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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]
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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, N.J.,
2009.
[bibtex-entry]
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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]
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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]
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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]
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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]
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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]
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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]
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R. Heiland,
M. P. Baker,
and 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]
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D. Armbruster,
R. Heiland,
and E. J. Kostelich.
KLTool: A tool to analyze spatiotemporal complexity.
Chaos,
4(2):421-424,
1994.
[bibtex-entry]
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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]
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R. Heiland,
C. Perry,
B. Ream,
and A. Lumsdaine.
Sculpture, Geometry, and Computer Science.
In SIAM Conference on Computational Science and Engineering,
Reno, NV,
March 2011.
[bibtex-entry]
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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]
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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]
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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]
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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]
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R. Heiland.
Python for CompuCell3D.
Presentation at the National Institute for Mathematical and Biological Synthesis (NIMBioS), Knoxville, TN,
May 2011.
[bibtex-entry]
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R. Heiland.
An Introduction to Python for CompuCell3D.
Presentation at CompuCell3D-SBW Workshop, Bloomington, IN,
August 2011.
[bibtex-entry]
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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]
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R. Heiland.
An Introduction to Python.
Presentation at CompuCell3D-SBW Workshop, Bloomington, IN,
August 2010.
[bibtex-entry]
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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]
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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]
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Randy Heiland.
CompuCell3D: an open source cellular modeling framework.
Presentation at the Supercomputing 2008 Conference, Austin, TX,
November 2008.
[bibtex-entry]
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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]
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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]
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