diff --git a/.DS_Store b/.DS_Store index 325b089..4e070b2 100644 Binary files a/.DS_Store and b/.DS_Store differ diff --git a/Dockerfile b/Dockerfile new file mode 100644 index 0000000..cd283b2 --- /dev/null +++ b/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-$(arch)-linux-gnu + +RUN R -e 'install.packages(c(\ + "shiny", "shinydashboard","DT","rlang", "ggplot2", "plotly", "remotes",\ + "tidyverse", "RColorBrewer", "stringr","reshape2","dplyr","shinyalert", "faq"\ + )\ + )' + +RUN R -e 'remotes::install_github("nvelden/NGLVieweR")' + +COPY ./MTSvieweR /srv/shiny-server/ + +CMD ["/usr/bin/shiny-server"] diff --git a/MTSvieweR/.DS_Store b/MTSvieweR/.DS_Store index ebec9dc..c577670 100644 Binary files a/MTSvieweR/.DS_Store and b/MTSvieweR/.DS_Store differ diff --git a/MTSvieweR/PDBs/.DS_Store b/MTSvieweR/PDBs/.DS_Store new file mode 100644 index 0000000..229c7be Binary files /dev/null and b/MTSvieweR/PDBs/.DS_Store differ diff --git a/MTSvieweR/global.R b/MTSvieweR/global.R index 9d612c9..2808d9f 100644 --- a/MTSvieweR/global.R +++ b/MTSvieweR/global.R @@ -1,12 +1,12 @@ -# Dashboard v 1.0.2, 2022/03/24 +# Dashboard v 1.0.3, 2023/09/28 # Developers: Andrew Bayne (andrew.bayne@mail.mcgill.ca), Jing Dong (jing.dong2@mail.mcgill.ca), and Saeid Amiri (saeid.amiri@mcgill.ca) # install.packages("devtools") # devtools::install_github("tidyverse/magrittr") # install.packages("scales") # install.packages("tidyverse") -# install.packages("remotes") -# remotes::install_github("nvelden/NGLVieweR") +#install.packages("remotes") +#remotes::install_github("nvelden/NGLVieweR") library(shiny) library(shinydashboard) diff --git a/MTSvieweR/google-analytics.html b/MTSvieweR/google-analytics.html new file mode 100644 index 0000000..b8f7801 --- /dev/null +++ b/MTSvieweR/google-analytics.html @@ -0,0 +1,9 @@ + + + \ No newline at end of file diff --git a/MTSvieweR/rsconnect/.DS_Store b/MTSvieweR/rsconnect/.DS_Store new file mode 100644 index 0000000..e11ffb0 Binary files /dev/null and b/MTSvieweR/rsconnect/.DS_Store differ diff --git a/MTSvieweR/ui.R b/MTSvieweR/ui.R index 27e5fb0..5c8590f 100644 --- a/MTSvieweR/ui.R +++ b/MTSvieweR/ui.R @@ -1,4 +1,5 @@ fluidPage( +tags$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
Andrew N. Bayne, Jing Dong, Saeid Amiri, Sali M.K. Farhan, Jean-Francois Trempe (2023)
PLOS ONE 18(4): e0284541.
DOI: https://doi.org/10.1371/journal.pone.0284541")) - ) - ) - + 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
Andrew N. Bayne, Jing Dong, Saeid Amiri, Sali M.K. Farhan, Jean-Francois Trempe (2023)
PLOS ONE 18(4): e0284541.
DOI: https://doi.org/10.1371/journal.pone.0284541")))) ) ) diff --git a/README.md b/README.md index ed66273..a96fb08 100644 --- a/README.md +++ b/README.md @@ -1,13 +1,20 @@ -# 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 @@ -15,11 +22,31 @@ Welcome to MTSviewer, a database for the study of mitochondrial proteins which i - 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