Software License Agreement

JSim Software (Source Code)

 
The University of Washington ("UW") and Dr. James B.
Bassingthwaighte and Erik Butterworth ("Developers")
give permission for ("you") and your institution
("Institution") to use the JSim software ("Software").
JSim software is a Java-based simulation system for
building quantitative numeric models and analyzing them
with respect to experimental reference data. UW and the
Developers allow you and your Institution to access
Software source code, and perform (run and execute),
copy and modify Software, for internal, non-profit
research purposes, on the following conditions:

The Software remains at your Institution and is not
published, distributed, or otherwise transferred or
made available to other than Institution employees and
students involved in research under your supervision.
If you wish to distribute modified Software you must
obtain written permission from UW.

If you wish to obtain Software for any commercial
purposes, you will need to execute a separate licensing
agreement with UW and pay a fee. This includes, but is
not limited to, using Software to provide services to
outside parties for a fee.

You retain in Software and any modifications to
Software, the copyright, trademark, or other notices
pertaining to Software as provided by UW. You agree to
provide the Developers with feedback on the use of the
Software in your research, and that the Developers and
UW are permitted to use any information you provide in
making changes to the Software at no charge.

You acknowledge that the Developers, UW and its
licensees may develop modifications to Software that
may be substantially similar to your modifications of
Software, and that the Developers, UW and its licensees
shall not be constrained in any way by you or your
Institution in UW's or its licensees' use or management
of such modifications.

If utilization of the Software results in outcomes
which will be published, please specify the version of
Software you used and cite source as follows:

  JSim software (version 1.6.xx) was developed at the National 
  Simulation Resource(physiome.org) at the University of Washington 
  with support from NIH grant ROI EB 001973.

Any risk associated with using the Software at your
Institution is with you and your Institution. Software
is experimental in nature and is made available as a
research courtesy "AS IS," without obligation by UW to
provide accompanying services or support.

UW AND THE DEVELOPERS EXPRESSLY DISCLAIM ANY AND ALL
WARRANTIES REGARDING THE SOFTWARE, WHETHER EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO WARRANTIES
PERTAINING TO MERCHANTABILITY, NON-INFRINGEMENT OR
FITNESS FOR A PARTICULAR PURPOSE.

Certain third party software is integrated in Software.
Table 1 lists the third party software and their
associated license agreements.  You and you Institution
agree to comply with the license agreements for the
third party software listed in Table 1 as a condition
of UW providing Software to you and your Institution.

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 SUNDIAL License http://www.llnl.gov/CASC/sundials/download/license.html source
Toms731 ACM Software Copyright and License Agreement http://www.acm.org/pubs/copyright_policy/softwareCRnotice.html source
NelderMead http://www.ee.ucl.ac.uk/~mflanaga/java/ source
For your convenience, the source distribution of
Software also contains third party software in addition
to JSim as listed in Table 2.  You and your Institution
understand and agree to the applicable license
agreements in Table 2 as a condition of UW providing
Software to you and your Institution.

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 Graphic Toolkit U.S. Department of Commerce (DOC) Software License for EPIC Software http://www.epic.noaa.gov/java/license.html binary
Xerces2 Java-based XML Parser Apache license, version 2.0 http://www.apache.org/licenses/LICENSE-2.0.html binary
JigCell SBML Parser https://biospice.org/BioCOMPLicense.html binary
JAMA http://math.nist.gov/javanumerics/jama/ binary