Resolve "Add missing Frozen entries"

.gitlab-ci.yml

@@ -6,15 +6,15 @@ variables:
 before_script:
   - bundle install && bundle update
 
-test:
-  stage: test
-  script:
-  - bundle exec jekyll build -d test
-  artifacts:
-    paths:
-    - test
-  except:
-  - master
+#test:
+#  stage: test
+#  script:
+#  - bundle exec jekyll build -d test
+#  artifacts:
+#    paths:
+#    - test
+#  except:
+#  - master
 
 pages:
   stage: deploy
@@ -23,5 +23,5 @@ pages:
   artifacts:
     paths:
     - public
-  only:
-  - master
+#  only:
+#  - master

Websites.md

----
-layout: default
-title: Websites
-order: 3
-permalink: /websites/
----
-
-# Websites hosted within the R3lab frame:
-
-## [TGM pipeline](https://core-services.pages.uni.lu/tgm-pipeline-doc/){:target="_blank"}
-a platform for visually-aided exploration, analysis and interpretation of high-throughput translational medicine data
-
-## [IMP](https://imp.pages.uni.lu/web/){:target="_blank"}
-Integrated Meta-omic Pipeline
-
-## [MINERVA](https://minerva.pages.uni.lu/doc/){:target="_blank"}
-a platform for Molecular Interaction NEtwoRk VisuAlization
-
-## [SYSCID](http://r3lab.uni.lu/web/imp/){:target="_blank"}
-Data Management Plan Information Collection
-
-## [CaSiAn](https://core-services.pages.uni.lu/casian-doc/){:target="_blank"}
-CaSiAn Website

_config.yml

@@ -13,14 +13,14 @@
 # you will see them accessed via {{ site.title }}, {{ site.email }}, and so on.
 # You can create any custom variable you would like, and they will be accessible
 # in the templates via {{ site.myvariable }}.
-title: R3.
+title: R3 pages 
 email: lcsb-sysadmins@example.com
 description: >- # this means to ignore newlines until "baseurl:"
   Write an awesome description for your new site here. You can edit this
   line in _config.yml. It will appear in your document head meta (for
   Google search results) and in your feed.xml site description.
 baseurl: "/r3-pages/" # the subpath of your site, e.g. /blog
-url: "https://core-services.pages.uni.lu" # the base hostname & protocol for your site, e.g. http://example.com
+url: "https://core-services.pages.uni.lu"
 
 banner: default  # When you have custom images, change this setting's value to the name of the folder containing them
 logo: small  # Change to "big" (without quotas) in case of having broad logo

frozen.md

 ---
 layout: default
-title: Frozen Pages
+title: Frozen pages
 order: 2
 permalink: /frozen/
 ---
@@ -8,19 +8,20 @@ permalink: /frozen/
 # Information
 Here you can find project pages that are related to a published scientific paper. Project pages must link to all components referenced in the paper and is not modified after the release of the paper.
 
-This website is under version control on the [LCSB Gitlab](https://git-r3lab.uni.lu).
+This website is under version control on the [LCSB Gitlab](https://git-r3lab.uni.lu/core-services/r3-pages).
 
 # Frozen pages
 
+* **[Modeling Parkinson's disease in midbrain like organoids]({{ "frozen/modeling-parkinsons-disease-in-midbrain-like-organoids" | relative_url }})**
 
-* ## [Modeling Parkinson's disease in midbrain like organoids]({{ "frozen/modelingParkinson" | relative_url }})
- Modeling Parkinson's disease in midbrain-like organoids
+* **[Synapse Alterations Precede Neuronal Damage And Storage Pathology In A Human Cerebral Organoid Model]({{ "frozen/synapse-alterations-precede-neuronal-damage-and-storage-pathology-in-a-human-cerebral-organoid-model" | relative_url }})**
 
-* ## [Integrated Metaomic Pipeline]({{ "frozen/imp" | relative_url }})
-IMP - Integrated Metaomic Pipeline
+* **[IMP - Integrated Metaomic Pipeline]({{ "frozen/imp" | relative_url }})**
 
-* ## [SmartR]({{ "frozen/smartr" | relative_url }})
-An open-source platform for interactive visual analytics for translational research data
+* **[Reproducible generation of human midbrain organoids for in vitro modeling of Parkinson's disease]({{ "frozen/reproducible-generation-of-human-midbrain-organoids-for-in-vitro-modeling-of-parkinsons-disease" | relative_url }})**
 
-* ## [Single-cell transcriptomics reveals multiple neuronal cell types in human midbrain-specific organoids]({{ "frozen/singlecell" | relative_url }}) 
-Single-cell transcriptomics reveals multiple neuronal cell types in human midbrain-specific organoids
\ No newline at end of file
+* **[SmartR]({{ "frozen/smartr" | relative_url }})** - an open-source platform for interactive visual analytics for translational research data
+
+* **[Single-cell transcriptomics reveals multiple neuronal cell types in human midbrain-specific organoids]({{ "frozen/single-cell-transcriptomics-reveals-multiple-neuronal-cell-types-in-human-midbrain-specific-organoids" | relative_url }})**
+
+* **[Machine learning-assisted neurotoxicity prediction in human midbrain organoids]({{ "frozen/machine-learning-assisted-neurotoxicity-prediction-in-human-midbrain-organoids" | relative_url }})**

frozen/machine_learning_assisted_neurotoxicity.md

+---
+layout: default
+order: -1
+title: Machine learning-assisted neurotoxicity prediction in human midbrain organoids  (PRE-VERSION)
+permalink: /frozen/machine-learning-assisted-neurotoxicity-prediction-in-human-midbrain-organoids/
+---
+
+
+{% rtitle Machine learning-assisted neurotoxicity prediction in human midbrain organoids  (PRE-VERSION) %}
+Please cite the article on [Paper](#).
+
+Anna S. Monzel†, Kathrin Hemmer, Tony Kaoma Mukendi, Philippe Lucarelli, Isabel Rosety, Alise Zagare, Silvia Bolognin, Paul Antony, Sarah L. Nickels, Rejko Krueger, Francisco Azuaje, Jens C. Schwamborn*
+{% endrtitle %} 
+
+
+{% rgridblock a-unique-id %}
+{% rblock  SOURCE CODE | fas fa-code %}
+The source code is available on [Github](https://github.com/LCSB-DVB/Monzel_2019) where you can traceback what have been done by the authors. Similarly, you can find the code used for the machine learning analysis [here](https://gitlab.com/biomodlih/tox-ml).
+{% endrblock %}
+
+{% rblock  Figures | fas fa-image %}
+The data for the figures can be found [here](https://webdav-r3lab.uni.lu/public/data/machine-learning-assisted-neurotoxicity-prediction-in-human-midbrain-organoid/).
+{% endrblock %}
+
+{% endrgridblock %} 

Frozen/modelingParkinson.md → frozen/modeling_parkinson.md

 ---
 layout: default
 order: -1
-title: Imp
-permalink: /frozen/modelingParkinson
+title: Modeling Parkinson's disease in midbrain-like organoids
+permalink: /frozen/modeling-parkinsons-disease-in-midbrain-like-organoids
 ---
 
 {% rtitle Modeling Parkinson's disease in midbrain-like organoids %}
 Please cite the article on [NPJ Parkinson's disease](https://doi.org/10.1038/s41531-019-0078-4).
+
 Lisa M Smits†, Lydia Reinhardt†, Peter Reinhardt, Michael Glatza, Anna S Monzel, Nacny Stanslowsky, Marcelo D Rosato-Siri, Alessandra Zanon, Paul M Antony, Jessica Bellmann, Sarah M Nicklas, Kathrin Hemmer, Xiaobing Qing, Emanuel Berger, Norman Kalmbach, Marc Ehrlich, Silvia Bolognin, Andrew A Hicks, Florian Wegner, Jared L. Sterneckert* & Jens C Schwamborn*
 {% endrtitle %} 
 
 
 {% rgridblock a-unique-id %}
-{% rblock  Raw data | fas fa-file-download %}
+{% rblock  Raw data | fas fa-image %}
 The complete **Dataset** is available [here](https://webdav-r3lab.uni.lu/public/data/modeling-parkinsons-disease-in-midbrain-like-organoids/).
 {% endrblock %}
 
 
-{% rblock source code %}
+{% rblock source code | fas fa-copy %}
 The source code used to make the publication is available on [Github](https://github.com/LCSB-DVB/Smits_Reinhardt_2019) where you can traceback what have been done by the authors.
 {% endrblock %}
 
 
 
-{%  rblock microarray data | fas fa-globe %}
+{%  rblock microarray data | fas fa-th %}
 Data is accessible through [NCBI GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE127967) website.
 {% endrblock %}
 {% endrgridblock %} 

frozen/reproducible_generation.md

+---
+layout: default
+order: -1
+title: Reproducible generation of human midbrain organoids for in vitro modeling of Parkinson's disease
+permalink: /frozen/reproducible-generation-of-human-midbrain-organoids-for-in-vitro-modeling-of-parkinsons-disease
+---
+
+{% rtitle Reproducible generation of human midbrain organoids for in vitro modeling of Parkinson`s disease %}
+Sarah Louise Nickels†, Jennifer Modamio, Bárbara Mendes-Pinheiro, Anna Sophia Monzel, Fay Betsou and Jens Christian Schwamborn*
+{% endrtitle %} 
+
+
+{% rgridblock a-unique-id %}
+{% rblock  Raw data | fas fa-video %}
+The complete Dataset is available  [here](https://webdav-r3lab.uni.lu/public/data/reproducible-generation-of-human-midbrain-organoids-for-in-vitro-modeling-of-parkinsons-disease/). It is subdivided into originals (raw data) and partials (analysis) specific to each figure and supplementary present in the manuscript.
+{% endrblock %}
+
+
+{% rblock source code %}
+The source code used to make the analysis/figures of the publication is available on [Github](https://github.com/LCSB-DVB/Nickels_2019).
+{% endrblock %}
+
+{% endrgridblock %} 

Frozen/singlecell.md → frozen/single_cell_transcriptomics.md

 ---
 layout: default
 order: -1
-title: Imp
-permalink: /frozen/singlecell
+title: Single-cell transcriptomics reveals multiple neuronal cell types in human midbrain-specific organoids
+permalink: /frozen/single-cell-transcriptomics-reveals-multiple-neuronal-cell-types-in-human-midbrain-specific-organoids/
 ---
 
 
 {% rtitle SINGLE-CELL TRANSCRIPTOMICS REVEALS MULTIPLE NEURONAL CELL TYPES IN HUMAN MIDBRAIN-SPECIFIC ORGANOIDS %}
 Please cite the article on [BioRxiv](https://www.biorxiv.org/content/10.1101/589598v1).
+
 Lisa M Smits†, Magni Stefano, Grzyb Kamil, Antony Paul MA, Krüger Rejko, Skupin Alexander, Bolognin Silvia, Jens C Schwamborn*
 {% endrtitle %} 
 
 
 {% rgridblock a-unique-id %}
 {% rblock  SOURCE CODE | fas fa-code %}
-The complete **Dataset** is available [here](https://webdav-r3lab.uni.lu/public/data/single-cell-transcriptomics-reveals-multiple-neuronal-cell-types-in-human-midbrain-specific-organoids/single-cell_transcriptomics/).
+The source code used to make the publication is available on [Github](https://github.com/LCSB-DVB/Smits_Reinhardt_2019) where you can traceback what have been done by the authors.
 {% endrblock %}
 
-{% rblock  SINGLE-CELL TRANSCRIPTOMICS | fas fa-file-download %}
+{% rblock  SINGLE-CELL TRANSCRIPTOMICS | fas fa-th %}
 Data is accessible through [LCSB WebDAV](https://webdav-r3lab.uni.lu/public/data/single-cell-transcriptomics-reveals-multiple-neuronal-cell-types-in-human-midbrain-specific-organoids/single-cell_transcriptomics/) website.
 {% endrblock %}
 
-{% rblock  RAW DATA | fas fa-file-download %}
-The complete Dataset is available [here](https://webdav-r3lab.uni.lu/public/data/single-cell-transcriptomics-reveals-multiple-neuronal-cell-types-in-human-midbrain-specific-organoids/raw-data/).
+{% rblock  RAW DATA | fas fa-image %}
+The complete **Dataset** is available [here](https://webdav-r3lab.uni.lu/public/data/single-cell-transcriptomics-reveals-multiple-neuronal-cell-types-in-human-midbrain-specific-organoids/raw-data/).
 {% endrblock %}
 {% endrgridblock %} 

frozen/synapse.md

+---
+layout: default
+order: -1
+title: Synapse Alterations Precede Neuronal Damage And Storage Pathology In A Human Cerebral Organoid Model  (PRE-VERSION)
+permalink: /frozen/synapse-alterations-precede-neuronal-damage-and-storage-pathology-in-a-human-cerebral-organoid-model/
+---
+
+
+{% rtitle Synapse Alterations Precede Neuronal Damage And Storage Pathology In A Human Cerebral Organoid Model  (PRE-VERSION) %}
+Please cite the article on [Paper](#).
+
+Gemma Gomez-Giro†, Jonathan Arias-Fuenzalida, Javier Jarazo, Dagmar Zeuschner, Muhammad Ali, Nina Possemis, Silvia Bolognin, Rashi Halder, Christian Jäger, Willemijn F.E. Kuper, Holm Zaehres, Antonio del Sol, Herman van der Putten, Hans R. Schöler & Jens C. Schwamborn*
+{% endrtitle %} 
+
+
+{% rgridblock a-unique-id %}
+{% rblock  Raw data | fas fa-th %}
+The complete dataset is available [here](https://webdav-r3lab.uni.lu/public/data/synapse-alterations-precede-neuronal-damage-and-storage-pathology-in-a-human-cerebral-organoid-model/). It is subdivided into originals (raw data) and partials (analysis) specific to each figure and supplementary present in the manuscript.
+{% endrblock %}
+
+{% rblock  RNA-Seq data | fas fa-th %}
+The RNA-seq data is accessible through the [NCBI GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE137420) website.
+{% endrblock %}
+
+{% rblock  Source code | fas fa-copy %}
+The source code used to make the analysis/figures of the publication is available on [GitHub](https://github.com/LCSB-DVB/Gomez-Giro_2019).
+{% endrblock %}
+{% endrgridblock %} 

index.md

@@ -9,16 +9,6 @@ Here you can find a collection of tools used @LCSB to provide support for reprod
 
 ## Associated services
 
-
-[![Gitlab]({{ "//images/gitlab-logo.png" | relative_url }}){:width="120px"}](https://git-r3lab.uni.lu/){:target="_blank"}
-**Gitlab** is an open source software that provide Version control and many other usefule features for devellopers and scientists.
-
-
-[![Docker]({{ "//images/docker-logo.png" | relative_url }}){:width="120px"}](https://docker-r3lab.uni.lu){:target="_blank"}
-**DOCKER** is an open source solution that allow us to package and freeze an application or framework and all it's dependencies into a single unit called a container.
-
-[![Webdav]({{ "//images/webdav-logo.png" | relative_url }}){:width="120px"}](https://webdav-r3lab.uni.lu/){:target="_blank"}
-**WEBDAV** is a file sharing system over the web that brings more advanced security and control that a traditionnal FTP server.
-
-
-
+| [![Gitlab]({{ "//images/gitlab-logo.png" | relative_url }}){:width="120px"}](https://git-r3lab.uni.lu/){:target="_blank"}   | **Gitlab** is an open source software that provide Version control and many other usefule features for devellopers and scientists.  |
+| [![Docker]({{ "//images/docker-logo.png" | relative_url }}){:width="120px"}](https://docker-r3lab.uni.lu){:target="_blank"} | **DOCKER** is an open source solution that allow us to package and freeze an application or framework and all it's dependencies into a single unit called a container.  |
+|  [![Webdav]({{ "//images/webdav-logo.png" | relative_url }}){:width="120px"}](https://webdav-r3lab.uni.lu/){:target="_blank"} | **WEBDAV** is a file sharing system over the web that brings more advanced security and control that a traditionnal FTP server.  |

pagination.md

----
-# To enable the pagination, do the following changes in this file:
-# published: true
-# pagination:
-#   enabled: true
-
-# And inside index.md, add `published: false`
-
-# You don't need to edit this file, it's empty on purpose.
-# Edit theme's home layout instead if you wanna make some changes
-# See: https://jekyllrb.com/docs/themes/#overriding-theme-defaults
-
-title: index 
-layout: paginated_index
-published: false
-pagination:
-  enabled: false
----
-

websites.md

+---
+layout: default
+title: Websites
+order: 3
+permalink: /websites/
+---
+
+# Websites hosted within the R3lab frame:
+
+* **[TGM pipeline](https://core-services.pages.uni.lu/tgm-pipeline-doc/){:target="_blank"}** - a platform for visually-aided exploration, analysis and interpretation of high-throughput translational medicine data
+
+* **[IMP](https://imp.pages.uni.lu/web/){:target="_blank"}** - Integrated Meta-omic Pipeline
+
+* **[MINERVA](https://minerva.pages.uni.lu/doc/){:target="_blank"}** - a platform for Molecular Interaction NEtwoRk VisuAlization
+
+* **[SYSCID](http://r3lab.uni.lu/web/imp/){:target="_blank"}** - Data Management Plan Information Collection
+
+* **[CaSiAn](https://core-services.pages.uni.lu/casian-doc/){:target="_blank"}** - CaSiAn Website