Commit 2e9f9132 authored by Jacek Lebioda's avatar Jacek Lebioda
Browse files

Merge branch '4-add-missing-frozen-entries' into 'master'

Resolve "Add missing Frozen entries"

Closes #4

See merge request core-services/r3-pages!3
parents 2371ffab 209353a2
Pipeline #44040 passed with stage
in 1 minute and 2 seconds
......@@ -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
---
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
......@@ -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
......
---
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 }})**
---
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 %}
---
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 %}
---
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 %}
---
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 %}
---
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 %}
......@@ -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. |
---
# 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
---
---
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
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