2010-10-08    <guravage@caterpie.sen.cwi.nl>

	* auxin_growth.xml: Added export_interval and export_fn_prefix parameters.

2010-06-23    <guravage@caterpie.sen.cwi.nl>

	* Added: tutorial3_init.xml

	tutorial4_init.xml

	tutorial5_init.xml

	* Removed: bend.xml

	circ.xml

	explant.xml

	init.xml

	one_acc_point_van3.xml

	one_acc_point_van3_growth.xml

	one_acc_point_van3_growth2.xml

	tissue.xml

<?xml version="1.0" encoding="UTF-8"?>

<!-- 

  $Rev$:  Revision of last commit

  $Author$:  Author of last commit

  $Source$:  Source file

  $Date$:  Date of last commit

  This file is part of the Virtual Leaf.

  The Virtual Leaf is free software: you can redistribute it and/or modify

  it under the terms of the GNU General Public License as published by

  the Free Software Foundation, either version 3 of the License, or

  (at your option) any later version.

  The Virtual Leaf is distributed in the hope that it will be useful,

  but WITHOUT ANY WARRANTY; without even the implied warranty of

  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the

  GNU General Public License for more details.

  You should have received a copy of the GNU General Public License

  along with the Virtual Leaf.  If not, see <http://www.gnu.org/licenses/>.

  Copyright 2010 Roeland Merks.

-->

<leaf name="/Users/roel/VLeafClean_plugin/Snapshot/VLeafMacOSX/auxin_growth.xml" date="Sat Aug 29 18:28:19 2009" simtime="11660">

  <parameter>

    <par name="export_interval" val="1000"/>

    <par name="arrowcolor" val="white"/>

    <par name="arrowsize" val="10"/>

    <par name="textcolor" val="red"/>

    <par name="cellnumsize" val="1"/>

    <par name="nodenumsize" val="1"/>

    <par name="node_mag" val="1"/>

    <par name="outlinewidth" val="1"/>

    <par name="cell_outline_color" val="forestgreen"/>

    <par name="resize_stride" val="10"/>

    <par name="T" val="1"/>

    <par name="lambda_length" val="100"/>

    <par name="lambda_celllength" val="0"/>

    <par name="target_length" val="60"/>

    <par name="cell_expansion_rate" val="10"/>

    <par name="cell_div_expansion_rate" val="10"/>

    <par name="auxin_dependent_growth" val="true"/>

    <par name="ode_accuracy" val="0.0001"/>

    <par name="mc_stepsize" val="0.4"/>

    <par name="mc_cell_stepsize" val="0.2"/>

    <par name="energy_threshold" val="1000"/>

    <par name="bend_lambda" val="0"/>

    <par name="alignment_lambda" val="0"/>

    <par name="rel_cell_div_threshold" val="2"/>

    <par name="rel_perimeter_stiffness" val="2"/>

    <par name="collapse_node_threshold" val="0.05"/>

    <par name="morphogen_div_threshold" val="0.2"/>

    <par name="morphogen_expansion_threshold" val="0.01"/>

    <par name="copy_wall" val="true"/>

    <par name="source" val="0"/>

    <par name="D">

      <valarray>

        <val v="1e-06"/>

        <val v="0"/>

        <val v="0"/>

        <val v="0"/>

      </valarray>

    </par>

    <par name="initval">

      <valarray>

        <val v="0"/>

        <val v="1"/>

        <val v="0"/>

        <val v="0"/>

      </valarray>

    </par>

    <par name="k1" val="1"/>

    <par name="k2" val="0.3"/>

    <par name="r" val="1"/>

    <par name="kr" val="1"/>

    <par name="km" val="1"/>

    <par name="Pi_tot" val="1"/>

    <par name="transport" val="0.36"/>

    <par name="ka" val="1"/>

    <par name="pin_prod" val="0"/>

    <par name="pin_prod_in_epidermis" val="0"/>

    <par name="pin_breakdown" val="0"/>

    <par name="pin_breakdown_internal" val="0.001"/>

    <par name="aux1prod" val="0.001"/>

    <par name="aux1prodmeso" val="0"/>

    <par name="aux1decay" val="0.001"/>

    <par name="aux1decaymeso" val="0.1"/>

    <par name="aux1transport" val="0.036"/>

    <par name="aux_cons" val="0"/>

    <par name="aux_breakdown" val="0.0001"/>

    <par name="kaux1" val="1"/>

    <par name="kap" val="1"/>

    <par name="leaf_tip_source" val="0.0001"/>

    <par name="sam_efflux" val="0.0001"/>

    <par name="sam_auxin" val="10"/>

    <par name="sam_auxin_breakdown" val="0"/>

    <par name="dt" val="0.1"/>

    <par name="rd_dt" val="10"/>

    <par name="datadir" val="auxin_growth"/>

    <par name="movie" val="true"/>

    <par name="nit" val="100000"/>

    <par name="maxt" val="1e+06"/>

    <par name="storage_stride" val="10"/>

    <par name="xml_storage_stride" val="500"/>

    <par name="rseed" val="-1"/>

    <par name="constituous_expansion_limit" val="16"/>

    <par name="vessel_inh_level" val="1"/>

    <par name="vessel_expansion_rate" val="0.25"/>

    <par name="d" val="0"/>

    <par name="e" val="0"/>

    <par name="f" val="0"/>

    <par name="c" val="0"/>

    <par name="mu" val="0"/>

    <par name="nu" val="0"/>

    <par name="rho0" val="0"/>

    <par name="rho1" val="0"/>

    <par name="c0" val="0"/>

    <par name="gamma" val="0"/>

    <par name="eps" val="0"/>

  </parameter>

  <code name="VirtualLeaf.cpp">#include &lt;fstream&gt;

#include <sstream>

#include <cstring>

#include <functional> 

#include <getopt.h>

#include <cerrno>

#include "mesh.h"

#include "parameter.h"

#include "random.h"

#include "pi.h"

#include "cellitem.h"

#include "canvas.h"

#include "cell.h"

#include "output.h"

#include <qwidget.h>

#include <q3process.h>

#include <qapplication.h>

#include <QDesktopWidget>

#include <QGraphicsScene>

#include <QMessageBox>

//Added by qt3to4:

#include <QMouseEvent>

#include <unistd.h>

#include <q3textstream.h> 

#ifdef HAVE_QWT

#include "data_plot.h"

#endif

#include <QPalette>

#include <QBrush>

#include <QToolTip>

#include "simplugin.h"

#include "testplugin.h"

/* #define _xstr_(s) _str_(s)

#define _str_(s) #s

#include _xstr_(REACTIONS_HEADER)

*/

extern Parameter par;

MainBase *main_window = 0;

double auxin_account = 0.;

TestPlugin *plugin = new TestPlugin();

#ifdef XFIGGRAPHICS

#define TIMESTEP double Graphics::TimeStep(void)

#endif

class PrintNode {

public:

  void operator() (const Node &n) const 

  {

    cerr << n.Index() << ": " << n <<  endl;

  }

};

class EdgeSource {

public:

  void operator() (Cell &c) {

    if (c.AtBoundaryP()) {

      cerr << "Cell " << c.Index() << " is a source cell.\n";

      c.SetSource(0,par.source);

    } else {

      cerr << "Cell " << c.Index() << " is _not_ a source cell.\n";

    }

  }

};

class CellInfo {

public:

  void operator() (Cell &c,std::ostream &os) const {

    os << "Cell " << c.index << " says: " << endl;

    os << "c.nodes.size() = " << c.nodes.size() << endl;

    for (list<Node *>::iterator i=c.nodes.begin();

	 i!=c.nodes.end();

	 i++) {

      cerr << (*i)->Index() << " ";

    }

    cerr << endl;

  }

};

double PINSum(Cell &c) {

	return c.Chemical(1) + c.SumTransporters(1);// + c.ReduceCellAndWalls<double>( complex_PijAj );

}

<h1>Friday 24 September 2010</h1>

<dl class="docutils">

<dt>To Do:</dt>

<dd><ol class="first last arabic simple">

<li>Publish our mercurial repositories (Chris/Martin). This may mesh with deploying Plone.</li>

<li>Create a vleaf mailing list (Henk).</li>

</ol>

</dd>

</dl>

<p>Found an article on SBRML - a markup language for associating systems

biology data with models. At a glance the schema seems bigger than

SED-ML's, but SBRML appears to be SBML specific.</p>

</div>

<div class="section" id="monday-27-september-2010">

<h1>Monday 27 September 2010</h1>

<p>Spoke with Chris about publishing the Mercurial repositories and

deploying Plone. Both can be accomplished in their own project space

on a server in the DMZ. Chris said he would supply me with login

credentials for both accounts. I will install Plone and Chris (or

Maarten) will help me configure Apache/nginx and Varnish. Chris will

install the required Mercurial packages; after which I can clone the

repositories to their new home.</p>

</div>

<div class="section" id="tuesday-5-october-20010">

<h1>Tuesday 5 October 20010</h1>

<div class="section" id="tutorial0-pro">

<h2>tutorial0.pro</h2>

<p>Added simplugin.h to list of header files. NB: this is the only

tutorial in which simplugin.h appears.</p>

</div>

<div class="section" id="auxingrowthplugin-h">

<h2>auxingrowthplugin.h</h2>

<p>Declared, and defined, a virtual function named <tt class="docutils literal">DefaultLeafML()</tt>

which merely returns a QString naming a LeafML filename sans path.</p>

</div>

<div class="section" id="virtualleaf-cpp">

<h2>VirtualLeaf.cpp</h2>

<p>Moved <tt class="docutils literal"><span class="pre">Cell::SetMagnification()</span></tt> and <tt class="docutils literal"><span class="pre">Cell::SetOffset()</span></tt> from

<tt class="docutils literal">main()</tt> to <tt class="docutils literal"><span class="pre">MainBase::Init()</span></tt>.</p>

</div>

<div class="section" id="canvas-h">

<h2>canvas.h</h2>

<p>Declare <tt class="docutils literal">exportCellData()</tt>.</p>

</div>

<div class="section" id="canvas-cpp">

<h2>canvas.cpp</h2>

<p>Add an 'Export cell areas' to the file dropdown menu which invokes - surprise - <tt class="docutils literal"><span class="pre">Main::exportCellData()</span></tt>:</p>

<pre class="literal-block">

void Main::exportCellData(void) {

  QFile file("areas.csv");

  if ( file.open( IO_WriteOnly ) ) {

    QTextStream stream( &file );

    mesh.CSVExportCellData(stream);

    mesh.CSVExportMeshData(stream);

    file.close();

  }

}

</pre>

</div>

<div class="section" id="mesh-h">

<h2>mesh.h</h2>

<p>Include <tt class="docutils literal">&lt;QTextStream&gt;</tt></p>

<p>Set the boundary_poloygon pointer to zero in the class constructor,

and delete it, if it exists, in the class destructor.</p>

<p>Declare <tt class="docutils literal">Compactness()</tt>, <tt class="docutils literal">CSVExportCellData()</tt> and <tt class="docutils literal">CSVExportMeshData()</tt>:</p>

<pre class="literal-block">

double Compactness(double *res_compactness=0, double *res_area=0, double *res_cell_area=0);

void CSVExportCellData(QTextStream &csv_stream) const;

void CSVExportMeshData(QTextStream &csv_stream);

</pre>

</div>

<div class="section" id="mesh-cpp">

<h2>mesh.cpp</h2>

<p>In <tt class="docutils literal"><span class="pre">mesh::clear()</span></tt>, delete the boundary_polygon only if the pointer hasn't been assigned:</p>

<pre class="literal-block">

if (boundary_polygon) {

   delete boundary_polygon;

   boundary_polygon=0;

 }

</pre>

<p>Ditto for <tt class="docutils literal"><span class="pre">mesh::clean()</span></tt>.</p>

<p>Define the code for <tt class="docutils literal">Compactness()</tt>, <tt class="docutils literal">CSVExportCellData()</tt> and <tt class="docutils literal">CSVExportMeshData()</tt>.</p>

</div>

<div class="section" id="modelcatalogue-cpp">

<h2>modelcatalogue.cpp</h2>

<p>In <tt class="docutils literal">InstallModel()</tt>, find and load the default LeafML file.</p>

</div>

<div class="section" id="simplugin-h">

<h2>simplugin.h</h2>

<p>Declare <tt class="docutils literal">DefaultLeafML()</tt>:</p>

<pre class="literal-block">

// Default LeafML-file to be read after model startup

virtual QString DefaultLeafML(void);

</pre>

</div>

<div class="section" id="simplugin-cpp">

<h2>simplugin.cpp</h2>

<p>Define <tt class="docutils literal">DefaultLeafML()</tt>. Returns an empty <tt class="docutils literal">QString</tt>:</p>

<pre class="literal-block">

QString SimPluginInterface::DefaultLeafML(void) { return QString(); }

</pre>

</div>

<div class="section" id="xmlwrite-cpp">

<h2>xmlwrite.cpp</h2>

<p>In <tt class="docutils literal"><span class="pre">Mesh::XMLReadCells()</span></tt> - Delete the boundary_ploygon only if its

pointer has been assigned.</p>

</div>

</div>

<div class="section" id="wednesday-6-october-2010">

<h1>Wednesday 6 October 2010</h1>

<p>Wrote Simon van Mourik about his missing libiconv-2.dll.</p>

</div>

<div class="section" id="thursday-7-october-2010">

<h1>Thursday 7 October 2010</h1>

<p>Added a Q3FileDialog in <tt class="docutils literal"><span class="pre">canvas.cpp:Main::exportCellData(void)</span></tt> to

choose where to write the exported cell data.</p>

</div>

<div class="section" id="friday-8-october-2010">

<h1>Friday 8 October 2010</h1>

<p>Added new parameters to control perodic cell exprt data.</p>

<p>Added code to relize perodic cell export.</p>

</div>

<div class="section" id="monday-11-october-2010">

<h1>Monday 11 October 2010</h1>

<div class="section" id="mercurial-hooks">

<h2>Mercurial hooks</h2>

<p>Tried several alternatives for Mercurial's <tt class="docutils literal">pretxnchangegroup.forbid_2heads</tt> hook.</p>

<ol class="arabic simple">

<li><a class="reference external" href="http://bitbucket.org/dgc/headcount">http://bitbucket.org/dgc/headcount</a>: <strong>Headcount</strong> <tt class="docutils literal">ui</tt> complains of a missing data member</li>

<li><a class="reference external" href="http://stackoverflow.com/questions/1705921/useful-mercurial-hooks">http://stackoverflow.com/questions/1705921/useful-mercurial-hooks</a>: <strong>forbid2_heads.py</strong> doesn't load</li>

<li><a class="reference external" href="http://davidherron.com/node/961">http://davidherron.com/node/961</a>: <strong>forbid2_heads.sh</strong> works as advertised</li>

</ol>

</div>

<div class="section" id="mercurial-repositories">

<h2>Mercurial Repositories</h2>

<p>Tried to install Rhode Code from: <a class="reference external" href="http://packages.python.org/RhodeCode">http://packages.python.org/RhodeCode</a>.</p>

<ol class="arabic simple">

<li><a class="reference external" href="http://bitbucket.org/marcinkuzminski/rhodecode">http://bitbucket.org/marcinkuzminski/rhodecode</a></li>

<li><a class="reference external" href="http://packages.python.org/RhodeCode">http://packages.python.org/RhodeCode</a>, <a class="reference external" href="http://pypi.python.org/pypi/RhodeCode/1.0.0rc3">http://pypi.python.org/pypi/RhodeCode/1.0.0rc3</a></li>

<li><a class="reference external" href="http://hg.python-works.com">http://hg.python-works.com</a> (demo,demo)</li>

<li><a class="reference external" href="http://bitbucket.org/bfrog/cutehg">http://bitbucket.org/bfrog/cutehg</a></li>

<li><a class="reference external" href="http://pypi.python.org/pypi/SIP">http://pypi.python.org/pypi/SIP</a>, <a class="reference external" href="http://www.riverbankcomputing.com/hg/sip">http://www.riverbankcomputing.com/hg/sip</a></li>

<li><a class="reference external" href="http://pypi.python.org/pypi/PyQt">http://pypi.python.org/pypi/PyQt</a></li>

<li><a class="reference external" href="http://ask.github.com/celery">http://ask.github.com/celery</a></li>

</ol>

<p>All goes tolerably until you tick in the url; at which point RhodeCode complains that:</p>

<pre class="literal-block">

Exception happened during processing of request from ('127.0.0.1', 35803)

Traceback (most recent call last):

 File "/ufs/guravage/.archive/mas/mr/rhodecode/lib/python2.6/site-packages/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py", line 1068, in process_request_in_thread

   self.finish_request(request, client_address)

 File "/ufs/guravage/opt/Python-2.6.2/lib/python2.6/SocketServer.py", line 320, in finish_request

   self.RequestHandlerClass(request, client_address, self)

 File "/ufs/guravage/opt/Python-2.6.2/lib/python2.6/SocketServer.py", line 615, in __init__

   self.handle()

 File "/ufs/guravage/.archive/mas/mr/rhodecode/lib/python2.6/site-packages/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py", line 442, in handle

   BaseHTTPRequestHandler.handle(self)

 File "/ufs/guravage/opt/Python-2.6.2/lib/python2.6/BaseHTTPServer.py", line 329, in handle

   self.handle_one_request()

 File "/ufs/guravage/.archive/mas/mr/rhodecode/lib/python2.6/site-packages/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py", line 437, in handle_one_request

   self.wsgi_execute()

 File "/ufs/guravage/.archive/mas/mr/rhodecode/lib/python2.6/site-packages/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py", line 287, in wsgi_execute

   self.wsgi_start_response)

 File "/ufs/guravage/.archive/mas/mr/rhodecode/lib/python2.6/site-packages/Paste-1.7.5.1-py2.6.egg/paste/cascade.py", line 130, in __call__

   return self.apps[-1](environ, start_response)

 File "/ufs/guravage/.archive/mas/mr/rhodecode/lib/python2.6/site-packages/Paste-1.7.5.1-py2.6.egg/paste/registry.py", line 379, in __call__

   app_iter = self.application(environ, start_response)

 File "/ufs/guravage/.archive/mas/mr/rhodecode/lib/python2.6/site-packages/RhodeCode-1.0.0rc1-py2.6.egg/rhodecode/lib/middleware/https_fixup.py", line 33, in __call__

   return self.application(environ, start_response)

 File "/ufs/guravage/.archive/mas/mr/rhodecode/lib/python2.6/site-packages/Pylons-1.0-py2.6.egg/pylons/middleware.py", line 163, in __call__

   self.app, new_environ, catch_exc_info=True)

 File "/ufs/guravage/.archive/mas/mr/rhodecode/lib/python2.6/site-packages/Pylons-1.0-py2.6.egg/pylons/util.py", line 48, in call_wsgi_application

   app_iter = application(environ, start_response)

 File "/ufs/guravage/.archive/mas/mr/rhodecode/lib/python2.6/site-packages/WebError-0.10.2-py2.6.egg/weberror/errormiddleware.py", line 156, in __call__

   return self.application(environ, start_response)

 File "/ufs/guravage/.archive/mas/mr/rhodecode/lib/python2.6/site-packages/RhodeCode-1.0.0rc1-py2.6.egg/rhodecode/lib/middleware/simplehg.py", line 55, in __call__

   return self.application(environ, start_response)

 File "/ufs/guravage/.archive/mas/mr/rhodecode/lib/python2.6/site-packages/Beaker-1.5.4-py2.6.egg/beaker/middleware.py", line 152, in __call__

   return self.wrap_app(environ, session_start_response)

 File "/ufs/guravage/.archive/mas/mr/rhodecode/lib/python2.6/site-packages/Routes-1.12.3-py2.6.egg/routes/middleware.py", line 131, in __call__

   response = self.app(environ, start_response)

 File "/ufs/guravage/.archive/mas/mr/rhodecode/lib/python2.6/site-packages/Pylons-1.0-py2.6.egg/pylons/wsgiapp.py", line 98, in __call__

   self.setup_app_env(environ, start_response)

 File "/ufs/guravage/.archive/mas/mr/rhodecode/lib/python2.6/site-packages/Pylons-1.0-py2.6.egg/pylons/wsgiapp.py", line 203, in setup_app_env

   pylons_obj.translator = _get_translator(lang, pylons_config=self.config)

 File "/ufs/guravage/.archive/mas/mr/rhodecode/lib/python2.6/site-packages/Pylons-1.0-py2.6.egg/pylons/i18n/translation.py", line 165, in _get_translator

   raise LanguageError('IOError: %s' % ioe)

LanguageError: IOError: [Errno 2] No translation file found for domain: 'rhodecode'

</pre>

</div>

<div class="section" id="re-install">

<h2>RE-INSTALL</h2>

<ol class="arabic simple">

<li>easy_install mercurial</li>

<li>mkdir src</li>

<li>cd src</li>

<li>hg clone <a class="reference external" href="http://www.riverbankcomputing.com/hg/sip">http://www.riverbankcomputing.com/hg/sip</a></li>

<li>cd sip</li>

<li>python build.py prepare</li>

<li>python configure.py</li>

<li>make</li>

<li>make install</li>

<li>cd ..</li>

<li>tar xzf PyQt-x11-gpl-4.7.7</li>

<li>cd PyQt-x11-gpl-4.7.7</li>

<li>python configure.py</li>

<li>make</li>

<li>make install</li>

<li>cd ..</li>

<li>hg clone <a class="reference external" href="https://litsol&#64;bitbucket.org/bfrog/cutehg">https://litsol&#64;bitbucket.org/bfrog/cutehg</a></li>

<li>cd cutehg</li>

<li>python setup.py build</li>

<li>python setup.py install</li>

</ol>

<p>This procedure fails as before.</p>

<p>However, upon inspection I saw that the i18n directory was missing

from my build but present in the rhodecode clone from bitbucket. While

I think that the <tt class="docutils literal">easy_install rhodecode</tt> invocation is necessary to

install the various subsidiary packages, moving the cloned rhodecode

into the site-packages directory seems to have made most functionality

work. e.g. graphical logs and diff highlighting.</p>

</div>

</div>

<div class="section" id="tuesday-12-october-2010">

<h1>Tuesday 12 October 2010</h1>

<div class="section" id="rhodecode">

<h2>RhodeCode</h2>

<p>I think that if Chris can install RhodeCode, I can serve individual

instance from my home directory.</p>

</div>

<div class="section" id="sed-ml-l1v1rc1">

<h2>SED-ML L1V1RC1</h2>

<p>Walking through the new SED-ML schema I see that they've dropped the

generic simulation class and added AddXML and RemoveXML model change

classes. Adding several more SED-ML examples for the symposium might

still be justified - though they become obsolete the moment I

introduce the new schema changes.</p>

</div>

</div>

</div>

<div class="footer">

<hr class="footer" />

###Page###

</div>

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