RADICAL Website

This is the repository for our RADICAL website. We use Jekyll to run our Github page. We welcome other people to contribute to our site not just lab members. Feel free to fork and create pull-requests!

This site is based on a clone of KordingLab.github.io

Run the website locally

To run locally, follow Jekyll's installation instructions, clone this repository and cd in its root directory.

Ubuntu

sudo gem install jekyll
sudo gem install rouge
sudo gem install jekyll-redirect-from
sudo gem install bundler
sudo gem install html-proofer
jekyll serve

macOS

First, install homebrew if not already installed, then do the following:

xcode-select --install
brew install ruby
echo 'export PATH="/usr/local/opt/ruby/bin:$PATH"' >> ~/.bash_profile
. ~/.bash_profile
gem install --user-install bundler jekyll rouge jekyll-redirect-from html-proofer jekyll-sitemap
echo 'export PATH="/Users/$USER/.local/share/gem/ruby/3.2.0/bin:$PATH"' >> ~/.bash_profile
. ~/.bash_profile

Note: this assumes that ruby 3.2.0 was installed. Change the last echo command if you have a different version.

Check that the installation was successful:

which ruby should return /usr/local/opt/ruby/bin/ruby if it returns /usr/bin/ruby you are using the one shipped with macos and jekyll will likely not work.
gem env should show /Users/$USER/.local/share/gem/ruby/3.2.0/bin:$PATH under SHELL PATH.

Issue:

jekyll serve

You should be able to see the website in your browser at http://127.0.0.1:4000. Any local change made to the website should be immediately reflected reloading the page.

Add a publication

All publications are located in the _publications folder. Each file contains a single publication and has a front matter and no body. The front matter contains both mandatory and optional variables:

Variable	Value	Category	Description
title	string	mandatory	Title of the publication
collection	`publications`	mandatory	Jekyll-related, has always the same value
permalink	`publications/file_name`	mandatory	Jekyll-related. `file_name` must be the same given to the file with this front matter
type	`pub`; `standard`	mandatory	`pub`, for a published paper, and `standard`, for standards, white papers and technical reports
date	year-month-day	mandatory	Date of publication
author	firt last,	mandatory	Comma-separated list of authors
venue	string	mandatory	Proceedings, journal or archive of the publication
paperurl	URL	mandatory	Official URL of the publication
arxiv	URL	mandatory	Arxiv URL of the publication
abstract	string	optional	Abstract of the publication. When added, a landing page for the publication is created with title, authors, abstract and links to the full paper

The name of the file in _publications must follow the format: Last name of the first author, year of the publication, and first word of the title. An example of a valid file name for a publication is: paraskevakos2018task.md.

Papers that have been uploaded to Arxiv are considered publications. It is the first author responsibility to update her/his paper with the most current information.

For reference, see the following paper front matter:

---
title: "Task-parallel Analysis of Molecular Dynamics Trajectories"
collection: publications
permalink: /publications/paraskevakos2018task
date: 2018-08-15
type: pub
author: "Ioannis Paraskevakos, Andre Luckow, Mahzad Khoshlessan, George Chantzialexiou, Thomas E. Cheatham, Oliver Beckstein, Geoffrey C. Fox and Shantenu Jha"
venue: "47th International Conference on Parallel Processing (ICPP 2018)"
paperurl: https://dl.acm.org/citation.cfm?id=3225128
arxiv: https://arxiv.org/abs/1801.07630
abstract: "Abstract."
---

This paper's filename is: paraskevakos2018task.md

When adding a publication to the webpage, create a branch named publication/<pub-filename> and create a pull request towards master of this repo. As soon as the request is merged, GitHub will render the page on the official website.

Add a project

All project pages are located in the _projects folder. Each file contains a single project and has a front matter and a body in the markdown and HTML format. The front matter contains both mandatory and optional variables:

Variable	Value	Category	Description
title	string	mandatory	Title of the project
collection	`projects`	mandatory	Jekyll-related, has always the same value
permalink	`projects/file_name`	mandatory	Jekyll-related. `file_name` must be the same given to the file with this front matter
abstract.	string	mandatory	A single sentence that describes the project. See current website for examples
status	`active`; `inactive`	mandatory	Ongoing projects are `active`, terminated projects are `inactive`
grant	{`funder`: string, `number`: string, `url`: URL}	optional	A collection with three keys. The whole collection and each of its keys are optional
repository	URL.	optional	URL of the code repository of the project (e.g., github, bitbucket)
logo	`file_name`	optional	Optional but almost mandatory :) 150x150px, possibly 144dpi
figure	{`name`: `file_name`, `width`: int}	optional	Optional but almost mandatory :) max 1000x1000px, possibly 144dpi in compressed jpg. `width` is used in the project landing page. Try to select a number that makes the image to take up to 1/3 of the width of the landing page.
website	URL	optional	The official website of the project

The body of the file contains a one-paragraph description of the project.

The name of the file in _projects has no mandatory formatting; just keep it short and descriptive of the project. An example of a descriptive and short project name is: power-of-many.md.

For reference, see the following project front matter:

---
title: "Extensible Tools for Advanced Sampling and analYsis (ExTASY)"
collection: projects
permalink: /projects/extasy
abstract: "Executing iterative, coupled molecular simulation and analysis kernels on high performance computing systems." 
logo: extasy_logo.jpg
status: active
figure:
  name: extasy.jpg
  width: 300
repository: https://bitbucket.org/extasy-project/extasy-workflows
grant:
  funder: NSF
  number: 1265929
  url: https://nsf.gov/awardsearch/showAward?AWD_ID=1265929
---

The Extensible Toolkit for Advanced Sampling and AnalYsis (ExTASY) is a lightweight software...

When adding a project to the website, create a branch named publication/<proj-filename> and add the logo and page images in images/projects. You must upload three images with the following naming convention: proj_name_original.jpg; proj_name_logo.jpg; proj_name.jpg. Create a pull request towards master of this repo. As soon as the request is merged, GitHub will render the page on the official website.

Add yourself

All RADICAL member pages are located in the _people folder. Each file contains a single personal page and has a front matter and a body in the markdown and HTML format. The front matter contains both mandatory and optional variables:

Variable	Value	Category	Description
name	string	mandatory	Title of the project
collection	`projects`	mandatory	Jekyll-related, has always the same value
permalink	`projects/file_name`	mandatory	Jekyll-related. `file_name` must be the same given to the file with this front matter
position	`undergrad`; `ms`; `phd`; `researcher`; `pi`	mandatory	Your position in the lab
title	string	mandatory	Your title in the lab
joined	year	mandatory	The year you joined the lab
avatar	`file_name`.jpg	optional	Optional but almost mandatory :) square, possibly 144dpi, <1MB
contacts	{`email`: string, `office`: string, `scholar`: URL, `github`: URL, `linkedin`: URL}	optional	A collection of contact-related information. The whole collection and each of its keys are optional
publications	{`id`: string, `cofirst`: true}	optional	The collection of your RADICAL publications. `id` must be the same as the name of the corresponding publication file in `_publications`; `cofirst` used only when you are a co-first author of the paper
projects	{`id`: string, `role`: string}	optional	The collection of RADICAL projects in which your are involved. `id` must be the same as the name of the corresponding project file in `_projects`; `role` indicates your official role in the project
students	[string]	optional	List of students name. Available if you are member of the Graduate School and advisor of one or more RADICAL students.

The body of the page can contain your brief bio or whatever else relates to your research and activity in the lab.

The name of the file in _people must follow the format: firstname_lastname. An example of a valid file name is: ioannis_paraskevakos.md.