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Copyright
Copyright © 2013 D2D development team. All rights reserved.
Contact: Andreas Raue - [email protected]
The Data 2 Dynamics (D2D) software is based on software developed by Andreas Raue (http://www.fdmold.uni-freiburg.de/~araue/). Since March 2013 the development is continued by the D2D development team on BitBucket.org and since June 2016 on GitHub.com. Decisions concerning copyright changes remain at Andreas Raue. The software is open source and freely available. Third party software included in the D2D software and their respective license information is given below.
Source: http://computation.llnl.gov/casc/sundials
Copyright © 2002, The Regents of the University of California. Produced at the Lawrence Livermore National Laboratory. All rights reserved.
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 disclaimer below.
- Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the disclaimer (as noted below) in the documentation and/or other materials provided with the distribution.
- Neither the name of the UC/LLNL 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 REGENTS OF THE UNIVERSITY OF CALIFORNIA, THE U.S. DEPARTMENT OF ENERGY 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 BSD Notice:
- This notice is required to be provided under our contract with the U.S. Department of Energy (DOE). This work was produced at the University of California, Lawrence Livermore National Laboratory under Contract No. W-7405-ENG-48 with the DOE.
- Neither the United States Government nor the University of California nor any of their employees, makes any warranty, express or implied, or assumes any liability or responsibility for the accuracy, completeness, or usefulness of any information, apparatus, product, or process disclosed, or represents that its use would not infringe privately-owned rights.
- Also, reference herein to any specific commercial products, process, or services by trade name, trademark, manufacturer or otherwise does not necessarily constitute or imply its endorsement, recommendation, or favoring by the United States Government or the University of California. The views and opinions of authors expressed herein do not necessarily state or reflect those of the United States Government or the University of California, and shall not be used for advertising or product endorsement purposes.
** Source: ** http://www.suitesparse.com
KLU, Copyright (C) 2004-2013, University of Florida by Timothy A. Davis and Ekanathan Palamadai.
KLU is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version, GNU LGPL.
Source: http://sources.redhat.com/pthreads-win32
Copyright © 2001,2006 Ross P. Johnson. All rights reserved.
Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed. Pthreads-win32 is covered by the GNU LESSER GENERAL PUBLIC LICENSE GNU LGPL.
Source: http://www.ra.cs.uni-tuebingen.de/software/EvA2
The EvA2 software is available under GNU LESSER GENERAL PUBLIC LICENSE GNU LGPL and incorporates the terms and conditions of version 3 of the GNU General Public License GNU GPL.
Source: http://strscne.de.unifi.it/
Authors:
- Stefania Bellavia - [email protected]
- Maria Macconi - [email protected]
- Benedetta Morini - [email protected]
STRSCNE code has non-commercial purposes. We assume no responsibility for any errors that may exist in the provided routines. We welcome questions, comments, recommended changes and bug reports.
If you use this code, the authors would appreciate your acknowledging having done so in the reports, publications, theses, etc., resulting from their use.
- Stefania Bellavia, M. Macconi, B. Morini, An affine scaling trust-region approach to bound-constrained nonlinear systems Applied Numer. Math., Vol. 44, pp. 257-180, 2003
- Stefania Bellavia, M. Macconi, B. Morini, STRSCNE: A Scaled Trust Region Solver for Constrained Nonlinear Equations, Computational Optimization and Applications, Vol. 98, pp. 31-50, 2004.
- Installation and system requirements
- Setting up models
- First steps
- Advanced events and pre-equilibration
- Computation of integration-based prediction bands
- How is the architecture of the code and the most important commands?
- What are the most important fields of the global variable ar?
- What are the most important functions?
- Optimization algorithms available in the d2d-framework
- Objective function, likelhood and chi-square in the d2d framework
- How to set up priors?
- How to set up steady state constraints?
- How do I restart the solver upon a step input?
- How to deal with integrator tolerances?
- How to implement a bolus injection?
- How to implement washing and an injection?
- How to implement a moment ODE model?
- How to run PLE calculations on a Cluster?