nano-lazar 1.1.0

data/public/css/jquery-ui.theme.min.css

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+/*! jQuery UI - v1.11.4 - 2015-03-11
+* http://jqueryui.com
+* Copyright 2015 jQuery Foundation and other contributors; Licensed MIT */
+
+.ui-widget{font-family:Trebuchet MS,Tahoma,Verdana,Arial,sans-serif;font-size:1.1em}.ui-widget .ui-widget{font-size:1em}.ui-widget input,.ui-widget select,.ui-widget textarea,.ui-widget button{font-family:Trebuchet MS,Tahoma,Verdana,Arial,sans-serif;font-size:1em}.ui-widget-content{border:1px solid #ddd;background:#eee url("images/ui-bg_highlight-soft_100_eeeeee_1x100.png") 50% top repeat-x;color:#333}.ui-widget-content a{color:#333}.ui-widget-header{border:1px solid #e78f08;background:#f6a828 url("images/ui-bg_gloss-wave_35_f6a828_500x100.png") 50% 50% repeat-x;color:#fff;font-weight:bold}.ui-widget-header a{color:#fff}.ui-state-default,.ui-widget-content .ui-state-default,.ui-widget-header .ui-state-default{border:1px solid #ccc;background:#f6f6f6 url("images/ui-bg_glass_100_f6f6f6_1x400.png") 50% 50% repeat-x;font-weight:bold;color:#1c94c4}.ui-state-default a,.ui-state-default a:link,.ui-state-default a:visited{color:#1c94c4;text-decoration:none}.ui-state-hover,.ui-widget-content 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repeat-x;opacity:.2;filter:Alpha(Opacity=20);border-radius:5px}

data/public/css/style.css

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+.tablesorter thead tr 
+  th.physchem {
+    min-width: 60px;}
+  th.tox {
+    background-color: #ffcc80 !important}
+.tablesorter tbody tr 
+  td.physchem {
+    min-width: 60px;}
+  td.tox {
+    background-color: #ffcc80 }
+.tablesorter tbody tr.static td {
+  background-color: #CCFFCC;
+}
+.th5 {
+  display: inline;
+}

data/public/css/theme.bootstrap.min.css

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+.tablesorter-bootstrap{width:100%}.tablesorter-bootstrap tfoot td,.tablesorter-bootstrap tfoot th,.tablesorter-bootstrap thead td,.tablesorter-bootstrap thead th{font:14px/20px Arial,Sans-serif;font-weight:700;padding:4px;margin:0 0 18px;background-color:#eee}.tablesorter-bootstrap .tablesorter-header{cursor:pointer}.tablesorter-bootstrap .tablesorter-header-inner{position:relative;padding:4px 18px 4px 4px}.tablesorter-bootstrap .tablesorter-header i.tablesorter-icon{font-size:11px;position:absolute;right:2px;top:50%;margin-top:-7px;width:14px;height:14px;background-repeat:no-repeat;line-height:14px;display:inline-block}.tablesorter-bootstrap .bootstrap-icon-unsorted{background-image:url(data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAAsAAAAOCAMAAADOvxanAAAAVFBMVEUAAABCQkJZWVkZGRnJyckgICAZGRkZGRn8/PweHh4dHR0aGhoaGhpUVFQbGxvQ0NDc3NxMTExSUlIbGxvr6+s4ODhKSkogICAtLS00NDQzMzMnJydSEPrQAAAAGHRSTlMA1ssZRLgdAQbDyisqsZo8QdXUq0r9xPepSRwiAAAAX0lEQVQI13XHSQKAIAwEwQAKxn13Ev7/T2Pu9qmarJKPXIicI4PH4hxaKNrhm2S8bJK5h4YzKHrzJNtK6yYT/TdXzpS5zuYg4MSQYF6i4IHExdw1UVRi05HPrrvT53a+qyMFC9t04gcAAAAASUVORK5CYII=)}.tablesorter-bootstrap .icon-white.bootstrap-icon-unsorted{background-image:url(data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAAsAAAAOBAMAAAALT/umAAAAKlBMVEUAAAD///////////////////////////////////////////////////+Gu8ovAAAADXRSTlMA4EXKBtQqvR0+sxmalc142gAAAFdJREFUCNdjYGDoamAAAjZbMxCVfvd6AgMDd+3du9UMDKx3hWSvMjBwXZww8RYDGuC53NB8h4GB8a617UUGBs7Yu3cjGRhYVO9eVQFKOskKOQApFmUgBwBZ+xXRTttNdAAAAABJRU5ErkJggg==)}.tablesorter-bootstrap>tbody>tr.odd>td,.tablesorter-bootstrap>tbody>tr.tablesorter-hasChildRow.odd:hover~tr.tablesorter-hasChildRow.odd~.tablesorter-childRow.odd>td{background-color:#f9f9f9}.tablesorter-bootstrap>tbody>tr.even:hover>td,.tablesorter-bootstrap>tbody>tr.hover>td,.tablesorter-bootstrap>tbody>tr.odd:hover>td,.tablesorter-bootstrap>tbody>tr.tablesorter-hasChildRow.even:hover~.tablesorter-childRow.even>td,.tablesorter-bootstrap>tbody>tr.tablesorter-hasChildRow.odd:hover~.tablesorter-childRow.odd>td{background-color:#f5f5f5}.caption,.tablesorter-bootstrap>tbody>tr.even>td,.tablesorter-bootstrap>tbody>tr.tablesorter-hasChildRow.even:hover~tr.tablesorter-hasChildRow.even~.tablesorter-childRow.even>td{background-color:#fff}.tablesorter-bootstrap .tablesorter-processing{background-image:url(data:image/gif;base64,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);background-position:center center!important;background-repeat:no-repeat!important}.tablesorter-bootstrap .tablesorter-filter-row input.tablesorter-filter,.tablesorter-bootstrap .tablesorter-filter-row select.tablesorter-filter{width:98%;margin:0;padding:4px 6px;color:#333;-webkit-box-sizing:border-box;-moz-box-sizing:border-box;box-sizing:border-box;-webkit-transition:height .1s ease;-moz-transition:height .1s ease;-o-transition:height .1s ease;transition:height .1s ease}.tablesorter-bootstrap .tablesorter-filter-row .tablesorter-filter.disabled{background-color:#eee;color:#555;cursor:not-allowed;border:1px solid #ccc;border-radius:4px;box-shadow:0 1px 1px rgba(0,0,0,.075)inset;box-sizing:border-box;transition:height .1s ease}.tablesorter-bootstrap .tablesorter-filter-row{background-color:#efefef}.tablesorter-bootstrap .tablesorter-filter-row td{background-color:#efefef;line-height:normal;text-align:center;padding:4px 6px;vertical-align:middle;-webkit-transition:line-height .1s ease;-moz-transition:line-height .1s ease;-o-transition:line-height .1s ease;transition:line-height .1s ease}.tablesorter-bootstrap .tablesorter-filter-row.hideme td{padding:2px;margin:0;line-height:0}.tablesorter-bootstrap .tablesorter-filter-row.hideme *{height:1px;min-height:0;border:0;padding:0;margin:0;opacity:0;filter:alpha(opacity=0)}.tablesorter .filtered{display:none}.tablesorter-bootstrap .tablesorter-pager select{padding:4px 6px}.tablesorter-bootstrap .tablesorter-pager .pagedisplay{border:0}.tablesorter-bootstrap tfoot i{font-size:11px}.tablesorter .tablesorter-errorRow td{text-align:center;cursor:pointer;background-color:#e6bf99}

data/public/css/theme.default.min.css

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+<h1>Read across toxicity predictions with nano-lazar</h1>
+
+</div>
+</div>
+<div class="presentation">
+<div class="slide" id="slide0">
+<h1 class="title">Read across toxicity predictions with nano-lazar</h1>
+
+<p class="center">Christoph Helma, Denis Gebele, Micha Rautenberg</p>
+<p class="center">in silico toxicology gmbh</p>
+<img alt="http://www.enanomapper.net/sites/all/themes/theme807/logo.png" class="center align-center" src="http://www.enanomapper.net/sites/all/themes/theme807/logo.png" />
+
+</div>
+<div class="slide" id="requirements-for-nanoparticle-read-across">
+<h1>Requirements for nanoparticle read-across</h1>
+<ul class="incremental simple">
+<li>Nanoparticle characterisation</li>
+<li>Toxicity measurements</li>
+</ul>
+</div>
+<div class="slide" id="enanomapper-particle-characterisation">
+<h1>eNanoMapper particle characterisation</h1>
+<ul class="incremental simple">
+<li>Nanoparticles imported: 464</li>
+<li>Nanoparticles with particle characterisation: 394</li>
+<li>Nanoparticles with toxicity data: 167</li>
+<li>Nanoparticles with toxicity data and particle characterisation: 160</li>
+</ul>
+</div>
+<div class="slide" id="enanomapper-toxicity-endpoints">
+<h1>eNanoMapper toxicity endpoints</h1>
+<ul class="incremental simple">
+<li>Toxicity endpoints: 41</li>
+<li>Toxicity endpoints with more than one measurement value: 22</li>
+<li>Toxicity endpoints with more than 10 measurements: 2</li>
+</ul>
+</div>
+<div class="slide" id="selected-data">
+<h1>Selected data</h1>
+<p>Protein corona dataset Au particles (105 particles)
+Toxicity endpoint: Net cell association (A549 cell line)</p>
+</div>
+<div class="slide" id="read-across-procedure">
+<h1>Read across procedure</h1>
+<ul class="incremental simple">
+<li>Identify relevant properties (statistically significant correlation with toxicity: 14 from 30 properties)</li>
+<li>Calculate similarities (weighted cosine similarity with correlation coefficients as weights)</li>
+<li>Identify neighbors (particles with similarity &gt; 0.95)</li>
+<li>Calculate prediction (weighted average from neighbors with similarities as weights)</li>
+</ul>
+<p class="incremental">Algorithms for feature selection, similarity calculation and predictions may change in the future.</p>
+</div>
+<div class="slide" id="future-development-i">
+<h1>Future development (I)</h1>
+<ul class="simple">
+<li>Validation of predictions</li>
+<li>Applicability domain/reliability of predictions</li>
+<li>Accuracy improvements:<ul>
+<li>additional data</li>
+<li>feature selection</li>
+<li>similarity calculation</li>
+<li>predictions (local regression models)</li>
+</ul>
+</li>
+</ul>
+</div>
+<div class="slide" id="id1">
+<h1>Future development (I)</h1>
+<ul class="simple">
+<li>Usability improvements:<ul>
+<li>additional data (extension of applicability domain, additional endpoints and chemistries)</li>
+<li>inclusion of ontologies</li>
+<li>inclusion of protein corona characterisation?</li>
+<li>particle characterisation without experimental data<ul>
+<li>descriptor calculation from core and coating chemistries</li>
+<li>ontological descriptors</li>
+</ul>
+</li>
+</ul>
+</li>
+</ul>
+</div>
+<div class="slide" id="nano-lazar">
+<h1>nano-lazar</h1>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field"><th class="field-name">Webinterface:</th><td class="field-body"><a class="reference external" href="https://nano-lazar.in-silico.ch/predict">https://nano-lazar.in-silico.ch/predict</a></td>
+</tr>
+<tr class="field"><th class="field-name">Presentation:</th><td class="field-body"><a class="reference external" href="https://nano-lazar.in-silico.ch/enm-workshop.html">https://nano-lazar.in-silico.ch/enm-workshop.html</a></td>
+</tr>
+<tr class="field"><th class="field-name">Source code:</th><td class="field-body"><a class="reference external" href="https://github.com/enanomapper/nano-lazar">https://github.com/enanomapper/nano-lazar</a></td>
+</tr>
+<tr class="field"><th class="field-name">Issues:</th><td class="field-body"><a class="reference external" href="https://github.com/enanomapper/nano-lazar/issues">https://github.com/enanomapper/nano-lazar/issues</a></td>
+</tr>
+</tbody>
+</table>
+<p>Your comments, ideas, recommendations?</p>
+</div>
+</div>
+</body>
+</html>

data/public/enm-workshop.rst

@@ -0,0 +1,98 @@
+.. |date| date::
+
+
+=============================================================
+Read across toxicity predictions with nano-lazar
+=============================================================
+
+.. class:: center
+
+  Christoph Helma, Denis Gebele, Micha Rautenberg
+
+  in silico toxicology gmbh
+
+  .. image:: http://www.enanomapper.net/sites/all/themes/theme807/logo.png
+    :align: center
+
+Requirements for nanoparticle read-across
+=========================================
+
+.. class:: incremental
+
+  - Nanoparticle characterisation
+  - Toxicity measurements
+
+eNanoMapper particle characterisation
+=====================================
+
+.. class:: incremental
+
+  - Nanoparticles imported: 464 
+  - Nanoparticles with particle characterisation: 394 
+  - Nanoparticles with toxicity data: 167 
+  - Nanoparticles with toxicity data and particle characterisation: 160
+
+
+eNanoMapper toxicity endpoints
+==============================
+
+.. class:: incremental
+
+  - Toxicity endpoints: 41
+  - Toxicity endpoints with more than one measurement value: 22
+  - Toxicity endpoints with more than 10 measurements: 2
+
+Selected data
+=============
+
+Protein corona dataset Au particles (105 particles)
+Toxicity endpoint: Net cell association (A549 cell line)
+
+Read across procedure
+=====================
+
+.. class:: incremental
+
+  - Identify relevant properties (statistically significant correlation with toxicity: 14 from 30 properties)
+  - Calculate similarities (weighted cosine similarity with correlation coefficients as weights)
+  - Identify neighbors (particles with similarity > 0.95)
+  - Calculate prediction (weighted average from neighbors with similarities as weights)
+
+  Algorithms for feature selection, similarity calculation and predictions may change in the future.
+
+Future development (I)
+======================
+
+- Validation of predictions
+- Applicability domain/reliability of predictions
+
+- Accuracy improvements:
+
+  - additional data
+  - feature selection
+  - similarity calculation
+  - predictions (local regression models)
+
+Future development (I)
+======================
+
+- Usability improvements:
+
+  - additional data (extension of applicability domain, additional endpoints and chemistries)
+  - inclusion of ontologies
+  - inclusion of protein corona characterisation?
+  - particle characterisation without experimental data
+
+    - descriptor calculation from core and coating chemistries
+    - ontological descriptors 
+
+nano-lazar
+=====================
+
+:Webinterface: https://nano-lazar.in-silico.ch/predict
+:Presentation: https://nano-lazar.in-silico.ch/enm-workshop.html
+:Source code: https://github.com/enanomapper/nano-lazar
+:Issues: https://github.com/enanomapper/nano-lazar/issues
+
+Your comments, ideas, recommendations?
+