diff options
Diffstat (limited to 'public/enm-workshop.html')
-rw-r--r-- | public/enm-workshop.html | 83 |
1 files changed, 53 insertions, 30 deletions
diff --git a/public/enm-workshop.html b/public/enm-workshop.html index f0c6781..05d4308 100644 --- a/public/enm-workshop.html +++ b/public/enm-workshop.html @@ -371,20 +371,20 @@ ul.auto-toc { <div class="slide" id="slide0"> <h1 class="title">Read across toxicity predictions with nano-lazar</h1> -<p class="center">Christoph Helma</p> +<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"> -<h1>Requirements</h1> -<ul class="simple"> +<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-data-import"> -<h1>eNanoMapper data import</h1> +<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> @@ -403,42 +403,65 @@ ul.auto-toc { <div class="slide" id="selected-data"> <h1>Selected data</h1> <p>Protein corona dataset Au particles (106 particles) -Toxicity endpoint:</p> +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 fragments (significant correlation with toxicity) -TODO list of fragments, number</li> -<li>Calculate similarities (weighted cosine similarity, correlation coefficients = weights)</li> -<li>Identify neighbors (particles with more than 0.95 similarity)</li> -<li>Calculate prediction (weighted average from neighbors, similarities = weights)</li> +<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 > 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"> -<h1>Future development</h1> +<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: -- additional data -- feature selection -- similarity calculation -- predictions (local regression models)</li> -<li>Usability improvements: -- additional data (extension of applicability domain, additional endpoints and chemistries) -- inclusion of ontologies -- descriptor calculation directly from core and coating chemistries</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="webinterface"> -<h1>Webinterface</h1> -<p><a class="reference external" href="https://nano-lazar.in-silico.ch/predict">https://nano-lazar.in-silico.ch/predict</a></p> -<p>Your recommendations?</p> +<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="source-code"> -<h1>Source code</h1> -<p><a class="reference external" href="https://github.com/opentox/nano-lazar">https://github.com/opentox/nano-lazar</a></p> +<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/predict/enm-workshop.html">https://nano-lazar.in-silico.ch/predict/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-gui">https://github.com/enanomapper/nano-lazar-gui</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-gui/issues">https://github.com/enanomapper/nano-lazar-gui/issues</a></td> +</tr> +</tbody> +</table> +<p>Your comments, ideas, recommendations?</p> </div> </div> </body> |