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authorChristoph Helma <helma@in-silico.ch>2017-01-25 12:47:49 +0100
committerChristoph Helma <helma@in-silico.ch>2017-01-25 12:47:49 +0100
commit93d0af1f4049534d26167f7437b8396aeb186762 (patch)
tree40b7f990cd35ab9c3f6ca4ea926f709829e57ea5 /markdown_blocks
parentd9a9348a68ecb4e83a3facd5be1d4c54fca09374 (diff)
corrections for services poster
Diffstat (limited to 'markdown_blocks')
-rw-r--r--markdown_blocks/services_aa.md4
-rw-r--r--markdown_blocks/services_infrastructure.md18
-rw-r--r--markdown_blocks/services_lazar-rest.md20
-rw-r--r--markdown_blocks/services_lazar.md25
-rw-r--r--markdown_blocks/services_nano-lazar-paper.md12
-rw-r--r--markdown_blocks/services_nano-lazar.md20
-rw-r--r--markdown_blocks/services_ontoviewer.md8
-rw-r--r--markdown_blocks/services_qsar-report.md22
-rw-r--r--markdown_blocks/services_sparql.md4
-rw-r--r--markdown_blocks/services_summary.md4
10 files changed, 75 insertions, 62 deletions
diff --git a/markdown_blocks/services_aa.md b/markdown_blocks/services_aa.md
index 44c12d3..b28afa5 100644
--- a/markdown_blocks/services_aa.md
+++ b/markdown_blocks/services_aa.md
@@ -1,4 +1,4 @@
-IST has conceived, setup and maintained an infrastructure for authentication and authorization.
+Infrastructure for eNanoMapper authentication and authorization.
* Single sign-on authorization & authentication service
- <https://openam.in-silico.ch/openam/> \ No newline at end of file
+ <https://openam.in-silico.ch/openam/>
diff --git a/markdown_blocks/services_infrastructure.md b/markdown_blocks/services_infrastructure.md
index d834dce..ddcc090 100644
--- a/markdown_blocks/services_infrastructure.md
+++ b/markdown_blocks/services_infrastructure.md
@@ -1,22 +1,22 @@
-IST support the eNanoMapper infrastructure with a brought range of services.
+eNanoMapper infrastructure services implemented and maintained by IST.
-* Bugzilla Issue tracker (project internal)
+* Bugzilla issue tracker for eNanoMapper
<https://bugzilla.enanomapper.net/>
* Mailman mailing list for partner, developers and associate-partners
<http://lists.enanomapper.net/>
-* Maintenance for scripts to query the eNM ontology at purl.enanomapper.net
- (e.g. <https://purl.enanomapper.net/php/ENM_0000018>)
-
* Registration form and user management
<https://purl.enanomapper.net/register/>
+* Online visualization of eNanoMapper specification documents
+ <http://specs.enanomapper.net>
+
+* Maintenance for scripts to query the eNM ontology at purl.enanomapper.net
+ (e.g. <https://purl.enanomapper.net/php/ENM_0000018>)
+
* LDAP user database server and replication server
<ldap.opentox.org>
-
-* eNanoMapper specification documents online visualization
- <http://specs.enanomapper.net>
-* Blog entries on eNanoMapper IST specific technical implementation
+* 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 12f80a3..9a1b028 100644
--- a/markdown_blocks/services_lazar-rest.md
+++ b/markdown_blocks/services_lazar-rest.md
@@ -1,22 +1,20 @@
-The nano-lazar Rest API interface provides a Restful web service. It is the web service implementation of
-the nano-lazar Ruby API for obtaining information on data in the nano-lazar framework and for
-performing predictions and descriptor calculations.
+`lazar-rest` provides an eNanoMapper compatible REST API for the `nano-lazar` read-across framework
-* Nano-lazar REST API GUI. Swagger UI based documentation for API visualization and interaction.
- \
+* `lazar-rest` Swagger UI documentation for API visualization and interaction. \cite{rautenberg_micha_2016_187328}
<https://enm.in-silico.ch>
-* Nano-lazar Swagger API definition file
+* `lazar-rest` Swagger API definition file
<https://enm.in-silico.ch/api/api.json>
-* Nano-lazar REST API services source code repository
+* `lazar-rest` source code
<https://github.com/opentox/lazar-rest>
-* Nano-lazar REST API services gem library\cite{rautenberg_micha_2016_187328}
+* `lazar-rest` Ruby gem library
<https://rubygems.org/gems/lazar-rest>
-* Nano-lazar REST API services Rubydocs gem library documentation
+* `lazar-rest` issue tracker
+ <https://github.com/opentox/lazar-rest/issues>
+
+* `lazar-rest` API documentation
<http://www.rubydoc.info/gems/lazar-rest>
-* Nano-lazar REST API issue tracker
- <https://github.com/opentox/lazar-rest/issues> \ No newline at end of file
diff --git a/markdown_blocks/services_lazar.md b/markdown_blocks/services_lazar.md
index fa870e9..e63888d 100644
--- a/markdown_blocks/services_lazar.md
+++ b/markdown_blocks/services_lazar.md
@@ -1,14 +1,19 @@
-* Lazar Ruby gem library\cite{helma_christoph_2016_215483}
- <https://rubygems.org/gems/lazar>
-
-* Lazar toxicity prediction UI
- <https://lazar.in-silico.ch>
+`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 (source code)
+* `lazar` source code \cite{helma_christoph_2016_215483}
<https://github.com/opentox/lazar>
-
-* Lazar issue tracker
+
+* `lazar` Ruby gem library
+ <https://rubygems.org/gems/lazar>
+
+* `lazar` issue tracker
<https://github.com/opentox/lazar/issues>
-* Lazar Rubydocs gem library documentation
- <http://www.rubydoc.info/gems/lazar> \ No newline at end of file
+- `lazar` methodology and validation
+ <https://github.com/enanomapper/nano-lazar-paper/blob/master/nano-lazar.pdf>
+
+* `lazar` tutorial
+ <https://github.com/opentox/lazar/blob/master/README.md>
+
+* `lazar` API documentation
+ <http://www.rubydoc.info/gems/lazar>
diff --git a/markdown_blocks/services_nano-lazar-paper.md b/markdown_blocks/services_nano-lazar-paper.md
index dca676a..c61390f 100644
--- a/markdown_blocks/services_nano-lazar-paper.md
+++ b/markdown_blocks/services_nano-lazar-paper.md
@@ -1,7 +1,13 @@
-IST
+Detailed description of `nano-lazar` methods and validation results. Results can be reproduced by external researchers with the accompanying docker image.
* Source code for nano-lazar publication (and oral presentations).
<https://github.com/enanomapper/nano-lazar-paper>
-* Dockerized reproducible nano-lazar paper generation.
- <https://hub.docker.com/r/insilicotox/nano-lazar-paper/> \ No newline at end of file
+* Manuscript submitted to Frontiers in Pharmacology
+ <https://github.com/enanomapper/nano-lazar-paper/blob/master/nano-lazar.pdf>
+
+* Tutorial for repeating `nano-lazar` validation experiments
+ <https://github.com/enanomapper/nano-lazar-paper/blob/master/README.md>
+
+* Docker image for inspection and reproduction of validation experiments
+ <https://hub.docker.com/r/insilicotox/nano-lazar-paper/>
diff --git a/markdown_blocks/services_nano-lazar.md b/markdown_blocks/services_nano-lazar.md
index 385654a..3122fda 100644
--- a/markdown_blocks/services_nano-lazar.md
+++ b/markdown_blocks/services_nano-lazar.md
@@ -1,12 +1,16 @@
-* Nano-lazar for toxicity predictions - graphical user interface\cite{gebele_denis_2017_250818}.
- \
+The `nano-lazar` GUI provides a public webinterface for `nano-lazar` models
+
+* `nano-lazar` public webinterface \cite{gebele_denis_2017_250818}.
<https://nano-lazar.in-silico.ch>
-* Nano-lazar source code repository
+* `nano-lazar` source code
<https://github.com/eNanoMapper/nano-lazar>
-
-* Nano-lazar Rubydocs gem library documentation
- <http://www.rubydoc.info/gems/nano-lazar>
-* Nano-lazar REST API issue tracker
- <https://github.com/eNanoMapper/nano-lazar/issues> \ No newline at end of file
+* `nano-lazar` Ruby gem library
+ <https://rubygems.org/gems/nano-lazar>
+
+* `nano-lazar` issue tracker
+ <https://github.com/eNanoMapper/nano-lazar/issues>
+
+* `nano-lazar` API documentation
+ <http://www.rubydoc.info/gems/nano-lazar>
diff --git a/markdown_blocks/services_ontoviewer.md b/markdown_blocks/services_ontoviewer.md
index ab4cd6c..d50c2d7 100644
--- a/markdown_blocks/services_ontoviewer.md
+++ b/markdown_blocks/services_ontoviewer.md
@@ -1,10 +1,10 @@
-The eNanoMapper ontology viewer application\cite{gebele_denis_2017_259384} visualizes SPARQL query results from eNM ontologies ad data.
+The eNanoMapper ontology viewer visualizes SPARQL query results from eNM ontologies and data.
-* eNanoMapper ontology viewer
+* eNanoMapper ontology viewer \cite{gebele_denis_2017_259384}
<https://query.enanomapper.net/>
-* eNanoMapper ontology viewer source code repository
+* eNanoMapper ontology viewer source code
<https://github.com/enanomapper/enm-ontoviewer>
-* eNanoMapper ontology viewer issues
+* 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 a347992..d29a97d 100644
--- a/markdown_blocks/services_qsar-report.md
+++ b/markdown_blocks/services_qsar-report.md
@@ -1,16 +1,16 @@
-The QSAR-report Ruby gem library was developed to extend nano-lazar with QMRF and QPRF reporting features.
+QMRF and QPRF reporting features for `nano-lazar`. This library is accessible from the `nano-lazar` GUI and the `lazar-rest` webservices.
-* QSAR report - Ruby gem library\cite{rautenberg_micha_2016_179038} for QMRF and QPRF reporting
- <https://rubygems.org/gems/qsar-report/>
-
-* QSAR report - Rubydoc documentation
- <http://www.rubydoc.info/gems/qsar-report>
-
-* QSAR report - Ruby gem library source code
+* `qsar-report` source code \cite{rautenberg_micha_2016_179038}
<https://github.com/opentox/qsar-report>
-* QSAR report - Ruby gem library issue tracker
+* `qsar-report` Ruby gem library
+ <https://rubygems.org/gems/qsar-report/>
+
+* `qsar-report` issue tracker
<https://github.com/opentox/qsar-report/issues>
-* QSAR report - Tutorial
- <http://opentox.github.io/usage/2016/10/05/qmrf-and-qprf-reporting-library-gem> \ No newline at end of file
+* `qsar-report` tutorial
+ <http://opentox.github.io/usage/2016/10/05/qmrf-and-qprf-reporting-library-gem>
+
+* `qsar-report` API documentation
+ <http://www.rubydoc.info/gems/qsar-report>
diff --git a/markdown_blocks/services_sparql.md b/markdown_blocks/services_sparql.md
index 0d89a0f..b2a9562 100644
--- a/markdown_blocks/services_sparql.md
+++ b/markdown_blocks/services_sparql.md
@@ -1,7 +1,7 @@
-A SPARQL query interface for eNanoMapper data and ontologies has been established.
+SPARQL query interface for eNanoMapper data and ontologies
* SPARQL endpoint
<https://sparql.enanomapper.net/>
-* Documentation in "Deliverable 3.2 Data Management System with extended search capabilities" - 3.2.3.1. SPARQL endpoint
+* Documentation
<http://enanomapper.net/deliverables/d3/20160420_eNanoMapper_D3.2_Data_Management_System_with_extended_search_capabilities_FINAL.pdf>
diff --git a/markdown_blocks/services_summary.md b/markdown_blocks/services_summary.md
index 3b7305c..9f13628 100644
--- a/markdown_blocks/services_summary.md
+++ b/markdown_blocks/services_summary.md
@@ -1,6 +1,6 @@
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
+augmented with new developments. This poster gives a comprehensive overview of
+all IST resources developed within eNanoMapper. Each service is presented
with a brief description and links to the public interface, source code,
documentation and download links for self-contained docker images.