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Cardiac Physiome Society workshop: November 6-9, 2017 , Toronto

Published Software of the National Simulation Resource


A short description of the published software available for distribution from the National Simulation Resource is given below. The citation for the application publication is given.

Each package includes the source code for the product, its test program, and all subprograms upon which they depend. Also included are a README file with notes about the files, a manual page (plain text and UNIX troff source versions), a Makefile to create and run the test program, and the auxiliary files required by the test program.

These software packages can be transferred using anonymous ftp by clicking on the name of the package desired. Transferred files are compressed tar archives. (Some browsers will uncompress the file automatically). Extracting files from the archive will create a new directory in the current directory into which the software files will be written.

Available Software Products


Description: Non-linear equilibrium binding blood-tissue exchange model for oxygen and water

Publication: Li, Zheng, T. Yipintsoi, and J. B. Bassingthwaighte. Nonliner model for capillary-tissue oxyten trantport and metabolism. Ann. Biomed. Eng. 25:604-619, 1997.


Description: Compute a frequency histogram of regional relative flows to model blood flow heterogeneity.

Publication: King, R. B., G. M. Raymond, and J. B. Bassingthwaighte. Modeling blood flow heterogeneity. Ann. Biomed. Eng. 24:352-372, 1996.


Description: Non-linear, least squares optimizer with sensitivity scaling.

Publication: Chan, I. S., A. A. Goldstein, and J. B. Bassingthwaighte. SENSOP: A derivative-free solver for non-linear least squares with sensitivity scaling. Ann. Biomed. Eng. 21:621-631, 1993.


Description: A non-exchanging vascular operator for modeling convection through large blood vessels.

Publication: King, R. B., A. Deussen, G. R. Raymond, and J. B. Bassingthwaighte. A vascular transport operator. Am. J. Physiol. 265 (Heart Circ. Physiol. 34) :H2196-H2208, 1993


Description: A three region, two barrier, distributed blood-tissue exchange operator with axial dispersion.

Publication: Bassingthwaighte, J. B., I. S. Chan, and C. Y. Wang. Computationally efficient algorithms for capillary convection-permeation-diffusion models for blood-tissue exchange. Ann. Biomed. Eng. 20:687-725, 1992


Description: Weighted, geometric mean linear regression.

Publication: Bassingthwaighte, J. B., M. A. Malone, T. C. Moffett, R. B. King, I. S. Chan, J. M. Link, and K. A. Krohn. Molecular and particulate depositions for regional myocardial flows in sheep. Circ. Res. 66:1328-1344, 1990


Description: A four region, three barrier, distributed blood-tissue exchange operator with axial dispersion.

Publication: Bassingthwaighte, J. B., I. S. Chan, and C. Y. Wang. Blood-tissue exchange via transport and transformation by endothelial cells. Circ. Res. 65:997-1020, 1989

Problems and Questions

To report any problems or obtain further information, send e-mail to:

Gary Raymond

Last modified 13May08, 12:28 pm.

Model development and archiving support at provided by the following grants: NIH/NIBIB BE08407 Software Integration, JSim and SBW 6/1/09-5/31/13; NIH/NHLBI T15 HL88516-01 Modeling for Heart, Lung and Blood: From Cell to Organ, 4/1/07-3/31/11; NSF BES-0506477 Adaptive Multi-Scale Model Simulation, 8/15/05-7/31/08; NIH/NHLBI R01 HL073598 Core 3: 3D Imaging and Computer Modeling of the Respiratory Tract, 9/1/04-8/31/09; as well as prior support from NIH/NCRR P41 RR01243 Simulation Resource in Circulatory Mass Transport and Exchange, 12/1/1980-11/30/01 and NIH/NIBIB R01 EB001973 JSim: A Simulation Analysis Platform, 3/1/02-2/28/07.