Articles in journals or book chapters (13)
  1. Shinya Ito, Michael Hansen, Randy Heiland, Andrew Lumsdaine, Alan M. Litke, and John M. Beggs. Extending Transfer Entropy Improves Identification of Effective Connectivity in a Spiking Cortical Network Model. PLoS ONE, 6(11):e27431, November 2011. [bibtex-entry]

  2. M. H. Swat, S. D. Hester, A. I. Balter, R. W. Heiland, B. L. Zaitlen, and J. A. Glazier. Multicell simulations of development and disease using the CompuCell3D simulation environment. In I. V. Maly, editor,Systems Biology, volume 500 of Methods in Molecular Biology, pages 361--428. Humana Press, Clifton, NJ, 2009. [bibtex-entry]

  3. X. Dong, K. E. Gilbert, R. Guha, R. Heiland, J. Kim, M. E. Pierce, and D. J. Wild G. C. Fox. Web Service Infrastructure for Chemoinformatics. Journal of Chemical Information and Modeling, 47(4):1303-1307, 2007. [bibtex-entry]

  4. A. Moad, C. Moad, R. Wampler J. Perry, G.S. Goeken, N. Begue, T. Shen, R. Heiland, and G. Simpson. NLOPredict: Visualization and data analysis software for nonlinear optics. Journal of Computational Chemistry, 28(12):1996-2002, 2007. [bibtex-entry]

  5. A. Singh, A. Olowoyeye, P. H. Baenziger, J. Dantzer, M. G. Kann, P. Radivojac, R. Heiland, and S.D. Mooney. MutDB: update on development of tools for the biochemical analysis of genetic variation. Nucleic Acids Research, 36(1):D815--D819, 2007. [bibtex-entry]

  6. R. D. Wampler, A. J. Moad, C. W. Moad, R. Heiland, and G. J. Simpson. Visual Methods for Interpreting Optical Nonlinearity at the Molecular Level. Accounts of Chemical Research, 40(10):953-960, 2007. [bibtex-entry]

  7. R. Heiland. XML for Bioinformatics. Briefings in Bioinformatics, February 2006. [bibtex-entry]

  8. B. Peters, C. Moad, E. Youn, K. Buffington, R. Heiland, and S.D. Mooney. Identification of Similar Regions of Protein Structures Using Integrated Sequence and Structure Analysis Tools. BMC Structural Biology, 6(4):1996-2002, 2006. [bibtex-entry]

  9. J. Dantzer, C. Moad, R. Heiland, and S.D. Mooney. MutDB services: interactive structural analysis of mutation data. Nucleic Acids Research, 33(2):W311--W314, 2005. [bibtex-entry]

  10. R. Heiland, M. P. Baker, and D. Tafti. VisBench: A Framework for Remote Data Visualization and Analysis. Springer Verlag Lecture Notes in Computer Science/ICCS, 2074:718-727, 2001. [bibtex-entry]

  11. D. Armbruster, E.F. Stone, and R.W. Heiland. Towards analyzing the dynamics of flames. In J. Chadam, M. Golubitsky, W. Langford, and B. Wetton, editors,Pattern Formation: Symmetry Methods and Applications, volume 5, pages 1--17. AMS and Fields Institute Communications, 1996. [bibtex-entry]

  12. D. Armbruster, R. Heiland, and E. J. Kostelich. KLTool: A tool to analyze spatiotemporal complexity. Chaos, 4(2):421-424, 1994. [bibtex-entry]

  13. D. Armbruster, R. Heiland, E. J. Kostelich, and B. Nicolaenko. Phase-space analysis of bursting behavior in Kolmogorov flow. Physica D, 58(1-4):392-401, 1992. [bibtex-entry]

Conference articles (6)
  1. R. Heiland, M. Swat, J. Sluka, B. Zaitlen, A. Shirinifard, G.L. Thomas, A. Lumsdaine, and J.A. Glazier. Visualizing Cells and their Connectivity Graphs for CompuCell3D. In BioVis 2012 Conference, Seattle, WA, October 2012. [bibtex-entry]

  2. R. Heiland, J. Belmonte, M. Swat, C. Silva, A. Lumsdaine, and J.A. Glazier. Enhancing CompuCell3D with Workflows and Data Provenance. In Virtual Physiological Human (VPH) 2010 Conference, Brussels, Belgium, September 2010. [bibtex-entry]

  3. R. Heiland, M. Swat, B. Zaitlen, J.A. Glazier, and A. Lumsdaine. Workflows for Parameter Studies of Multi-Cell Modeling. In Proceedings of HPC 2010, pages 140--145, April 2010. [bibtex-entry]

  4. R. Heiland, S. D. Mooney, J. Boverhof, K. Jackson, M. Christie, M. Swat, A. Balter, and J. Insley. Python for Scientific Gateways Development. In Proceedings of International Workshop on Grid Computing Environments, November 2007. [bibtex-entry]

  5. M.P. Baker, R. Heiland, E. Bachta, and M. Das. VisPort: Web-Based Access to Community-Based Visualization Functionality. In TeraGrid Conference, Madison, WI, June 2007. [bibtex-entry]

  6. J. Leigh, A.E. Johnson, T.A. DeFanti et al, R. Heiland, and et al. A review of tele-immersive applications in the CAVE research network. In Virtual Reality, 1999. Proceedings., IEEE, pages 180 -187, March 1999. [bibtex-entry]

Posters and Presentations (15)
  1. R. Heiland, J. Champlin, S. Ito, A. Litke, A. Lumsdaine, and J. Beggs. Introduction to Modeling and Computational Neuroscience using Python. Presentation at Society for Mathematical Biology Annual Meeting and Conference, July 2012. [bibtex-entry]

  2. R. Heiland. An Introduction to Python for CompuCell3D. Presentation at CompuCell3D-SBW Workshop, Bloomington, IN, August 2011. [bibtex-entry]

  3. R. Heiland. Python for CompuCell3D. Presentation at the National Institute for Mathematical and Biological Synthesis (NIMBioS), Knoxville, TN, May 2011. [bibtex-entry]

  4. R. Heiland, C. Perry, B. Ream, and A. Lumsdaine. Sculpture, Geometry, and Computer Science. Presentation at SIAM Conference on Computational Science and Engineering, March 2011. [bibtex-entry]

  5. R. Heiland, M. Swat, C. Silva, J.A. Glazier, and A. Lumsdaine. CompuCell3D, Workflows, and Parameter Studies. Presentation at the Supercomputing 2010 Conference, New Orleans, LA, November 2010. [bibtex-entry]

  6. R. Heiland. An Introduction to Python. Presentation at CompuCell3D-SBW Workshop, Bloomington, IN, August 2010. [bibtex-entry]

  7. R. Heiland and J.A. Glazier. Multi-Cell Simulations of Gastrulation and Somitogenesis Using CompuCell3D. International Conference on Computational Bioengineering (ICCB), Bertinoro, Italy, September 2009. [bibtex-entry]

  8. B. Zaitlen and R. Heiland. Spatial Geometry in CompuCell3D. Presentation at the CellML-SBGN-SBO-BioPAX-MIASE Workshop, Auckland, New Zealand, April 2009. [bibtex-entry]

  9. R. Heiland. CompuCell3D: an open source cellular modeling framework. Presentation at the Supercomputing 2008 Conference, Austin, TX, November 2008. [bibtex-entry]

  10. R. Heiland, D. Milsho, and K. Browning. Using Squeak to graphically model symmetries in nature. Poster presentation at the ITAP Teaching and Learning with Technology Conference, West Lafayette, IN, February 2005. [bibtex-entry]

  11. R. Heiland, C. Moad, and S. Mooney. Python-based Tools and Web Services for Structural Bioinformatics. Presentation at SciPy Conference, CalTech, September 2004. [bibtex-entry]

  12. R. Heiland, M.P. Baker, and B.D. Semeraro. A Survey of Visualization Tools for High Performance Computing. Poster presentation at SIAM Parallel Processing for Scientific Computing, San Antonio, TX, March 1999. [bibtex-entry]

  13. R. Heiland and M.P. Baker. Coprocessing: Experience with CUMULVS and pV3. CEWES MSRC/PET TR/99-05, January 1999. [bibtex-entry]

  14. R. Heiland. Object-oriented parallel polygon rendering. Presentation at the GVis Conference, Richland, WA, September 1994. [bibtex-entry]

  15. R. Heiland, E. Kostelich, and D. Armbruster. Extracting large-scale structures from spatiotemporal data with KLTool. Presentation at the Dynamics Days conference, Austin, TX, January 1992. [bibtex-entry]



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