JSIM Software License


Copyright (C) 1999-2009 University of Washington

Developed by the National Simulation Resource

Department of Bioengineering,  Box 355061

University of Washington, Seattle, WA 98195-5061.

Dr. J. B. Bassingthwaighte, Director


Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:


* Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.


* Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.


* Neither the name of the University of Washington nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.


THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS

"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT

LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR

A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR

CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,

EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,

PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR

PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF

LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING

NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS

SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.


ADDITIONAL CONDITIONS


Certain third party code is integrated in this software. Use of this software is conditioned upon complying with the license agreements for those third party codes listed in Table 1.


Table 1


External code

License Name

License url

Distribution Format

Radau

 

http://www.unige.ch/~hairer/prog/licence.txt

source

Dopri5

 

http://www.unige.ch/~hairer/prog/licence.txt

source

CVODE solver

SUNDIALS License

http://www.llnl.gov/CASC/sundials/download/license.html

source

Toms731 solver

ACM Software Copyright and License Agreement

http://www.acm.org/pubs/copyright_policy/softwareCRnotice.html

source

NelderMead optimizer

 

http://www.ee.ucl.ac.uk/~mflanaga/java/

source



For your convenience, certain third party codes are distributed along with this software. Use of this software is conditioned upon complying with the license agreements for those third party codes listed in Table 2.


Table 2


External code

License name

License url

Distribution Format

Java

Sun Microsystems, inc.
Binary code license agreement

http://www.java.com/en/download/license.jsp

binary

CUP parser generator

CUP Parser Generator Copyright Notice, License, and Disclaimer

http://www.cs.princeton.edu/~appel/modern/java/CUP/#LICENSE

binary

JLex lexical analyzer generator

Jlex copyright notice, license and disclaimer

http://www.cs.princeton.edu/~appel/modern/java/JLex/#LICENSE

binary

Scientific Graphics Toolkit

U.S. Department of Commerce (DOC)
Software License for EPIC Software

http://www.epic.noaa.gov/java/license.html

binary

Xerces2 Java Parser

Apache license, version 2.0

http://www.apache.org/licenses/LICENSE-2.0.html

binary

libsbml SBML Library

 

http://sbml.org/Software/libSBML/LibSBML_License

binary

JAMA Java Matrix package

 

http://math.nist.gov/javanumerics/jama/

binary