From 7da754f80a414810a8c4721e1e4ed9b4c2d706d7 Mon Sep 17 00:00:00 2001
From: Christoph Helma <helma@in-silico.ch>
Date: Fri, 22 Jan 2016 13:36:01 +0100
Subject: workshop presentation, enm source data added again

---
 presentation/enm-workshop.rst | 57 +++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 57 insertions(+)
 create mode 100644 presentation/enm-workshop.rst

(limited to 'presentation/enm-workshop.rst')

diff --git a/presentation/enm-workshop.rst b/presentation/enm-workshop.rst
new file mode 100644
index 0000000..7adae46
--- /dev/null
+++ b/presentation/enm-workshop.rst
@@ -0,0 +1,57 @@
+# Nanoparticle read across toxicity predictions with nano-lazar
+
+# Requirements
+
+- Nanoparticle characterisation
+- Toxicity measurements
+
+# eNanoMapper data import
+
+Nanoparticles imported: 464
+Nanoparticles with particle characterisation: 394
+Nanoparticles with toxicity data: 167
+Nanoparticles with toxicity data and particle characterisation: 160
+
+# eNanoMapper toxicity endpoints
+
+.. alles ohne falsch? zugewiesene protein corona tox endpoints
+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 (106 particles)
+Toxicity endpoint: 
+
+# Read across procedure
+
+- Identify relevant fragments (significant correlation with toxicity)
+  TODO list of fragments, number
+- Calculate similarities (weighted cosine similarity, correlation coefficients = weights)
+- Identify neighbors (particles with more than 0.95 similarity)
+- Calculate prediction (weighted average from neighbors, similarities = weights)
+
+# Future development
+
+- Validation of predictions
+- Applicability domain/reliability of predictions
+
+- Accuracy improvements:
+  - additional data
+  - feature selection
+  - similarity calculation
+  - predictions (local regression models)
+
+- Usability improvements:
+  - additional data (extension of applicability domain, additional endpoints and chemistries)
+  - inclusion of ontologies
+  - Descriptor calculation directly from core and coating chemistries
+
+# Webinterface
+
+Your recommendations?
+
+# Source code
+
+https://github.com/opentox/nano-lazar
-- 
cgit v1.2.3


From fbc7ec1f342767052e23d6430ea94f0ae7c8d27f Mon Sep 17 00:00:00 2001
From: Christoph Helma <helma@in-silico.ch>
Date: Fri, 22 Jan 2016 16:55:39 +0100
Subject: rendered workshop presentation

---
 presentation/enm-workshop.rst | 70 +++++++++++++++++++++++++++++++------------
 1 file changed, 51 insertions(+), 19 deletions(-)

(limited to 'presentation/enm-workshop.rst')

diff --git a/presentation/enm-workshop.rst b/presentation/enm-workshop.rst
index 7adae46..26a3524 100644
--- a/presentation/enm-workshop.rst
+++ b/presentation/enm-workshop.rst
@@ -1,30 +1,57 @@
-# Nanoparticle read across toxicity predictions with nano-lazar
+.. |date| date::
 
-# Requirements
+
+
+=============================================================
+Read across toxicity predictions with nano-lazar
+=============================================================
+
+.. class:: center
+
+  Christoph Helma
+
+  in silico toxicology gmbh
+
+  .. image:: http://www.enanomapper.net/sites/all/themes/theme807/logo.png
+    :align: center
+
+Requirements
+============
 
 - Nanoparticle characterisation
 - Toxicity measurements
 
-# eNanoMapper data import
 
-Nanoparticles imported: 464
-Nanoparticles with particle characterisation: 394
-Nanoparticles with toxicity data: 167
-Nanoparticles with toxicity data and particle characterisation: 160
+eNanoMapper data import
+=======================
 
-# eNanoMapper toxicity endpoints
+.. class:: incremental
 
-.. alles ohne falsch? zugewiesene protein corona tox endpoints
-Toxicity endpoints: 41
-Toxicity endpoints with more than one measurement value: 22
-Toxicity endpoints with more than 10 measurements: 2
+  - Nanoparticles imported: 464 
+  - Nanoparticles with particle characterisation: 394 
+  - Nanoparticles with toxicity data: 167 
+  - Nanoparticles with toxicity data and particle characterisation: 160
 
-# Selected data
+
+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 (106 particles)
-Toxicity endpoint: 
+Toxicity endpoint:
+
+Read across procedure
+=====================
 
-# Read across procedure
+.. class:: incremental
 
 - Identify relevant fragments (significant correlation with toxicity)
   TODO list of fragments, number
@@ -32,7 +59,8 @@ Toxicity endpoint:
 - Identify neighbors (particles with more than 0.95 similarity)
 - Calculate prediction (weighted average from neighbors, similarities = weights)
 
-# Future development
+Future development
+==================
 
 - Validation of predictions
 - Applicability domain/reliability of predictions
@@ -46,12 +74,16 @@ Toxicity endpoint:
 - Usability improvements:
   - additional data (extension of applicability domain, additional endpoints and chemistries)
   - inclusion of ontologies
-  - Descriptor calculation directly from core and coating chemistries
+  - descriptor calculation directly from core and coating chemistries
+
+Webinterface
+============
 
-# Webinterface
+https://nano-lazar.in-silico.ch/predict
 
 Your recommendations?
 
-# Source code
+Source code
+===========
 
 https://github.com/opentox/nano-lazar
-- 
cgit v1.2.3