# 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