From 05f1631236472c2931f571fa0fb987143a1cd105 Mon Sep 17 00:00:00 2001 From: rautenberg Date: Mon, 6 Feb 2017 16:29:05 +0100 Subject: add NMSA presentation --- .../nmsa-malaga/malaga-presentation.html | 252 +++++++++++++++++++++ views/presentations.haml | 3 + 2 files changed, 255 insertions(+) create mode 100644 public/presentations/nmsa-malaga/malaga-presentation.html diff --git a/public/presentations/nmsa-malaga/malaga-presentation.html b/public/presentations/nmsa-malaga/malaga-presentation.html new file mode 100644 index 0000000..38a613e --- /dev/null +++ b/public/presentations/nmsa-malaga/malaga-presentation.html @@ -0,0 +1,252 @@ + + + + + + + + + nano-lazar: A framework for nanoparticle read across risk assessment + + + + + + +
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nano-lazar: A framework for nanoparticle read across risk assessment

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+Christoph Helma, Micha Rautenberg, Denis Gebele +

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in silico toxicology gmbh, Basel, Switzerland
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nano-lazar framework

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Framework for reproducible read-across (k-nearest-neighbor) predictions

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For a given query substance (nanoparticle)

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nano-lazar algorithms

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Free choice of algorithms and parameters for

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Reasonable default algorithms and parameters

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nano-lazar experiments

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Endpoint:
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Net cell association (121 Gold and Silver particles) +
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Descriptors:
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Calculated fingerprints (new development), measured physchem properties, protein interactions +
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Feature selection:
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Correlation filter (measured properties) +
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Similarity:
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Weighted cosine (measured properties), Tanimoto/Jaccard (fingerprints) +
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Local regression:
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Weighted average, partial least squares (PLS), random forests (RF) +
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nano-lazar validation results

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DescriptorsAlgorithmRMSEr2% measurements within prediction interval
MP2DWA2.04 2.0 2.02 2.07 2.070.24 0.27 0.25 0.22 0.22NA
MP2DPLS2.14 2.11 2.21 1.99 1.90.27 0.26 0.26 0.32 0.3694 97 91 91 97
MP2DRF1.84 1.67 1.68 1.69 1.710.4 0.5 0.49 0.48 0.4794 96 96 94 94
P-CHEMWA1.91 1.93 1.91 2.03 2.020.48 0.47 0.49 0.41 0.42NA
P-CHEMPLS2.2 2.33 2.11 2.27 2.210.34 0.28 0.38 0.31 0.3397 92 96 93 91
P-CHEMRF1.8 1.82 1.77 1.68 1.860.54 0.53 0.56 0.6 0.5194 96 97 97 93
ProteomicsWA1.94 1.63 1.7 1.61 1.760.49 0.64 0.6 0.64 0.57NA
ProteomicsPLS1.67 1.63 1.86 1.74 1.80.62 0.64 0.53 0.59 0.5690 88 84 89 88
ProteomicsRF1.66 1.69 1.81 1.68 1.60.62 0.61 0.57 0.6 0.6589 89 89 87 89
P-CHEM ProteomicsWA1.61 1.56 1.71 1.66 2.410.64 0.66 0.6 0.62 0.33NA
P-CHEM ProteomicsPLS1.74 1.67 1.78 1.71 2.180.6 0.62 0.59 0.61 0.4391 90 86 85 86
P-CHEM ProteomicsRF1.78 1.62 1.56 1.82 1.770.57 0.64 0.66 0.55 0.6188 87 87 89 90
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Gold and silver particles included!

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nano-lazar prediction/measurement correlation

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Correlation of predicted vs. measured values for five independent crossvalidations with Proteomics descriptors and local random forest models

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nano-lazar validation summary

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nano-lazar GUI

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nano-lazar GUI

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Reproducible research

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Manuscript submitted to Frontiers in Pharmacology

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+ + + diff --git a/views/presentations.haml b/views/presentations.haml index ad5cb7a..ca593fa 100644 --- a/views/presentations.haml +++ b/views/presentations.haml @@ -1,5 +1,8 @@ View recent presentations and slides : %ul + %li + %a{:href => "/presentations/nmsa-malaga/malaga-presentation.html", :rel => "external"} nano-lazar: A framework for nanoparticle read across risk assessment + (New Tools and Approaches for Nanomaterial Safety Assessment (NMSA), Malaga, Spain, 7-9 February 2017) %li %a{:href => "/presentations/opentox-rheinfelden/opentox-workshop.html", :rel => "external"} Nanomaterial read across predictions with nano-lazar (eNanoMapper modelling workshop in Rheinfelden OpenTox Euro 2016) -- cgit v1.2.3