Built on 2023-09-28

Dockerfile

@@ -0,0 +1,17 @@
+# Prepared by Saeid Amiri
+FROM rocker/shiny:latest
+
+RUN apt-get update && apt-get install -y libcurl4-gnutls-dev \
+    libssl-dev libopenblas-dev && update-alternatives --config libblas.so.3-$(arch)-linux-gnu
+
+RUN R -e 'install.packages(c(\
+              "shiny", "shinydashboard","DT","rlang", "ggplot2", "plotly", "remotes",\
+              "tidyverse", "RColorBrewer", "stringr","reshape2","dplyr","shinyalert", "faq"\
+            )\
+          )'
+
+RUN R -e 'remotes::install_github("nvelden/NGLVieweR")'
+
+COPY ./MTSvieweR /srv/shiny-server/
+
+CMD ["/usr/bin/shiny-server"]

MTSvieweR/global.R

@@ -1,12 +1,12 @@
-# Dashboard v 1.0.2, 2022/03/24
+# Dashboard v 1.0.3, 2023/09/28
 # Developers: Andrew Bayne ([email protected]), Jing Dong ([email protected]), and Saeid Amiri ([email protected])
 
 # install.packages("devtools")
 # devtools::install_github("tidyverse/magrittr")
 # install.packages("scales")
 # install.packages("tidyverse")
-# install.packages("remotes")
-# remotes::install_github("nvelden/NGLVieweR")
+#install.packages("remotes")
+#remotes::install_github("nvelden/NGLVieweR")
 
 library(shiny)
 library(shinydashboard)

MTSvieweR/google-analytics.html

@@ -0,0 +1,9 @@
+<!-- Google tag (gtag.js) -->
+<script async src="https://www.googletagmanager.com/gtag/js?id=G-MMYJFKZYNT"></script>
+<script>
+  window.dataLayer = window.dataLayer || [];
+  function gtag(){dataLayer.push(arguments);}
+  gtag('js', new Date());
+
+  gtag('config', 'G-MMYJFKZYNT');
+</script>

MTSvieweR/ui.R

@@ -1,4 +1,5 @@
 fluidPage(
+tags$head(includeHTML(("google-analytics.html"))),
   titlePanel(
     title = 
       tags$a( target = "_blank",
@@ -124,13 +125,7 @@ fluidPage(
 
 
     tabPanel("How to cite us", 
-             mainPanel(
-               br(),
-               h4("When using MTSviewer please cite:"),
-               h5(HTML("MTSviewer: a database to visualize mitochondrial targeting sequences, cleavage sites, and mutations on protein structures<br>Andrew N. Bayne, Jing Dong, Saeid Amiri, Sali M.K. Farhan, Jean-Francois Trempe (2023)<br>PLOS ONE 18(4): e0284541.<br>DOI: <a href='https://doi.org/10.1371/journal.pone.0284541'>https://doi.org/10.1371/journal.pone.0284541</a>"))
-             )
-    )
-
+             mainPanel(br(), h4("When using MTSviewer please cite: "), h5(HTML("MTSviewer: a database to visualize mitochondrial targeting sequences, cleavage sites, and mutations on protein structures<br>Andrew N. Bayne, Jing Dong, Saeid Amiri, Sali M.K. Farhan, Jean-Francois Trempe (2023)<br>PLOS ONE 18(4): e0284541.<br>DOI: <a href='https://doi.org/10.1371/journal.pone.0284541'>https://doi.org/10.1371/journal.pone.0284541</a>"))))
   )
 )
 

README.md

@@ -1,25 +1,52 @@
-# MTSvieweR
-Welcome to MTSviewer, a database for the study of mitochondrial proteins which integrates AlphaFold stuctures, cleavage predictions, N-terminomics, and genetic variants.  
+# MTSvieweR: a database of mitochondrial proteins integrating
 
+[![](https://img.shields.io/badge/online-dashboard-red)](https://neurobioinfo.github.io/MTSvieweR)  [![](https://img.shields.io/badge/Docker-mtsviewer-blue)](https://hub.docker.com/r/saeidamiri1/mtsviewer) [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.7768427.svg)](https://doi.org/10.5281/zenodo.7768427) 
 
+-------------
 
-[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.7768427.svg)](https://doi.org/10.5281/zenodo.7768427)
+Welcome to MTSviewer's repository, a database for the study of mitochondrial proteins which integrates AlphaFold structures, cleavage predictions, N-terminomics, and genetic variants.
 
+## Contents
+-  [Features](#features)
+-  [Online Dashboard](#online-dashboard)
+-  [Docker](#docker)
+-  [Contributing](#contributing)
+-  [Citing](#citing)
 
 
-## Features
+### Features
 - MTS predictions
 - MPP cleavage sites
 - Genetic variants
 - Pathogenicity predictions
 - N-terminomics data
 - Structural visualization using AlphaFold models
 
+All of the raw data and in-house Python scripts used in the MTSviewer build are accessible and free to [download](https://drive.google.com/drive/folders/1L32pcbeUH-WR8ZTU4xTFvDV0XxG1WPbr?usp=sharing).
+
+:hammer: **Please note: if you only scroll through the "Gene List", the list will be truncated alphabetically after all genes starting with S. To overcome this, you must search your gene of interest, or type the beginning letter and all of the genes will be available!**
+
+### Online Dashboard
 It is accessible via [https://neurobioinfo.github.io/MTSvieweR](https://neurobioinfo.github.io/MTSvieweR)
 
-[All of the raw data and in-house Python scripts used in the MTSviewer build are accessible and free to download.](https://drive.google.com/drive/folders/1L32pcbeUH-WR8ZTU4xTFvDV0XxG1WPbr?usp=sharing).
 
-:hammer: **Please note: if you only scroll through the "Gene List", the list will be truncated alphabetically after all genes starting with S. To overcome this, you must search your gene of interest, or type the beginning letter and all of the genes will be available!**
+### Docker
+The MTSvieweR container is accessible on [docker's hub](https://hub.docker.com/r/saeidamiri1/mtsviewer). If you'd like to run it using Docker, please follow these instructions:
+```
+docker run --rm -p 3838:3838 saeidamiri1/mtsviewer:1.0.3
+```
+
+### Contributing
+Any contributions or suggestions are greatly appreciated. To initiate a discussion about a new feature or a bug fix, it's typically best to open a GitHub issue. Once we reach a consensus on the way forward, you can fork the repository, make the necessary changes (using the dev branch), and then create a pull request (PR). Please ensure that PRs are targeted towards the dev branch.
+
+If you come across a bug, kindly submit a comprehensive GitHub issue, and we'll respond promptly to address the issue.
+
+### Citing
+If you use MTSviewer in your research, please consider citing our paper: 
+
+Bayne, A. N., Dong, J., Amiri, S., Farhan, S. M., & Trempe, J. F. (2023). MTSviewer: A database to visualize mitochondrial targeting sequences, cleavage sites, and mutations on protein structures. Plos one, 18(4), e0284541. [https://doi.org/10.1371/journal.pone.0284541](https://doi.org/10.1371/journal.pone.0284541)
+
+See also our paper on [PlOS ONE](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0284541).
 
-## License
+### License
 This project is licensed under the MIT License - see the [LICENSE.md](https://github.com/neurobioinfo/MTSvieweR/blob/main/LICENSE) file for details