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---
title: '<a name="top"></a><img src="https://raw.githubusercontent.com/samWieczorek/Prostar/master/inst/ProstarApp/www/images/LogoProstarComplet.png" width="135"/>
**p r o s t a r - p r o t e o m i c s .org**'
output:
html_document:
toc: true
toc_float: true
theme: united
toc_depth: 3 # up to three depths of headings (specified by #, ## and ###)
highlight: tango # specifies the syntax highlighting style
#css: my.css # you can add your custom css, should be in same folder
includes:
in_header: GA_Script.html
---
<style>
body {
text-align: justify}
</style>
\usepackage{xspace}
newcommand{\version}{1.28.5\xspace}
------
# Home
\color{blue}{\scriptsize{\version}}
## News
**Enjoy the [Zero-install version of Prostar](#zero-install) as well as the new [Online demo](#online-demo)!**
**25/08/2022**
* Prostar version 1.28.5 has been released on the Bioconductor (release 3.15) and is deployed as a [Zero-install](#zero-install) zip.
**27/04/2022**
* Prostar version 1.28.0 has been released on the Bioconductor (release 3.15) and is deployed as a [Zero-install](#zero-install) zip.
**22/06/2021**
* Prostar for metabolomics 1.22.8 (beta version) is now available as a [Zero-install](#zero-install) zip.
## About
Prostar is a software tool devoted to the differential analysis of quantitative data resulting from discovery proteomics experiments.
Prostar is easy to install (see our [Zero-install page](#zero-install)),
easy to use (thanks to its [Shiny](https://shiny.rstudio.com/)-based click-button interface)
and well-documented (see our [reference page](#useful-links)).
Moreover, it has been regularly updated along years to provide state-of-the-art data science methodologies.
## Citation
**Maintaining Prostar as free software is a heavy duty. Please cite the following reference**
> *S. Wieczorek, F. Combes, C. Lazar, Q. Giai-Gianetto, L. Gatto, A. Dorffer, A.-M. Hesse, Y. Couté, M. Ferro, C. Bruley and T. Burger*.
DAPAR & ProStaR: software to perform statistical analyses in quantitative discovery proteomics.
**Bioinformatics** 33(1), 135-136, 2017.
<a href="http://doi.org/10.1093/bioinformatics/btw580" target="_blank">http://doi.org/10.1093/bioinformatics/btw580.</a>
## Presentation
[[./docs/md/presentation.md]]
------
# Software
1. [**Zero-install**](#zero-install)
The easiest way, so far only available on Microsoft Windows desktop machines.
Prostar is deployed either as a zip archive or as a Docker image (bêta).
2. [**Stand-alone Bioconductor install**](#bioconductor-installs)
The standard method to install Bioconductor distributed software.
This method works for any operating systems (Unix/Linux, Mac OS X and Windows)
as long as R is installed.
3. **Server install**
When one wants Prostar to run on a Unix server, on which remote users connect.
This more advanced type of install is detailed in the [user manual](#useful-links).
4. [**Online demo**](#online-demo)
Before installing Prostar on your desktop machine, test our online demo!
## Zero-install
**Remarks:**
1. It is not necessary to have R already installed.
2. For now, Zero-install is only available for Microsoft Windows machines.
3. At first launch, an internet connection is necessary to finish the install.
4. To ensure full compatibility and debugging, the zip file is available up to one month after each Bioconductor release.
### Zip file (only for Windows)
Just download the zip file below and unzip it! The unzipped folder contains an executable file which directly launches Prostar.
Download <a href="http://prabig-prostar.univ-lyon1.fr/ProstarZeroInstall/Prostar_1.28.5.zip" onclick="gtag('event', 'send', { 'event_category': 'download', 'event_label': 'Download Prostar_1.28.5.zip'});">**Prostar 1.28.5 zip file**</a>
(Release date: 22/08/2022)
Download <a href="http://prabig-prostar.univ-lyon1.fr/ProstarZeroInstall/Prostar4metabolomics_1.22.8.zip" onclick="gtag('event', 'send', { 'event_category': 'download', 'event_label': 'Download Prostar4metabolomics_1.22.8.zip'});">**Prostar4metabolomics 1.22.8 zip file**</a>
(Release date: 22/06/2021)
### Docker image (Bêta)
This feature is deployed as a Beta-test so as to give an alternative to the zip
file. The version of Prostar embebbed in this image follows the same logics of update
as for the zip file. So, the versions of Prostar are identical.
As a prerequisite, Docker must be installed on the computer and the service must be started. Prostar is available as a Docker image on the Github repository for images. To download the image and install it from the command line (wsl console on Windows), type:
```
docker pull ghcr.io/prostarproteomics/prostar:1.28.5
docker tag ghcr.io/prostarproteomics/prostar:1.28.5 prostar
```
There are two ways to launch Prostar's container. From the command line, type:
```
docker run -it -p 3838:3838 prostar
```
Then, open your default web browser and go to the address http://localhost:3838.
If one want to use an executable file, then create the launch script called 'docker_launch_prostar.sh' with the following
lines
```
#! /bin/sh
docker run -it -p 3838:3838 prostar
python -m webbrowser http://localhost:3838
```
Then, make the script runnable and launch Prostar
```
chmod +x docker_launch_prostar.sh
./docker_launch_prostar.sh
```
## Bioconductor installs
Only stand-alone install is detailed below. For server install, please refer to the user manual.
This type of install works with any operating system among Unix/Linux, Mac OS X and Windows.
However, it is necessary to have the latest version of R (R-4.2.0 for Prostar 1.28) installed in a directory where the user has read/write permissions.
1. Install Bioconductor package manager by copy-paste of the following commands (see
<a href="https://cran.r-project.org/web/packages/BiocManager/vignettes/BiocManager.html" target="_blank">this page</a>
for details):
```R
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install(version='3.15')
```
2. Install Prostar:
```R
BiocManager::install("Prostar")
```
3. Launch Prostar:
```R
library(Prostar)
Prostar()
```
## Online demo
An online demo of Prostar software is available at:
<a href="http://live.prostar-proteomics.org/" target="_blank">**http://live.prostar-proteomics.org**</a>
**Remark:** The server hosting the online demo has limited capacities.
Thus, uploading your own dataset may lead to server overload.
To test the online demo, please rely on the toy datasets that are available in "Demo data" (from "Data manager" menu).
## Release notes
[[./docs/md/versionNotes.md]]
[[./docs/md/formerReleases.md]]
------
# Support & resources
## Useful links
[[./docs/md/links.md]]
## Frequently asked questions
[[./docs/md/FAQ.md]]
## Forum
Our community forum is hosted by the Bioconductor:
<a href="https://support.bioconductor.org/t/prostar/" target="_blank">**https://support.bioconductor.org/t/prostar/**</a>
------
# Community
## Team presentation
### Core team
<a href="https://scholar.google.fr/citations?hl=fr&user=K4CBghYAAAAJ" target="_blank">**Samuel Wieczorek**</a>
<img src="https://github.com/samWieczorek/Prostar_website/raw/master/docs/img/Sam.png" width="155"/>
After a first career as IT support technician, Sam obtained an engineering degree (2004) at "Conservatoire National des Arts et Métiers",
followed by a MS degree in computer sciences and a PhD in machine learning (2009) at Grenoble-Alpes University.
Since then, he has been working as a research engineer at EDyP-lab, where he has been developing and maintaining software tools for proteomics.
Sam has been involved in Prostar project since its beginning.
He is the code guru and supervises all the software aspects of the project, such as coding, packaging, deployment,
debugging, graphical user interfaces, etc.
<a href="https://sites.google.com/site/thomasburgerswebpage" target="_blank">**Thomas Burger**</a>
<img src="https://github.com/samWieczorek/Prostar_website/raw/master/docs/img/Thomas-Burger-155.jpg" width="155"/>
After two MS degrees in computer sciences and in applied mathematics (2004),
Thomas defended a PhD in pattern recognition (2007) at Grenoble-Alpes University.
From 2008 to 2011, he held an associate professor position in statistics (South Britany University).
In November 2011, he obtained a full time CNRS researcher position at EDyP-lab, and started addressing computational proteomics questions.
He is the principal investigator of Prostar project.
His expertise focuses on the statistical, methodological and algorithmic aspects of proteomics data analysis.
**Contact us** - [email protected]
### Occasional contributors
* <a href="https://scholar.google.fr/citations?hl=fr&user=IJj2oUsAAAAJ" target="_blank">Florence Combes</a>
* <a href="https://research.pasteur.fr/fr/member/quentin-giai-gianetto/" target="_blank">Quentin Giai-Gianetto</a> (Institut Pasteur, France)
* <a href="https://lgatto.github.io/" target="_blank">Laurent Gatto</a>
(Université catholique de Louvain, Belgique)
* <a href="https://scholar.google.fr/citations?hl=fr&user=gHyBfNwAAAAJ" target="_blank">Cosmin Lazar</a>
* <a href="https://scholar.google.fr/citations?hl=fr&user=yYroo3gAAAAJ" target="_blank">Helene Borges</a>
* <a href="https://scholar.google.fr/citations?user=pUQIR6wAAAAJ&hl=fr" target="_blank">Yohann Couté</a>
* <a href="https://scholar.google.fr/citations?hl=fr&user=pnV6KrsAAAAJ" target="_blank">Christophe Bruley</a>
* <a href="https://scholar.google.fr/citations?hl=fr&user=DfkciI8AAAAJ" target="_blank">Anne-Marie Hesse</a>
* Alexia Dorffer
* Enora Fremy
### Beta-testing & co.
<img src="https://raw.githubusercontent.com/samWieczorek/Prostar/master/inst/ProstarApp/www/images/edyp.png" width="155"/>
The entire EDyP proteomics platform (see <a href="http://www.edyp.fr" target="_blank">www.edyp.fr</a>):
Prostar being permanently hosted by EDyP lab, the first users (the original ones, but also the testers) are naturally the lab members.
They are all warmly acknowledged for their contributions.
## Bug report
To report any issue with Prostar, it is best to use the devoted tab in Prostar software (click on **Bug report** in the **Help menu**),
as it allows easy sharing of the session logs and data (essential to efficient debugging).
However, it is also possible to contact the development team by email (see [team presentation](#team-presentation)).
## Happiness report
**If you are pleased with your Prostar experience**, you can also send us a message (messages are not restricted to bug reports)!
:-)
Do not forget to [cite Prostar in your publications](#citation)!
<div align="right"><a href="#top"> ↑ Top</a></div>