Christopher Mueller and Andrew Lumsdaine. LCPC 2006
  
  
• Runtime Synthesis of High-Performance Code from Scripting Languages
  Christopher Mueller and Andrew Lumsdaine. Dynamic Language Symposium 2006
  
  
• A Lightweight Pattern for Managing Distributed Computational Experiments
  Christopher Mueller, Douglas Gregor, and Andrew Lumsdaine.
  In prepration.
  
  
• Distributed Force-Directed Graph Layout and Visualization Christopher Mueller, Douglas Gregor, and Andrew Lumsdaine.
  In Eurographics Symposium on Parallel Graphics and Visualization (EGPVG'06), May 2006.
  
  
• High-Performance Direct Pairwise Comparison of Large Genomic Sequences
  Christopher Mueller, Mehmet Dalkilic, and Andrew Lumsdaine.
  In Proceedings of the Fourth IEEE International Workshop on High Performance Computational Biology (HiCOMB 2005), April 2005.
  
  
• Interactive Poster: Enlightenment: An Integrated Visualization and Analysis Tool for Drug Discovery
  Christopher E. Mueller.
  In Poster Compendium, IEEE Conference on Visualization, IEEE Symposium on Information Visualization, Seattle, Washington, October 19-24, 2003, Alan Keahey, Matt Ward, et. al. poster chairs.
  
  

Other Conferences and Workshops

• Position Paper for the Workshop on Information Visualization Software Infrastructures
  Chris Mueller. submitted to and presented at IVSI2004, October 9, 2004
  
  
• Extended Abstract: Accessible Peta-scale Computing for the Life Sciences
  Christopher Mueller and Andrew Lumsdaine Accepted to EuroPar Workshop on Peta-scale Computational Biology 2006. Redacted due to travel conflicts. October 9, 2004

Classes

• Synthetic Similarity Matrix Generation
  Chris Mueller. For I590: Programming for Science Informatics, April 28, 2006
• Applying Visual Similarity Matrices to Chemical Databases
  Chris Mueller. For I571: Chemical Information Technology, December 1, 2005
• Vertex Reordering Algorithms for Cluster Identification
  Christopher Mueller. For L529: Algorithms for Bioinformatics, May 6, 2005
• Structural Evolution of Web Content
  Christopher Mueller and Matthew M. Liggett. For B659: Web Mining, May 5, 2005 (note: an updated version of this paper is being prepared for journal submission)
• Sparse Matrix Reordering Algorithms for Cluster Identification
  Chris Mueller. For I532: Machine Learning in Bioinformatics, December 17, 2004
• The Java Generic Programming System
  Chris Mueller and Scott Jensen. For B629: Generic Programming, May 12, 2004
• High Resolution Dot Matrix Status Report
  Chris Mueller. For L519: Introduction to Bioinformatics, May 7, 2004
• Typed DLAs
  Chris Mueller. For P700: Fractals and Pattern Formation, March 12, 2004

Software Architecture Documents

• Web Minging Database Schema (png)
  Christopher Mueller and Matthew M. Liggett. For B659: Web Mining, Spring 2005
• Component-based PDE Solver UML Diagram v1.2
  For P573: Scientific Computing, Spring 2004 (v1.0 pdf) (v1.1 pdf)
• Python/CompuCell GUI Integration
  Chris Mueller. August 12, 2004
• CompuCell 3D UML Diagram
  Chris Mueller. August 12, 2004
• Potts Model 2.0 Collaboration Requirements
  Chris Mueller. September 20, 2003

Software Manuals

• ION Script User's Guide
  June, 1999 edition. Boulder, CO: Research Systems, Inc.
• ION Java User's Guide
  June, 1999 edition. Boulder, CO: Research Systems, Inc.