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<h1> DDE-BIFTOOL v. |version|</h1>
<ul>
<li><a href="#install">Installation</a></li>
<li><a href="#refdoc">Reference and documentation</a></li>
<li><a href="#authors">Contributors</a></li>
<li><a href="#citation">Citation</a></li>
<li><a href="#copyright">Copyright, License and No-warranty notice</a></li>
</ul>
<hr>
<a name="install"></a>
<h2>Installation</h2>
<ul><li>Unzipping ddebiftool.zip creates a "dde_biftool" directory (named "dde_biftool") containing the subfolders:
<ul>
<li><a href="ddebiftool/index.html">ddebiftool</a> (basic DDE-BIFTOOL routines),</li>
<li><a href="demos/index.html">demos</a> (example scripts illustrating the use of DDE-BIFTOOL),</li>
<li><a href="ddebiftool_extra_psol/html/index.html">ddebiftool_extra_psol</a> (extension for local bifurcations of periodic orbits),</li>
<li><a href="ddebiftool_extra_nmfm/index.html">ddebiftool_extra_nmfm</a> (extension for normal form coefficient computations at local bifurcations of equilibria in DDEs with constant delay),</li>
<li><a href="ddebiftool_utilities/html/index.html">ddebiftool_utilities</a> (auxiliary functions),</li>
<li><a href="ddebiftool_extra_rotsym/html/index.html">ddebiftool_extra_rotsym</a> (extension for systems with rotational symmetry).</li>
<li><a href="external_tools/Readme.html">external_tools</a> (support scripts, such as a Mathematica and a Maple script for generating derivative functions used in DDE-BIFTOOL).</li>
</ul></li>
<li>To test the tutorial demo "<a href="demos/neuron/html/demo1.html">neuron</a>" (the instructions below assume familiarity with Matlab or octave):</li>
<ul>
<LI>Start Matlab (version 7.0 or higher) or octave (tested with version 3.8.1)</LI>
<li>Inside Matlab or octave change working directory to demos/neuron using the "cd" command</li>
<li>Execute script "rundemo" to perform all steps of the tutorial demo</li>
<li>Compare the outputs on screen and in figure windows with the published output in <a href="demos/neuron/html/demo1.html">demos/neuron/html/demo1.html</a>.</li>
</ul>
</li>
</ul>
<hr>
<a name="refdoc"></a>
<h2>Reference and documentation</h2>
<dl>
<dt>Current download URL on Sourceforge (including access to versions from 3.1 onward)</dt><dd><a href="https://sourceforge.net/projects/ddebiftool/"> https://sourceforge.net/projects/ddebiftool/<a></dd>
<dt>URL of original DDE-BIFTOOL website (including access to versions
up to
3.0)</dt><dd><a href="http://twr.cs.kuleuven.be/research/software/delay/ddebiftool.shtml">
http://twr.cs.kuleuven.be/research/software/delay/ddebiftool.shtml<a></dd>
<dt>Contact (bug reports, questions etc)</dt><dd><a href="https://sourceforge.net/projects/ddebiftool/support">https://sourceforge.net/projects/ddebiftool/support</a></dd>
<dt>Manual for version 2.0x</dt><dd>K. Engelborghs, T. Luzyanina, G. Samaey. DDE-BIFTOOL v. 2.00:
a Matlab package for bifurcation analysis of delay differential
equations. Technical Report TW-330</dd>
<dt>Manual for current version</dt><dd><a href="doc/manual.pdf">manual.pdf</a> (v. |version|), stored on arxiv: <a href="http://arxiv.org/abs/1406.7144">arxiv.org/abs/1406.7144</a></dd>
<dt>Changes for v. 2.03</dt><dd><a href="doc/Addendum_Manual_DDE-BIFTOOL_2_03.pdf">Addendum_Manual_DDE-BIFTOOL_2_03.pdf</a> (by K. Verheyden)</dd>
<dt>Changes for v. 3.0</dt><dd><a href="doc/Changes-v3.pdf">Changes-v3.pdf</a> (by J. Sieber)</dd>
<dt>Description of extensions ddebiftool_extra_psol and ddebiftool_extra_rotsym</dt><dd><a href="doc/Extra_psol_extension.pdf">Extra_psol_extension.pdf</a> (by J. Sieber)</dd>
<dt>Description of the extention ddebiftool_extra_nmfm<br>
</dt>
<dd><a href="doc/nmfm_extension_description.pdf">nmfm_extension_desctiption.pdf</a>
(by M. Bosschaert, B. Wage, Yu.A. Kuznetsov)</dd>
<dt>Overview of documented demos</dt><dd><a href="demos/index.html">demos/index.html</a></dd>
</dl>
<hr>
<a name="authors"></a>
<h2> Contributors</h2>
<h5>Original code and documentation (v. 2.03)</h5>
K. Engelborghs, T. Luzyanina, G. Samaey. D. Roose, K. Verheyden<br>
K.U.Leuven<br>
Department of Computer Science<br>
Celestijnenlaan 200A<br>
B-3001 Leuven<br>
Belgium<br>
<h5>Revision for v. 3.0, 3.1.x</h5>
<h5> Bifurcations of periodic orbits</h5>
J. Sieber<br>
College for Engineering, Mathematics and Physical Sciences, University of Exeter (UK),<br>
<a href="http://emps.exeter.ac.uk/mathematics/staff/js543">emps.exeter.ac.uk/mathematics/staff/js543</a>
<h5>Normal form coefficients for bifurcations of equilibria</h5>
S. Janssens, B. Wage, M. Bosschaert, Yu.A. Kuznetsov<br>
Utrecht University<br>
Department of Mathematics<br>
Budapestlaan 6<br>
3584 CD Utrecht<br>
The Netherlands<br>
<a href="http://www.staff.science.uu.nl/%7Ekouzn101/">www.staff.science.uu.nl/~kouzn101/ ((Y.A. Kuznetsov)</a>
<h5>Revision for v. 3.2a</h5>
<h5>Code generation with symbolic Matlab/octave toolbox</h5>
<h5>Branching off from steady-state codimension-2 bifurcation</h5>
Maikel Bosschaert, Jan Sieber, Y. Kuznetsov
<h5>Automatic generation of right-hand sides and derivatives in Mathematica</h5>
D. Pieroux (Universite Libre de Bruxelles, ULB, Belgium)
<h5>Demo for phase oscillator</h5>
A. Yeldesbay (Potsdam University, Germany)
<h5>Methods and parts of implementation for neutral DDEs and demo</h5>
D.A.W. Barton (University of Bristol, UK)<br>
Soizic Terrien (University of Auckland, NZ)<br>
Dennis Hessel, Svetlana Gurevich (University of Münster, Germany)<br>
Julien Javaloyes (University of Palma de Mallorca, Spain)<br>
<h5>External code</h5>
(included)<br>
<a href="http://www.chebfun.org">chebfun</a> (legpts.m)<br>
<a href="http://csclab.murraystate.edu/bob.pilgrim/445/munkres.html">Munkres'
Assignment Algorithm, Modified for Rectangular Matrices</a> (munkres.m) version
2.3 by Yi Cao at Cranfield University on 11th September 2011
<hr>
<a name="citation"></a>
<h2>Citation</h2>
Scientific publications, for which the package DDE-BIFTOOL has been used, shall mention usage of the package DDE-BIFTOOL, and shall cite the following publications to ensure proper attribution and reproducibility:
<ul>
<li> K. Engelborghs, T. Luzyanina, and D. Roose, Numerical bifurcation analysis of delay differential equations using DDE-BIFTOOL, ACM Trans. Math. Softw. 28 (1), pp. 1-21, 2002.</li>
<li> K. Engelborghs, T. Luzyanina, G. Samaey. DDE-BIFTOOL v. 2.00: a Matlab package for bifurcation analysis of delay differential equations. Technical Report TW-330, Department of Computer Science, K.U.Leuven, Leuven, Belgium, 2001.</li>
<li>[Manual of current version, permanent link]<br> J. Sieber, K. Engelborghs, T. Luzyanina, G. Samaey, D. Roose: DDE-BIFTOOL Manual - Bifurcation analysis of delay differential equations. <a href="http://arxiv.org/abs/1406.7144">arxiv.org/abs/1406.7144</a>.</li>
<li>[Theoretical background for computation of normal form
coefficients, permanent link]<br clear="all">
Sebastiaan Janssens: On a Normalization Technique for
Codimension Two Bifurcations of Equilibria of Delay Differential
Equations. Master Thesis, Utrecht University (NL), supervised by
Yu.A. Kuznetsov and O. Diekmann, <a href="http://dspace.library.uu.nl/handle/1874/312252">dspace.library.uu.nl/handle/1874/312252</a>,
2010.<br>
</li>
<li>[Normal form implementation for Hopf-related cases, permanent
link]<br clear="all">
Bram Wage: Normal form computations for Delay Differential Equations in DDE-BIFTOOL. Master Thesis, Utrecht University (NL), supervised by Y.A. Kuznetsov,
<a href="http://dspace.library.uu.nl/handle/1874/296912">dspace.library.uu.nl/handle/1874/296912</a>, 2014.<br/>
</li>
<li> [Switching from codim-2 bifurcations]<br clear="all">
M. M. Bosschaert, S. G. Janssens, Y. A. Kuznetsov: Switching to nonhyperbolic cycles from codimension two bifurcations of equilibria of delay differential equations. Preprint <a href="https://arxiv.org/abs/1903.08276">arxiv</a>, 2017.
</li>
<li> [Collocation of neutral DDEs]<br clear="all">
D.A.W. Barton, B. KrauskopF, and R. E. Wilson: Collocation schemes for periodic solutions of neutral delay
differential equations. Journal of Difference Equations and Applications
12(11):1087-1101, 2006.</li>
</ul>
<hr>
<a name="copyright"></a>
<h2>Copyright, License and No-warranty Notice</h2>
<p>
|license|
</p>
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