add more rest / integration PDF diagram

17 files changed, 46 insertions, 40 deletions

diff --git a/beamerthemeIST.sty b/beamerthemeIST.sty
index 39d3346..edfbf18 100644
--- a/beamerthemeIST.sty
+++ b/beamerthemeIST.sty
@@ -44,14 +44,14 @@
 \setbeamertemplate{bibliography item}[text]
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 \setbeamertemplate{block begin}{
-  \vskip3ex
+  \vskip2ex
   \begin{beamercolorbox}[rounded=true,shadow=true,sep=0ex,ht=3.4ex,dp=-0.2ex,colsep=0.9ex]{block title}%
     \usebeamerfont{block title}\textbf{\insertblocktitle}
   \end{beamercolorbox}%
   %{\ifbeamercolorempty[bg]{block body}{}{\nointerlineskip\vskip-0.5pt}}%
   \usebeamerfont{block body}%
-  \begin{beamercolorbox}[colsep*=.75ex,sep=.75ex,vmode]{block body}%
-    \ifbeamercolorempty[bg]{block body}{\vskip-.25ex}{\vskip-.75ex}\vbox{}%
+  \begin{beamercolorbox}[colsep*=.0ex,sep=.0ex,vmode]{block body}%
+    \ifbeamercolorempty[bg]{block body}{\vskip-.1ex}\vbox{}%
   }
   \setbeamertemplate{block end}{
   \end{beamercolorbox}
diff --git a/images/integration.pdf b/images/integration.pdf
new file mode 100644
index 0000000..b5fcf75
--- /dev/null
+++ b/images/integration.pdf
diff --git a/images/rest_interaction.png b/images/rest_interaction.png
new file mode 100644
index 0000000..e75ce07
--- /dev/null
+++ b/images/rest_interaction.png
diff --git a/images/rest_model_get.png b/images/rest_model_get.png
new file mode 100644
index 0000000..fd42a9e
--- /dev/null
+++ b/images/rest_model_get.png
diff --git a/images/rest_swagger_ui.png b/images/rest_swagger_ui.png
new file mode 100644
index 0000000..94e402b
--- /dev/null
+++ b/images/rest_swagger_ui.png
diff --git a/markdown_blocks/integration_diagram.md b/markdown_blocks/integration_diagram.md
new file mode 100644
index 0000000..48fbb6e
--- /dev/null
+++ b/markdown_blocks/integration_diagram.md
@@ -0,0 +1 @@
+![nano-lazar integration](./images/integration.pdf "nano-lazar integration"){width=3040px}
\ No newline at end of file
diff --git a/markdown_blocks/rest_interaction.md b/markdown_blocks/rest_interaction.md
new file mode 100644
index 0000000..2effd83
--- /dev/null
+++ b/markdown_blocks/rest_interaction.md
@@ -0,0 +1,3 @@
+The lazar-rest webservice text ...
+
+![nano-lazar Swagger UI](./images/rest_interaction.png "nano-lazar Swagger UI") 
\ No newline at end of file
diff --git a/markdown_blocks/rest_lazar-rest.md b/markdown_blocks/rest_lazar-rest.md
new file mode 100644
index 0000000..3c887ca
--- /dev/null
+++ b/markdown_blocks/rest_lazar-rest.md
@@ -0,0 +1,3 @@
+lazar-rest is a gem library written in Ruby. It provides a REST API webservice to lazar and nano-lazar. 
+The API is documented in the Swagger RESTful API documentation specification version 2.0. 
+This specification is conform to the Open API Iniciative specification.  
\ No newline at end of file
diff --git a/markdown_blocks/rest_lazar_description.md b/markdown_blocks/rest_lazar_description.md
index 523de05..2096877 100644
--- a/markdown_blocks/rest_lazar_description.md
+++ b/markdown_blocks/rest_lazar_description.md
@@ -1,4 +1,4 @@
-*lazar* (lazy structure–activity relationships) is a modular framework for read across predictions of chemical toxicities. 
+*lazar* (lazy structure–activity relationships)\cite{Maunz2013} is a modular framework for read across predictions of chemical toxicities. 
 Within the European Union’s FP7 eNanoMapper project lazar was extended with capabilities to handle nanomaterial data, 
 interfaces to other eNanoMapper services (databases and ontologies) and a stable and user-friendly graphical interface 
 for nanoparticle read-across predictions. lazar provides a ruby gem library to this developments.
\ No newline at end of file
diff --git a/markdown_blocks/rest_links.md b/markdown_blocks/rest_links.md
index 2049630..682e16e 100644
--- a/markdown_blocks/rest_links.md
+++ b/markdown_blocks/rest_links.md
@@ -2,12 +2,18 @@
   \
   <https://enm.in-silico.ch>
 
+* Nano-lazar Swagger API definition file
+  <https://enm.in-silico.ch/api/api.json> 
+
 * Nano-lazar Restful API services source code repository
   <https://github.com/opentox/lazar-rest>
   
-* Nano-lazar Restful API services Rubydocs documentation
+* Nano-lazar Restful API services Rubydocs gem library documentation
   <http://www.rubydoc.info/gems/lazar-rest>
 
+* Nano-lazar Restful API issue tracker
+  <https://github.com/opentox/lazar-rest/issues>
+
 * Lazar (source code)
   <https://github.com/opentox/lazar>
 
diff --git a/markdown_blocks/rest_screenshot.md b/markdown_blocks/rest_screenshot.md
deleted file mode 100644
index 1ad6fc7..0000000
--- a/markdown_blocks/rest_screenshot.md
+++ /dev/null
@@ -1 +0,0 @@
-![Swagger UI](./images/rest_swagger.png "This a short caption (alt text)"){width=1540px}
\ No newline at end of file
diff --git a/markdown_blocks/rest_screenshot_1.md b/markdown_blocks/rest_screenshot_1.md
new file mode 100644
index 0000000..51116f2
--- /dev/null
+++ b/markdown_blocks/rest_screenshot_1.md
@@ -0,0 +1,8 @@
+![nano-lazar Swagger UI](./images/rest_swagger_ui.png "nano-lazar Swagger UI"){width=1540px}
+\
+\tiny Figure 1: nano-lazar Swagger UI - service overview
+\ 
+![nano-lazar to GET a model](./images/rest_model_get.png "nano-lazar get a model"){width=1540px}
+\
+\tiny Figure 2: nano-lazar GET model data
+\ 
diff --git a/markdown_blocks/rest_summary.md b/markdown_blocks/rest_summary.md
index 0f2fc5c..7785192 100644
--- a/markdown_blocks/rest_summary.md
+++ b/markdown_blocks/rest_summary.md
@@ -1,4 +1,4 @@
-During the eNanoMapper project in silico toxicologies (IST) webservices were
+During the eNanoMapper project *in silico* toxicologies (IST) webservices were
 adapted in order to provide REST interfaces that adhere to eNanoMapper
 standards and specifications and supplemented with interactive SWAGGER
 documentation. This poster will give an overview of ISTs eNanoMapper API
diff --git a/markdown_blocks/services_summary.md b/markdown_blocks/services_summary.md
index 55273c9..3b7305c 100644
--- a/markdown_blocks/services_summary.md
+++ b/markdown_blocks/services_summary.md
@@ -1,4 +1,4 @@
-During the eNanoMapper project in silico toxicologies (IST) public server
+During the eNanoMapper project *in silico* toxicologies (IST) public server
 infrastructure was adapted to the requirements of the eNanoMapper project and
 augmented with new developments. This poster will give a comprehensive overview
 all IST resources developed within eNanoMapper. Each service will be presented
diff --git a/nmsa-ist-integration.tex b/nmsa-ist-integration.tex
index c929441..da3f77d 100644
--- a/nmsa-ist-integration.tex
+++ b/nmsa-ist-integration.tex
@@ -27,30 +27,11 @@
         \input{./markdown_blocks/integration_summary}
       \end{block}
 
-      \begin{block}{Screenshot}
-        \input{./markdown_blocks/screenshot}
-      \end{block}
-
-      \begin{block}{Markdown tables}
-        \input{./markdown_blocks/table}
-      \end{block}
 
     \end{textblock}
 
     \begin{textblock}{40.5}(42.6,16)
 
-      \begin{block}{Maths example}
-        \input{./markdown_blocks/maths}
-      \end{block}
-
-      \begin{alertblock}{Highlighted Box}
-        \input{./markdown_blocks/exampletext}
-      \end{alertblock}
-
-      \begin{block}{Code}
-        \input{./markdown_blocks/code}
-      \end{block}
-
       \begin{exampleblock}{Links}
         \input{./markdown_blocks/services_links}
       \end{exampleblock}
@@ -61,8 +42,8 @@
 
     \end{textblock}
 
-    \begin{textblock}{82.1}(1,88)
-      \input{./markdown_blocks/exampletext}
+    \begin{textblock}{82.1}(1,42)
+      \input{./markdown_blocks/integration_diagram}
     \end{textblock}
 
   \end{frame}
diff --git a/nmsa-ist-rest.tex b/nmsa-ist-rest.tex
index 583e92f..f41b75c 100644
--- a/nmsa-ist-rest.tex
+++ b/nmsa-ist-rest.tex
@@ -33,23 +33,31 @@
         \input{./markdown_blocks/rest_lazar_description}
       \end{block}
 
-      \begin{block}{Swagger API GUI}
-        \input{./markdown_blocks/rest_screenshot}
+      \begin{block}{lazar-rest services}
+        \justifying
+        \input{./markdown_blocks/rest_lazar-rest}
+      \end{block}
+
+      \begin{block}{lazar-rest Swagger UI graphical interface}
+        \vskip.6ex
+        \input{./markdown_blocks/rest_screenshot_1}
       \end{block}
 
+
+
     \end{textblock}
 
     \begin{textblock}{40.5}(42.6,14)
 
+      \begin{block}{Interaction with other services}
+        \input{./markdown_blocks/rest_interaction}
+      \end{block}
+
       \begin{block}{Authorization \& Authentication}
         \justifying        
         \input{./markdown_blocks/rest_aa}
       \end{block}
 
-      \begin{alertblock}{Highlighted Box}
-        \input{./markdown_blocks/exampletext}
-      \end{alertblock}
-
       \begin{block}{Practical Linux cURL Command Examples}
         \input{./markdown_blocks/rest_examples}
       \end{block}
@@ -65,10 +73,6 @@
 
     \end{textblock}
 
-    \begin{textblock}{82.1}(1,98)
-      \input{./markdown_blocks/exampletext}
-    \end{textblock}
-
   \end{frame}
 
 \end{document}
diff --git a/references.bib b/references.bib
index 5e73eec..30d32b0 100644
--- a/references.bib
+++ b/references.bib
@@ -136,7 +136,8 @@
   number={1},
   pages={1},
   year={2010},
-  publisher={Springer International Publishing}
+  publisher={Springer International Publishing},
+  doi = {10.1186/1758-2946-2-7}
 }
 
 @article{Guetlein2012,