Commit c532cf1c authored by Elisabeth Guerard's avatar Elisabeth Guerard
Browse files

Finish layout #2

parent 601beeaa
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...@@ -5,4 +5,80 @@ title: Imp ...@@ -5,4 +5,80 @@ title: Imp
permalink: /frozen/imp permalink: /frozen/imp
--- ---
Test IMP {: .rtitle}
<div>
## IMP: a pipeline for reproducible reference-independent integrated metagenomic and metatranscriptomic analyses
Please cite the article on [Genome Biology][urlGenomeBiology].
Shaman Narayanasamy†, Yohan Jarosz†, Emilie E. L. Muller, Anna Heintz-Buschart, Malte Herold, Anne Kaysen, Cédric C. Laczny, Nicolás Pinel, Patrick May and Paul Wilmes*
</div>
{: .rblock}
<div>
### <i class="fas fa-globe"></i> Website
<hr>
The **IMP** website hosted within *R3lab* frame is available [here][urlIMP].
</div>
{: .rblock}
<div>
### <i class="fas fa-code"></i> Source code
<hr>
The source code of IMP is available on the [LCSB Gitlab][urlGitIMP] where you can traceback what have been done by the authors.
</div>
{: .rblock}
<div>
### <i class="fas fa-code"></i> Additionnal source code
<hr>
Some additionnal analysis made on the paper as also available on the [LCSB Gitlab][urlGitIMPDoc].
</div>
{: .rblock}
<div>
### <i class="fas fa-cogs"></i> Workflow
<hr>
Snakemake, a reproducible workflow engine that allow us IMP users execute the same workflow for each analysis. From [Köster, Johannes and Rahmann, Sven. “Snakemake - A scalable bioinformatics workflow engine”. Bioinformatics 2012.][urlBioinformatic]
</div>
{: .rblock}
<div>
### <i class="fas fa-dolly-flatbed"></i> Tool repository
<hr>
The **IMP** tool repository is hosted on the [LCSB webdav storage][urlWebdavIMP]. You will find some of the tools installed within IMP. IMP versions are stored under the dist folder.
</div>
{: .rblock}
<div>
### <i class="fab fa-docker"></i> Environment
<hr>
All tools dependencies of IMP are frozen inside a docker container. The files used to build the container can be found on Gitlab and versioned tarballs of the containers are found under the [webdav][urlWebdavIMPDep].
</div>
{: .rblock}
<div>
### <i class="fas fa-wrench"></i> R toolkit
<hr>
We use the [checkpoint][urlLibraryCheck] library to ensure that all of the necessary R packages are installed with the correct versions.
</div>
{: .rblock}
<div>
### <i class="fas fa-book"></i> Report
<hr>
**IMP** report contains all information needed to reproduce the same workflow, from the version of **IMP** used to make the analysis to the configuration file used to start the workflow. Everything is condensed and organized within an HTML report. Some reports can be found [here][urlIMPReport].
</div>
[urlIMP]:https://imp.pages.uni.lu/web/
[urlGenomeBiology]:https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-1116-8
[urlGitIMP]:https://git-r3lab.uni.lu/IMP/IMP
[urlGitIMPDoc]:https://git-r3lab.uni.lu/IMP/IMP_manuscript_analysis
[urlBioinformatic]:https://academic.oup.com/bioinformatics/article/28/19/2520/290322
[urlWebdavIMP]:https://webdav-r3lab.uni.lu/public/R3lab/IMP/
[urlWebdavIMPDep]:https://webdav-r3lab.uni.lu/public/R3lab/IMP/dist/
[urlLibraryCheck]:https://cran.r-project.org/web/packages/checkpoint/vignettes/checkpoint.html
[urlIMPReport]:https://webdav-r3lab.uni.lu/public/R3lab/IMP/reports/
\ No newline at end of file
---
layout: default
order: -1
title: Imp
permalink: /frozen/modelingParkinson
---
{: .rtitle}
<div>
## Modeling Parkinson's disease in midbrain-like organoids
Please cite the article on [NPJ Parkinson's disease][urlDoi].
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*
</div>
{: .rblock}
<div>
### <i class="fas fa-file-download"></i> RAW DATA
<hr>
The complete **Dataset** is available [here][urlWebdav].
</div>
{: .rblock}
<div>
### <i class="fas fa-code"></i> Source code
<hr>
The source code used to make the publication is available on [Github][urlGithub] where you can traceback what have been done by the authors.
</div>
{: .rblock}
<div>
### <i class="fas fa-globe"></i> Microarray data
<hr>
Data is accessible through [NCBI GEO][urlNCBI] website.
</div>
[urlDoi]:https://doi.org/10.1038/s41531-019-0078-4
[urlWebdav]:https://webdav-r3lab.uni.lu/public/data/modeling-parkinsons-disease-in-midbrain-like-organoids/
[urlGithub]:https://github.com/LCSB-DVB/Smits_Reinhardt_2019
[urlNCBI]: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE127967
\ No newline at end of file
---
layout: default
order: -1
title: Imp
permalink: /frozen/singlecell
---
{: .rtitle}
<div>
## SINGLE-CELL TRANSCRIPTOMICS REVEALS MULTIPLE NEURONAL CELL TYPES IN HUMAN MIDBRAIN-SPECIFIC ORGANOIDS
Please cite the article on [BioRxiv][urlBioRxiv].
Lisa M Smits†, Magni Stefano, Grzyb Kamil, Antony Paul MA, Krüger Rejko, Skupin Alexander, Bolognin Silvia, Jens C Schwamborn*
</div>
{: .rblock}
<div>
### <i class="fas fa-code"></i> SOURCE CODE
<hr>
The complete **Dataset** is available [here][urlWebdav].
</div>
{: .rblock}
<div>
### <i class="fas fa-file-download"></i> SINGLE-CELL TRANSCRIPTOMICS
<hr>
Data is accessible through [LCSB WebDAV][urlWebdav] website.
</div>
{: .rblock}
<div>
### <i class="fas fa-file-download"></i> RAW DATA
<hr>
The complete Dataset is available [here][urlWebdavall].
</div>
[urlBioRxiv]:https://www.biorxiv.org/content/10.1101/589598v1
[urlWebdavall]: https://webdav-r3lab.uni.lu/public/data/single-cell-transcriptomics-reveals-multiple-neuronal-cell-types-in-human-midbrain-specific-organoids/raw-data/
[urlWebdav]:https://webdav-r3lab.uni.lu/public/data/single-cell-transcriptomics-reveals-multiple-neuronal-cell-types-in-human-midbrain-specific-organoids/single-cell_transcriptomics/
\ No newline at end of file
...@@ -5,4 +5,44 @@ title: Smartr ...@@ -5,4 +5,44 @@ title: Smartr
permalink: /frozen/smartr permalink: /frozen/smartr
--- ---
Test Frozen {: .rtitle}
<div>
## SmartR: An open-source platform for interactive visual analytics for translational research data
<hr>
Please cite the article on [Oxford Bioinformatics][urlDoi].
Sascha Herzinger, Wei Gu, Venkata Satagopam, Serge Eifes, Kavita Rege, Adriano Barbosa-Silva, Reinhard Schneider, on behalf of the eTRIKS Consortium
</div>
{: .rblock}
<div>
### <i class="fas fa-globe"></i> Website
<hr>
The **SmartR** website hosted by **R3lab** is available [here][urlSmartR].
</div>
{: .rblock}
<div>
### <i class="fas fa-code"></i> Source code
<hr>
The source code of SmartR is available on [GitHub][urlSourceSmartR].
</div>
{: .rblock}
<div>
### <i class="fas fa-book"></i> Documentation
<hr>
All available documentation can be found [here][urlDocSmartR]
</div>
{: .rblock}
<div>
### <i class="fas fa-video"></i> Videos
<hr>
Several videos have been recorded to showcase the capabilities of SmartR. They can be accessed via [YouTube][urlYouTubeSmartR].
</div>
[urlYouTubeSmartR]: https://www.youtube.com/channel/UC0LP15lmuMkgYYLaFj3SKew
[urlDocSmartR]: https://github.com/transmart/SmartR/tree/master/doc
[urlSourceSmartR]:https://github.com/transmart/SmartR
[urlSmartR]: http://smartr.lcsb.uni.lu/
[urlDoi]: https://doi.org/10.1093/bioinformatics/btx137
...@@ -9,7 +9,7 @@ source "https://rubygems.org" ...@@ -9,7 +9,7 @@ source "https://rubygems.org"
# #
# This will help ensure the proper Jekyll version is running. # This will help ensure the proper Jekyll version is running.
# Happy Jekylling! # Happy Jekylling!
gem "jekyll", "~> 3.7.3" gem "jekyll", "~> 3.8.5"
gem "bundler", "> 1.16.1" gem "bundler", "> 1.16.1"
# This is the default theme for new Jekyll sites. You may change this to anything you like. # This is the default theme for new Jekyll sites. You may change this to anything you like.
...@@ -17,6 +17,7 @@ gem "minima", "~> 2.0" ...@@ -17,6 +17,7 @@ gem "minima", "~> 2.0"
gem 'jekyll-theme-primer', '~> 0.5.2' gem 'jekyll-theme-primer', '~> 0.5.2'
gem 'jekyll-theme-lcsb-default', '~> 0.2.5', :git => "https://git-r3lab.uni.lu/core-services/jekyll-theme-lcsb-default.git", :branch => "master" gem 'jekyll-theme-lcsb-default', '~> 0.2.5', :git => "https://git-r3lab.uni.lu/core-services/jekyll-theme-lcsb-default.git", :branch => "master"
# If you want to use GitHub Pages, remove the "gem "jekyll"" above and # If you want to use GitHub Pages, remove the "gem "jekyll"" above and
# uncomment the line below. To upgrade, run `bundle update github-pages`. # uncomment the line below. To upgrade, run `bundle update github-pages`.
# gem "github-pages", group: :jekyll_plugins # gem "github-pages", group: :jekyll_plugins
......
GIT GIT
remote: https://git-r3lab.uni.lu/core-services/jekyll-theme-lcsb-default.git remote: https://git-r3lab.uni.lu/core-services/jekyll-theme-lcsb-default.git
revision: f1eaba1cc613481c624b3b1a08129f3a91d79819 revision: 0d8c02bd35f4b0ebf563ee09f668cc6ac2e80935
branch: master branch: master
specs: specs:
jekyll-theme-lcsb-default (0.2.18) jekyll-theme-lcsb-default (0.2.20)
jekyll (~> 3.7) jekyll (~> 3.8)
jekyll-seo-tag (~> 2.1) jekyll-seo-tag (~> 2.5)
GEM GEM
remote: https://rubygems.org/ remote: https://rubygems.org/
specs: specs:
addressable (2.5.2) addressable (2.6.0)
public_suffix (>= 2.0.2, < 4.0) public_suffix (>= 2.0.2, < 4.0)
colorator (1.1.0) colorator (1.1.0)
concurrent-ruby (1.0.5) concurrent-ruby (1.1.5)
em-websocket (0.5.1) em-websocket (0.5.1)
eventmachine (>= 0.12.9) eventmachine (>= 0.12.9)
http_parser.rb (~> 0.6.0) http_parser.rb (~> 0.6.0)
eventmachine (1.2.7)
eventmachine (1.2.7-x64-mingw32) eventmachine (1.2.7-x64-mingw32)
faraday (0.15.3) faraday (0.15.4)
multipart-post (>= 1.2, < 3) multipart-post (>= 1.2, < 3)
ffi (1.9.25) ffi (1.10.0-x64-mingw32)
ffi (1.9.25-x64-mingw32)
forwardable-extended (2.6.0) forwardable-extended (2.6.0)
http_parser.rb (0.6.0) http_parser.rb (0.6.0)
i18n (0.9.5) i18n (0.9.5)
concurrent-ruby (~> 1.0) concurrent-ruby (~> 1.0)
jekyll (3.7.4) jekyll (3.8.5)
addressable (~> 2.4) addressable (~> 2.4)
colorator (~> 1.0) colorator (~> 1.0)
em-websocket (~> 0.5) em-websocket (~> 0.5)
...@@ -40,25 +38,25 @@ GEM ...@@ -40,25 +38,25 @@ GEM
pathutil (~> 0.9) pathutil (~> 0.9)
rouge (>= 1.7, < 4) rouge (>= 1.7, < 4)
safe_yaml (~> 1.0) safe_yaml (~> 1.0)
jekyll-feed (0.11.0) jekyll-feed (0.12.1)
jekyll (~> 3.3) jekyll (>= 3.7, < 5.0)
jekyll-github-metadata (2.9.4) jekyll-github-metadata (2.12.1)
jekyll (~> 3.1) jekyll (~> 3.4)
octokit (~> 4.0, != 4.4.0) octokit (~> 4.0, != 4.4.0)
jekyll-paginate-v2 (1.9.4) jekyll-paginate-v2 (1.9.4)
jekyll (~> 3.0) jekyll (~> 3.0)
jekyll-sass-converter (1.5.2) jekyll-sass-converter (1.5.2)
sass (~> 3.4) sass (~> 3.4)
jekyll-seo-tag (2.5.0) jekyll-seo-tag (2.6.0)
jekyll (~> 3.3) jekyll (~> 3.3)
jekyll-theme-primer (0.5.3) jekyll-theme-primer (0.5.3)
jekyll (~> 3.5) jekyll (~> 3.5)
jekyll-github-metadata (~> 2.9) jekyll-github-metadata (~> 2.9)
jekyll-seo-tag (~> 2.0) jekyll-seo-tag (~> 2.0)
jekyll-watch (2.0.0) jekyll-watch (2.2.1)
listen (~> 3.0) listen (~> 3.0)
kramdown (1.17.0) kramdown (1.17.0)
liquid (4.0.0) liquid (4.0.3)
listen (3.1.5) listen (3.1.5)
rb-fsevent (~> 0.9, >= 0.9.4) rb-fsevent (~> 0.9, >= 0.9.4)
rb-inotify (~> 0.9, >= 0.9.7) rb-inotify (~> 0.9, >= 0.9.7)
...@@ -69,44 +67,44 @@ GEM ...@@ -69,44 +67,44 @@ GEM
jekyll-feed (~> 0.9) jekyll-feed (~> 0.9)
jekyll-seo-tag (~> 2.1) jekyll-seo-tag (~> 2.1)
multipart-post (2.0.0) multipart-post (2.0.0)
octokit (4.12.0) octokit (4.14.0)
sawyer (~> 0.8.0, >= 0.5.3) sawyer (~> 0.8.0, >= 0.5.3)
pathutil (0.16.1) pathutil (0.16.2)
forwardable-extended (~> 2.6) forwardable-extended (~> 2.6)
public_suffix (3.0.3) public_suffix (3.0.3)
rb-fsevent (0.10.3) rb-fsevent (0.10.3)
rb-inotify (0.9.10) rb-inotify (0.10.0)
ffi (>= 0.5.0, < 2) ffi (~> 1.0)
rouge (3.2.1) rouge (3.3.0)
ruby_dep (1.5.0) ruby_dep (1.5.0)
safe_yaml (1.0.4) safe_yaml (1.0.5)
sass (3.6.0) sass (3.7.4)
sass-listen (~> 4.0.0) sass-listen (~> 4.0.0)
sass-listen (4.0.0) sass-listen (4.0.0)
rb-fsevent (~> 0.9, >= 0.9.4) rb-fsevent (~> 0.9, >= 0.9.4)
rb-inotify (~> 0.9, >= 0.9.7) rb-inotify (~> 0.9, >= 0.9.7)
sawyer (0.8.1) sawyer (0.8.2)
addressable (>= 2.3.5, < 2.6) addressable (>= 2.3.5)
faraday (~> 0.8, < 1.0) faraday (> 0.8, < 2.0)
thread_safe (0.3.6) tzinfo (2.0.0)
tzinfo (1.2.5) concurrent-ruby (~> 1.0)
thread_safe (~> 0.1) tzinfo-data (1.2019.1)
tzinfo-data (1.2018.5)
tzinfo (>= 1.0.0) tzinfo (>= 1.0.0)
wdm (0.1.1)
PLATFORMS PLATFORMS
ruby
x64-mingw32 x64-mingw32
DEPENDENCIES DEPENDENCIES
bundler (> 1.16.1) bundler (> 1.16.1)
jekyll (~> 3.7.3) jekyll (~> 3.8.5)
jekyll-feed (~> 0.6) jekyll-feed (~> 0.6)
jekyll-paginate-v2 (~> 1.7) jekyll-paginate-v2 (~> 1.7)
jekyll-theme-lcsb-default (~> 0.2.5)! jekyll-theme-lcsb-default (~> 0.2.5)!
jekyll-theme-primer (~> 0.5.2) jekyll-theme-primer (~> 0.5.2)
minima (~> 2.0) minima (~> 2.0)
tzinfo-data tzinfo-data
wdm (~> 0.1.0)
BUNDLED WITH BUNDLED WITH
1.16.4 2.0.1
...@@ -7,17 +7,17 @@ permalink: /websites/ ...@@ -7,17 +7,17 @@ permalink: /websites/
# Websites hosted within the R3lab frame: # Websites hosted within the R3lab frame:
## TGM pipeline ## [TGM pipeline](https://gitlab-pages-doc.pages.uni.lu/tgm-pipeline-doc/)
a platform for visually-aided exploration, analysis and interpretation of high-throughput translational medicine data a platform for visually-aided exploration, analysis and interpretation of high-throughput translational medicine data
## [IMP]({{ "frozen/imp" | relative_url }}) ## [IMP](https://imp.pages.uni.lu/web/)
[Integrated Meta-omic Pipeline]({{ "frozen/imp" | relative_url }}) Integrated Meta-omic Pipeline
## [MINERVA](https://minerva.pages.uni.lu/doc/) ## [MINERVA](https://minerva.pages.uni.lu/doc/)
[a platform for Molecular Interaction NEtwoRk VisuAlization](https://minerva.pages.uni.lu/doc/) a platform for Molecular Interaction NEtwoRk VisuAlization
## SYSCID ## [SYSCID](http://r3lab.uni.lu/web/imp/)
Data Management Plan Information Collection Data Management Plan Information Collection
## CaSiAn ## [CaSiAn](https://gitlab-pages-doc.pages.uni.lu/casian-doc/)
CaSiAn Website CaSiAn Website
...@@ -24,7 +24,7 @@ url: "https://core-services.pages.uni.lu" # the base hostname & protocol for you ...@@ -24,7 +24,7 @@ url: "https://core-services.pages.uni.lu" # the base hostname & protocol for you
banner: default # When you have custom images, change this setting's value to the name of the folder containing them 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 logo: small # Change to "big" (without quotas) in case of having broad logo
date: "2018"
twitter_username: uni_lu twitter_username: uni_lu
facebook_username: uni.lu facebook_username: uni.lu
...@@ -32,11 +32,15 @@ linkedin_schoolname: university-of-luxembourg ...@@ -32,11 +32,15 @@ linkedin_schoolname: university-of-luxembourg
# Build settings # Build settings
markdown: kramdown markdown: kramdown
kramdown:
parse_block_html: true
theme: jekyll-theme-lcsb-default theme: jekyll-theme-lcsb-default
plugins: plugins:
- jekyll-feed - jekyll-feed
- jekyll-paginate-v2 - jekyll-paginate-v2
# Produces a cleaner folder structure when using categories # Produces a cleaner folder structure when using categories
permalink: /:year/:month/:title.html permalink: /:year/:month/:title.html
......
...@@ -12,8 +12,15 @@ This website is under version control on the [LCSB Gitlab](https://git-r3lab.uni ...@@ -12,8 +12,15 @@ This website is under version control on the [LCSB Gitlab](https://git-r3lab.uni
# Frozen pages # Frozen pages
* ## [Integrated Metaomic Pipeline](https://imp.lcsb.uni.lu)
* ## [Modeling Parkinson's disease in midbrain like organoids]({{ "frozen/modelingParkinson" | relative_url }})
Modeling Parkinson's disease in midbrain-like organoids
* ## [Integrated Metaomic Pipeline]({{ "frozen/imp" | relative_url }})
IMP - Integrated Metaomic Pipeline IMP - Integrated Metaomic Pipeline
* ## SmartR * ## [SmartR]({{ "frozen/smartr" | relative_url }})
An open-source platform for interactive visual analytics for translational research data 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/singlecell" | relative_url }})
Single-cell transcriptomics reveals multiple neuronal cell types in human midbrain-specific organoids
\ No newline at end of file
...@@ -9,13 +9,12 @@ Here you can find a collection of tools used @LCSB to provide support for reprod ...@@ -9,13 +9,12 @@ Here you can find a collection of tools used @LCSB to provide support for reprod
## Associated services ## Associated services
* ### GITLAB [![Gitlab]({{ "//images/gitlab-logo.png" | relative_url }}){:width="120px"}](https://git-r3lab.uni.lu/)
Gitlab is an open source software that provide Version control and many other usefule features for devellopers and scientists. **Gitlab** is an open source software that provide Version control and many other usefule features for devellopers and scientists.
* ### DOCKER
![Docker]({{ "//images/docker-logo.png" | relative_url }}){:width="120px"} [![Docker]({{ "//images/docker-logo.png" | relative_url }}){:width="120px"}](https://docker-r3lab.uni.lu)
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. **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 [![Webdav]({{ "//images/webdav-logo.png" | relative_url }}){:width="120px"}](https://webdav-r3lab.uni.lu/)
![Webdav]({{ "//images/webdav-logo.png" | relative_url }}){:width="120px"} **WEBDAV** is a file sharing system over the web that brings more advanced security and control that a traditionnal FTP server.
Webdav is a file sharing system over the web that brings more advanced security and control that a traditionnal FTP server.
\ No newline at end of file
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