diff options
| author | gebele <gebele@in-silico.ch> | 2017-01-26 11:58:39 +0100 |
|---|---|---|
| committer | gebele <gebele@in-silico.ch> | 2017-01-26 11:58:39 +0100 |
| commit | c76a0f9a26a52a43ae404333460acbca847fa3c1 (patch) | |
| tree | 5d084588dc90006f0a10e23d1dae799788b9ba77 | |
| parent | d1e1cb1ca6984782eb149c8ab8e516c322ac85f4 (diff) | |
| parent | 002f75eeff84a0eda49c7bc564e1f90bcdbbf10f (diff) | |
Merge branch 'master' of https://github.com/opentox/lazar-poster
33 files changed, 155 insertions, 96 deletions
@@ -35,9 +35,9 @@ nmsa-ist-ontoviewer: nmsa-ist-integration: ./md2tex.sh nmsa-ist-integration.tex $(PDFLATEX) nmsa-ist-integration.tex - # $(BIBTEX) nmsa-ist-integration - # $(PDFLATEX) nmsa-ist-integration.tex - # $(PDFLATEX) nmsa-ist-integration.tex + $(BIBTEX) nmsa-ist-integration + $(PDFLATEX) nmsa-ist-integration.tex + $(PDFLATEX) nmsa-ist-integration.tex #./dockercmd.sh /bin/sh -c "./md2tex.sh nmsa-ist-integration.tex && pdflatex nmsa-ist-integration.tex" # Poster enm-rest diff --git a/beamercolorthemeIST.sty b/beamercolorthemeIST.sty index fac5443..5ad6397 100644 --- a/beamercolorthemeIST.sty +++ b/beamercolorthemeIST.sty @@ -50,7 +50,7 @@ \lstloadlanguages{Bash} \lstset{% language=Bash, - basicstyle=\footnotesize\ttfamily\color{black}, + basicstyle=\ttfamily\color{black}, commentstyle = \ttfamily\color{darkgrey}, keywordstyle=\ttfamily\color{black}, stringstyle=\color{red}, diff --git a/markdown_blocks/integration_diagram.md b/markdown_blocks/integration_diagram.md index 4d7bc3d..8330eeb 100644 --- a/markdown_blocks/integration_diagram.md +++ b/markdown_blocks/integration_diagram.md @@ -1 +1 @@ -{width=100%}
\ No newline at end of file +{width=100%}
\ No newline at end of file diff --git a/markdown_blocks/integration_links.md b/markdown_blocks/integration_links.md index 96139e7..666ee0e 100644 --- a/markdown_blocks/integration_links.md +++ b/markdown_blocks/integration_links.md @@ -2,11 +2,11 @@ * eNM ontologies <https://github.com/enanomapper/ontologies> -* nano-lazar GUI <http://nano-lazar.in-silico.ch> +* `nano-lazar` GUI <https://nano-lazar.in-silico.ch> -* eNM ontology viewer <https://query.enanomapper.net/enm-viewer> +* eNM `ontology viewer` <https://query.enanomapper.net/enm-viewer> -* nano-lazar REST interface <https://enm.enanomapper.net> +* `nano-lazar` REST interface <https://enm.in-silico.ch> * eNM SPARQL interface <https://sparql.enanomapper.net> diff --git a/markdown_blocks/integration_summary.md b/markdown_blocks/integration_summary.md index 871516a..852bb1b 100644 --- a/markdown_blocks/integration_summary.md +++ b/markdown_blocks/integration_summary.md @@ -1,6 +1,6 @@ -During the eNanoMapper project in silico toxicologies (IST) public services +During the eNanoMapper project *in silico* toxicologies (IST) public services were adapted to the specification of the eNanoMapper API and new nanoparticle -specific developments were implemented. This poster depict the +specific developments were implemented. This poster depicts the interaction of IST services with eNanoMapper resources of other partners which covers use cases like data download/mirroring, augmentation of GUIs with ontology queries and nanoparticle descriptor calculation. diff --git a/markdown_blocks/integration_text.md b/markdown_blocks/integration_text.md index e69de29..5e11d31 100644 --- a/markdown_blocks/integration_text.md +++ b/markdown_blocks/integration_text.md @@ -0,0 +1,33 @@ +**`lazar`** \cite{helma_2017}\cite{helma_christoph_2016_215483} + + - Mirrors eNanoMapper data for read-across models + - Creates read-across predictions for the `nano-lazar` webinterface + - Responds to requests from the `lazar-rest` interface (e.g. nanoparticle predictions, model creation and validation, descriptor calculation) + +**RDF store** + + - Mirrors eNanoMapper data and ontologies + - Responds to SPARQL queries from the ontology viewer and the SPARQL interface + +**`nano-lazar` GUI** \cite{gebele_denis_2017_250818} + + - Obtains nanoparticle toxicity predictions from the `lazar` library + - Uses ontologies (eNanoMapper, BioPortal, UniProt) to explain domain specific terms in the user interface + - Uses ontologies and eNanoMapper data as supporting information for read-across predictions + +**eNM `ontology viewer`** + + - Sends SPARQL queries to the RDF store + - Visualises RDF response from the RDF store + +**`nano-lazar` REST interface** \cite{rautenberg_micha_2016_187328} + + - Interacts with the `lazar` library (e.g. for toxicity predictions, model creation and validation, descriptor calculation) + - Will be maintained and developed in the FP7 OpenRiskNet project + +**eNM SPARQL interface** + + - Sends SPARQL queries to the RDF store + - Receives SPARQL query results in different formats + + diff --git a/markdown_blocks/rest_aa.md b/markdown_blocks/rest_aa.md index 3dca640..ba82911 100644 --- a/markdown_blocks/rest_aa.md +++ b/markdown_blocks/rest_aa.md @@ -1,6 +1,6 @@ Data confidentiality, authentication and authorization (AA) is a common requirement for many resources. -Within the OpenTox\cite{hardy2010collaborative} project, in-silico toxicology gmbh has implemented a single-sign-on method with an OpenLDAP backend for user management -and OpenAM for authentication and authorization. +Within the OpenTox\cite{hardy2010collaborative} project, *in-silico* toxicology gmbh has implemented a single-sign-on method with an +OpenLDAP backend for user management and OpenAM for authentication and authorization. This system was updated and revised for eNanoMapper and provides access control for the current services. Conforming to the OpenTox web service architecture principles\cite{hardy2010collaborative}, eNanoMapper services can be decoupled from AA. -This provides the opportunity to deploy a service without A&A, if required (e.g. for local installations).
\ No newline at end of file +This provides the opportunity to deploy a service without AA, if required (e.g. for local installations).
\ No newline at end of file diff --git a/markdown_blocks/rest_examples.md b/markdown_blocks/rest_examples.md index 7bd49d6..ef4def2 100644 --- a/markdown_blocks/rest_examples.md +++ b/markdown_blocks/rest_examples.md @@ -1,14 +1,20 @@ Get an URI list for all models: +\footnotesize + ```Bash curl -X GET --header 'Accept: text/uri-list' -H 'accept:text/uri-list' 'https://enm.in-silico.ch/model' ``` - +\normalsize Retrieve an JSON representation of a model: -```bash +\footnotesize + +```Bash curl -X GET -H 'Accept: application/json' -H 'accept: application/json' 'https://enm.in-silico.ch/model/<MODELID>' ``` - +\normalsize Predict a nano-particle: +\footnotesize + ```Bash curl -X POST -H 'Content-Type: application/x-www-form-urlencoded' -H 'Accept:text/html' -d 'identifier= https://enm.in-silico.ch/nanoparticle/<NANOPARTICLEID>' 'https://enm.in-silico.ch/model/<MODELID>' ```
\ No newline at end of file diff --git a/markdown_blocks/rest_integration.md b/markdown_blocks/rest_integration.md index d63f909..26bd8dc 100644 --- a/markdown_blocks/rest_integration.md +++ b/markdown_blocks/rest_integration.md @@ -1,9 +1,9 @@ -lazar-rest provides a REST webservice for the nano-lazar framework. -The lazar framework integrates internal libraries, eNanoMapper +`lazar-rest` provides a REST webservice for the `nano-lazar` framework. +The `lazar` framework integrates internal libraries, eNanoMapper resources (Data Warehouse and Ontologies) and external resources like UniProt and -BioPortal. lazar-rest services make the lazar framework accessible +BioPortal. `lazar-rest` services make the `lazar` framework accessible for other webservices and web applications and for users who prefer the command line over graphical user interfaces. -{width=1400px}
\ No newline at end of file +{width=1400px}
\ No newline at end of file diff --git a/markdown_blocks/rest_lazar-rest.md b/markdown_blocks/rest_lazar-rest.md index 1058e38..a866886 100644 --- a/markdown_blocks/rest_lazar-rest.md +++ b/markdown_blocks/rest_lazar-rest.md @@ -1,3 +1,3 @@ -lazar-rest is a Ruby library, that provides a REST interface for nano-lazar. +`lazar-rest` is a Ruby library, that provides a REST interface for `nano-lazar`. The API is compatible with eNanoMapper specifications and documented with the Swagger API framework (version 2.0), which conforms with the Open API Initiative specification.
\ No newline at end of file diff --git a/markdown_blocks/rest_lazar_description.md b/markdown_blocks/rest_lazar_description.md index 1272146..9df224f 100644 --- a/markdown_blocks/rest_lazar_description.md +++ b/markdown_blocks/rest_lazar_description.md @@ -1,3 +1,3 @@ -*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 and interfaces -to other eNanoMapper services (databases and ontologies). lazar libraries are publicly distributed as Ruby gems.
\ No newline at end of file +`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 and interfaces +to other eNanoMapper services (databases and ontologies). `lazar` libraries are publicly distributed as Ruby gems.
\ No newline at end of file diff --git a/markdown_blocks/rest_links.md b/markdown_blocks/rest_links.md index 356f473..847ed8b 100644 --- a/markdown_blocks/rest_links.md +++ b/markdown_blocks/rest_links.md @@ -1,23 +1,23 @@ -* Nano-lazar REST API GUI. Swagger UI based documentation for API visualization and interaction. +* `nano-lazar` REST API GUI. Swagger UI based documentation for API visualization and interaction. \ <https://enm.in-silico.ch> -* Nano-lazar Swagger API definition file +* `nano-lazar` Swagger API definition file <https://enm.in-silico.ch/api/api.json> -* Nano-lazar REST API services source code repository +* `nano-lazar` REST API services source code repository <https://github.com/opentox/lazar-rest> -* Nano-lazar REST API services gem library +* `nano-lazar` REST API services gem library <https://rubygems.org/gems/lazar-rest> -* Nano-lazar REST API services Rubydocs gem library documentation +* `nano-lazar` REST API services Rubydocs gem library documentation <http://www.rubydoc.info/gems/lazar-rest> -* Nano-lazar REST API issue tracker +* `nano-lazar` REST API issue tracker <https://github.com/opentox/lazar-rest/issues> -* Lazar (source code) +* `lazar` (source code) <https://github.com/opentox/lazar> * Swagger framework for APIs diff --git a/markdown_blocks/rest_qmrf.md b/markdown_blocks/rest_qmrf.md index 6a3997b..62a8112 100644 --- a/markdown_blocks/rest_qmrf.md +++ b/markdown_blocks/rest_qmrf.md @@ -1,6 +1,4 @@ -lazar-rest supports (Q)SAR Model Reporting Format (QMRF). The integrated QSAR-report library\cite{rautenberg_micha_2016_179038} -generates QMRF reports in XML format with basic model information (e.g. -validation results according to OECD guidelines). The QMRF report -library is independent of other IST libraries (e.g. lazar, -nano-lazar-gui, lazar-rest) and can be used by other applications that -need QMRF reporting.
\ No newline at end of file +`lazar-rest` supports (Q)SAR Model Reporting Format (QMRF). The integrated QSAR-report library\cite{rautenberg_micha_2016_179038} +generates QMRF reports in XML format with basic model information (e.g. validation results according +to OECD guidelines). The QMRF report library is independent of other IST libraries (e.g. `lazar`, +`nano-lazar`-gui, `lazar-rest`) and can be used by other applications that need QMRF reporting.
\ No newline at end of file diff --git a/markdown_blocks/rest_rest.md b/markdown_blocks/rest_rest.md index d8d670e..63abcb5 100644 --- a/markdown_blocks/rest_rest.md +++ b/markdown_blocks/rest_rest.md @@ -1,4 +1,4 @@ Representational State Transfer or RESTful API is an architectural style to design webservices. REST uses HTTP protocol requests GET, POST, PUT, DELETE for the communication between distributed webservices. -nano-lazar as a part of the eNanoMapper analysis and modelling infrastructure is built upon the OpenTox web services framework following -the principles of the Representational State Transfer (REST) design model.
\ No newline at end of file +`nano-lazar`\cite{helma_2017} as a part of the eNanoMapper analysis and modelling infrastructure is built upon the OpenTox +web services framework following the principles of the Representational State Transfer (REST) design model.
\ No newline at end of file diff --git a/markdown_blocks/rest_screenshot.md b/markdown_blocks/rest_screenshot.md index 4d6140c..642a125 100644 --- a/markdown_blocks/rest_screenshot.md +++ b/markdown_blocks/rest_screenshot.md @@ -1 +1 @@ -{width=1540px}
\ No newline at end of file +{width=1540px}
\ No newline at end of file diff --git a/markdown_blocks/rest_swagger_ui.md b/markdown_blocks/rest_swagger_ui.md index 2e8e5eb..1047bc7 100644 --- a/markdown_blocks/rest_swagger_ui.md +++ b/markdown_blocks/rest_swagger_ui.md @@ -1 +1 @@ -Swagger UI is used as an interactive documentation and visualization platform for the lazar-rest API.
\ No newline at end of file +Swagger UI is used as an interactive documentation and visualization platform for the `lazar-rest` API.
\ No newline at end of file diff --git a/markdown_blocks/services_infrastructure.md b/markdown_blocks/services_infrastructure.md index ddcc090..aff37a3 100644 --- a/markdown_blocks/services_infrastructure.md +++ b/markdown_blocks/services_infrastructure.md @@ -4,7 +4,9 @@ eNanoMapper infrastructure services implemented and maintained by IST. <https://bugzilla.enanomapper.net/> * Mailman mailing list for partner, developers and associate-partners - <http://lists.enanomapper.net/> + <http://lists.enanomapper.net/cgi-bin/mailman/listinfo/partner> + <http://lists.enanomapper.net/cgi-bin/mailman/listinfo/developers> + <http://lists.enanomapper.net/cgi-bin/mailman/listinfo/associate-partner> * Registration form and user management <https://purl.enanomapper.net/register/> @@ -16,7 +18,7 @@ eNanoMapper infrastructure services implemented and maintained by IST. (e.g. <https://purl.enanomapper.net/php/ENM_0000018>) * LDAP user database server and replication server - <ldap.opentox.org> + <http://ldap.opentox.org> * Blog entries with technical details about eNanoMapper implementations <http://opentox.github.io/archive> diff --git a/markdown_blocks/services_lazar-rest.md b/markdown_blocks/services_lazar-rest.md index 9a1b028..866e6b6 100644 --- a/markdown_blocks/services_lazar-rest.md +++ b/markdown_blocks/services_lazar-rest.md @@ -1,6 +1,6 @@ -`lazar-rest` provides an eNanoMapper compatible REST API for the `nano-lazar` read-across framework +`lazar-rest` provides an eNanoMapper compatible REST API for the `nano-lazar` read-across framework. -* `lazar-rest` Swagger UI documentation for API visualization and interaction. \cite{rautenberg_micha_2016_187328} +* `lazar-rest` Swagger UI documentation for API visualization and interaction \cite{rautenberg_micha_2016_187328} <https://enm.in-silico.ch> * `lazar-rest` Swagger API definition file diff --git a/markdown_blocks/services_lazar.md b/markdown_blocks/services_lazar.md index e63888d..ab271a9 100644 --- a/markdown_blocks/services_lazar.md +++ b/markdown_blocks/services_lazar.md @@ -1,4 +1,4 @@ -`lazar` is a framework for read-across predictions. Within eNanoMapper `lazar` was extended with interfaces for the eNanoMapper infrastructure and capabilities to predict nanomaterial toxicities. +`lazar`\cite{Maunz2013} is a framework for read-across predictions. Within eNanoMapper `lazar` was extended with interfaces for the eNanoMapper infrastructure and capabilities to predict nanomaterial toxicities. * `lazar` source code \cite{helma_christoph_2016_215483} <https://github.com/opentox/lazar> diff --git a/markdown_blocks/services_links.md b/markdown_blocks/services_links.md index 45b72c0..0d9b255 100644 --- a/markdown_blocks/services_links.md +++ b/markdown_blocks/services_links.md @@ -1,13 +1,13 @@ -* Lazar (source code) +* `lazar` (source code) <https://github.com/opentox/lazar> -* Nano-lazar GUI (graphical user interface) +* `nano-lazar` GUI (graphical user interface) <https://github.com/eNanoMapper/nano-lazar> -* Nano-lazar Restful API services +* `nano-lazar` Restful API services <https://github.com/opentox/lazar-rest> -* Nano-lazar paper manuscript (source code repository) +* `nano-lazar` paper manuscript (source code repository) <https://github.com/enanomapper/nano-lazar-paper> * Docker image diff --git a/markdown_blocks/services_nano-lazar-paper.md b/markdown_blocks/services_nano-lazar-paper.md index c61390f..ff7db57 100644 --- a/markdown_blocks/services_nano-lazar-paper.md +++ b/markdown_blocks/services_nano-lazar-paper.md @@ -1,6 +1,7 @@ -Detailed description of `nano-lazar` methods and validation results. Results can be reproduced by external researchers with the accompanying docker image. +Detailed description of `nano-lazar` methods and validation results \cite{helma_2017}. +Results can be reproduced by external researchers with the accompanying docker image. -* Source code for nano-lazar publication (and oral presentations). +* Source code for `nano-lazar` publication (and oral presentations). <https://github.com/enanomapper/nano-lazar-paper> * Manuscript submitted to Frontiers in Pharmacology diff --git a/markdown_blocks/services_nano-lazar.md b/markdown_blocks/services_nano-lazar.md index 3122fda..cf65a1b 100644 --- a/markdown_blocks/services_nano-lazar.md +++ b/markdown_blocks/services_nano-lazar.md @@ -1,6 +1,6 @@ -The `nano-lazar` GUI provides a public webinterface for `nano-lazar` models +The `nano-lazar` GUI provides a public webinterface for `nano-lazar` models. -* `nano-lazar` public webinterface \cite{gebele_denis_2017_250818}. +* `nano-lazar` public webinterface \cite{gebele_denis_2017_250818} <https://nano-lazar.in-silico.ch> * `nano-lazar` source code @@ -14,3 +14,6 @@ The `nano-lazar` GUI provides a public webinterface for `nano-lazar` models * `nano-lazar` API documentation <http://www.rubydoc.info/gems/nano-lazar> + +* `nano-lazar` dockerized service on Docker Hub + <https://hub.docker.com/u/insilicotox/nano-lazar>
\ No newline at end of file diff --git a/markdown_blocks/services_ontoviewer.md b/markdown_blocks/services_ontoviewer.md index d50c2d7..80a5251 100644 --- a/markdown_blocks/services_ontoviewer.md +++ b/markdown_blocks/services_ontoviewer.md @@ -1,10 +1,10 @@ -The eNanoMapper ontology viewer visualizes SPARQL query results from eNM ontologies and data. +The eNanoMapper `ontology viewer` visualizes SPARQL query results from eNM ontologies and data. -* eNanoMapper ontology viewer \cite{gebele_denis_2017_259384} +* eNanoMapper `ontology viewer` \cite{gebele_denis_2017_259384} <https://query.enanomapper.net/> -* eNanoMapper ontology viewer source code +* eNanoMapper `ontology viewer` source code <https://github.com/enanomapper/enm-ontoviewer> -* eNanoMapper ontology viewer issue tracker +* eNanoMapper `ontology viewer` issue tracker <https://github.com/enanomapper/enm-ontoviewer/issues> diff --git a/markdown_blocks/services_qsar-report.md b/markdown_blocks/services_qsar-report.md index d29a97d..efc8ae2 100644 --- a/markdown_blocks/services_qsar-report.md +++ b/markdown_blocks/services_qsar-report.md @@ -1,6 +1,6 @@ QMRF and QPRF reporting features for `nano-lazar`. This library is accessible from the `nano-lazar` GUI and the `lazar-rest` webservices. -* `qsar-report` source code \cite{rautenberg_micha_2016_179038} +* `qsar-report` source code\cite{rautenberg_micha_2016_179038} <https://github.com/opentox/qsar-report> * `qsar-report` Ruby gem library diff --git a/markdown_blocks/services_sparql.md b/markdown_blocks/services_sparql.md index b2a9562..1b51e8c 100644 --- a/markdown_blocks/services_sparql.md +++ b/markdown_blocks/services_sparql.md @@ -5,3 +5,6 @@ SPARQL query interface for eNanoMapper data and ontologies * Documentation <http://enanomapper.net/deliverables/d3/20160420_eNanoMapper_D3.2_Data_Management_System_with_extended_search_capabilities_FINAL.pdf> + +* Docker image + <https://hub.docker.com/r/insilicotox/ist-enm-virtuoso/>
\ No newline at end of file diff --git a/markdown_blocks/services_testing.md b/markdown_blocks/services_testing.md new file mode 100644 index 0000000..6aedde2 --- /dev/null +++ b/markdown_blocks/services_testing.md @@ -0,0 +1,3 @@ +IST uses the Ruby MiniTest framework for Test Driven Development (TDD). +Automated nightly tests keep track of code changes and ensure the +interoperability within IST components and with external services.
\ No newline at end of file diff --git a/nmsa-ist-integration.pdf b/nmsa-ist-integration.pdf Binary files differnew file mode 100644 index 0000000..f6b77a4 --- /dev/null +++ b/nmsa-ist-integration.pdf diff --git a/nmsa-ist-integration.tex b/nmsa-ist-integration.tex index c472e36..2f473ff 100644 --- a/nmsa-ist-integration.tex +++ b/nmsa-ist-integration.tex @@ -1,31 +1,40 @@ \documentclass[final]{beamer} \usetheme{IST} -\usepackage[orientation=portrait,size=a0,scale=1.4,debug]{beamerposter} % poster size +\usepackage[orientation=portrait,size=a0,scale=1.3,debug]{beamerposter} % poster size \usepackage[absolute,overlay]{textpos} \usepackage[utf8]{inputenc} \setlength{\TPHorizModule}{1cm} \setlength{\TPVertModule}{1cm} -\title{Integration of the in silico toxicology services in the eNanoMapper infrastructure } +\title{Integration of in silico toxicology services in the \\ eNanoMapper infrastructure } \author{C. Helma, D. Gebele, M. Rautenberg} \institute{\emph{in silico} toxicology gmbh, Basel, Switzerland} -\footer{Contact: \texttt{support@in-silico.ch}. Information: \texttt{www.in-silico.ch}} +\footer{Contact: \texttt{support@in-silico.ch}. Information: \texttt{www.in-silico.ch} \\ \emph{in silico} toxicology gmbh - Rastatterstrasse 41 - CH-4057 Basel, Switzerland } \begin{document} \begin{frame}{} - \begin{textblock}{40.5}(1,11) + \begin{textblock}{40.5}(1,10) \begin{block}{Abstract} \input{./markdown_blocks/integration_summary} \end{block} + \begin{exampleblock}{Links} + \input{./markdown_blocks/integration_links} + \end{exampleblock} + + + \begin{block}{References} + \small\bibliography{references} + \end{block} + \end{textblock} - \begin{textblock}{40.5}(42.6,11) + \begin{textblock}{40.5}(42.6,10) - \begin{block}{Text} + \begin{block}{Integration details} \input{./markdown_blocks/integration_text} \end{block} @@ -33,23 +42,17 @@ - \begin{textblock}{82.1}(1,28) + \begin{textblock}{82.1}(1,50) \input{./markdown_blocks/integration_diagram} \end{textblock} - \begin{textblock}{40.5}(1,90) + \begin{textblock}{40.5}(1,82) - \begin{exampleblock}{Links} - \input{./markdown_blocks/integration_links} - \end{exampleblock} \end{textblock} - \begin{textblock}{40.5}(42.6,90) + \begin{textblock}{40.5}(42.6,82) - \begin{block}{References} - \small\bibliography{references} - \end{block} \end{textblock} diff --git a/nmsa-ist-rest.pdf b/nmsa-ist-rest.pdf Binary files differnew file mode 100644 index 0000000..a2ee10a --- /dev/null +++ b/nmsa-ist-rest.pdf diff --git a/nmsa-ist-rest.tex b/nmsa-ist-rest.tex index 4f89784..4f840f1 100644 --- a/nmsa-ist-rest.tex +++ b/nmsa-ist-rest.tex @@ -10,7 +10,7 @@ \title{In silico toxicology eNanoMapper REST services} \author{M. Rautenberg, C. Helma, D. Gebele} \institute{\emph{in silico} toxicology gmbh, Basel, Switzerland} -\footer{Contact: \texttt{support@in-silico.ch}. Information: \texttt{www.in-silico.ch} \\ \emph{in silico toxicology gmbh} - Rastatterstrasse 41 - CH-4057 Basel, Switzerland } +\footer{Contact: \texttt{support@in-silico.ch}. Information: \texttt{www.in-silico.ch} \\ \emph{in silico} toxicology gmbh - Rastatterstrasse 41 - CH-4057 Basel, Switzerland } \begin{document} @@ -22,7 +22,7 @@ \input{./markdown_blocks/rest_summary} \end{block} - \begin{block}{lazar} + \begin{block}{\tt{lazar}} \justifying \input{./markdown_blocks/rest_lazar_description} \end{block} @@ -32,12 +32,12 @@ \input{./markdown_blocks/rest_rest} \end{block} - \begin{block}{lazar-rest services} + \begin{block}{\tt{lazar-rest} services} \justifying \input{./markdown_blocks/rest_lazar-rest} \end{block} - \begin{block}{lazar-rest Swagger interface} + \begin{block}{\tt{lazar-rest} Swagger interface} \vskip.2ex \input{./markdown_blocks/rest_swagger_ui} \vskip.2ex diff --git a/nmsa-ist-services.pdf b/nmsa-ist-services.pdf Binary files differnew file mode 100644 index 0000000..5803260 --- /dev/null +++ b/nmsa-ist-services.pdf diff --git a/nmsa-ist-services.tex b/nmsa-ist-services.tex index 542faba..9ab14ef 100644 --- a/nmsa-ist-services.tex +++ b/nmsa-ist-services.tex @@ -1,6 +1,6 @@ \documentclass[final]{beamer} \usetheme{IST} -\usepackage[orientation=portrait,size=a0,scale=1.3,debug]{beamerposter} % poster size +\usepackage[orientation=portrait,size=a0,scale=1.35,debug]{beamerposter} % poster size \usepackage[absolute,overlay]{textpos} \usepackage[utf8]{inputenc} @@ -21,51 +21,50 @@ \input{./markdown_blocks/services_summary} \end{block} - \begin{block}{lazar} + \begin{block}{\tt{lazar}} \input{./markdown_blocks/services_lazar} \end{block} - \begin{block}{nano-lazar} + \begin{block}{\tt{nano-lazar}} \input{./markdown_blocks/services_nano-lazar} \end{block} - \begin{block}{nano-lazar-paper} + \begin{block}{\tt{nano-lazar}-paper} \input{./markdown_blocks/services_nano-lazar-paper} \end{block} - \begin{block}{lazar-rest} + \begin{block}{\tt{lazar-rest}} \input{./markdown_blocks/services_lazar-rest} \end{block} - \begin{block}{eNM ontoviewer} - \input{./markdown_blocks/services_ontoviewer} - \end{block} - - \begin{block}{SPARQL endpoint to eNM ontology and data} + \begin{block}{SPARQL endpoint for eNM ontology and data} \input{./markdown_blocks/services_sparql} \end{block} - \end{textblock} \begin{textblock}{40.5}(42.6,8.6) - \begin{block}{Docker} - \input{./markdown_blocks/services_docker} + \begin{block}{eNM ontoviewer} + \input{./markdown_blocks/services_ontoviewer} \end{block} - \begin{block}{Authorization \& Authentication} - \input{./markdown_blocks/services_aa} + \begin{block}{\tt{qsar-report}} + \input{./markdown_blocks/services_qsar-report} \end{block} - \begin{block}{QSAR-reporting} - \input{./markdown_blocks/services_qsar-report} + \begin{block}{Authorization \& authentication} + \input{./markdown_blocks/services_aa} \end{block} \begin{block}{eNanoMapper infrastructure} \input{./markdown_blocks/services_infrastructure} \end{block} + \begin{block}{Testing framework} + \input{./markdown_blocks/services_testing} + \end{block} + \begin{block}{References} \small\bibliography{references} \end{block} diff --git a/references.bib b/references.bib index e5decae..9b5cee8 100644 --- a/references.bib +++ b/references.bib @@ -1,3 +1,11 @@ +@article{helma_2017, + author = {Helma, Christoph and Rautenberg, Micha and Gebele, Denis}, + title = {nano-lazar: {R}ead across predictions for nanoparticle toxicities with calculated and measured properties address.}, + journal={Frontiers in Pharmacology}, + note = {Submitted to Frontiers in Pharmacology 2017 Jan, Predictive Toxicology section}, + year={2017}, + publisher={Frontiers Media SA} +} @misc{gebele_denis_2017_259384, author = {Gebele, Denis and Rautenberg, Micha and @@ -44,7 +52,7 @@ author = {Rautenberg, Micha and Helma, Christoph and Gebele, Denis}, - title = {qsar-report ruby gem library}, + title = {qsar-report {R}uby gem library}, month = sep, year = 2016, doi = {10.5281/zenodo.179038}, |