Coley Research Group Website

This is the repo for the website of the Coley Research group at MIT. It is modified on top of a Jekyll template developed by the Allan Lab.

Contributor Guide

All Coley Group members are free to make changes and additions to the website (such as adding/removing themselves to/from the "People" page) through this repo, pending approval. The existing templating combined with the following guide should hopefully make this process as painless as possible. Stylistic or template change suggestions are also welcome but may require navigating some messy templates or CSS.

Before you do anything, make sure you have Git installed on your machine. Then, (1) fork this repo and (2) clone the forked repo to your local machine with the command:

$ git clone https://github.com/{your_username}/coley.mit.edu.git

Local deployment

If you are making non-trivial changes (i.e. beyond just adding yourself to the "People" page), it is highly encouraged to locally deploy the website on your machine to preview the website before making a pull request. First, install Jekyll if you have not done so, following the official guide corresponding to your OS.

In the folder corresponding to your cloned repo, simply run the following to serve the website at http://localhost:4000.

$ jekyll serve

Making changes and pull requests

First, working in your forked repo, create and checkout a new branch (give it a descriptive name) with the command

$ git checkout -b BRANCH_NAME

After you make your changes, commit and push your changes to the branch:

$ git add .
$ git commit -m "COMMIT MESSAGE"
$ git push --set-upstream origin BRANCH_NAME

Finally, perform a pull request so that your changes can be reviewed and merged into the main repo. This can be done easily through the Github UI on the browser from your fork repo page.

Adding you or someone else to the "People" page

Adding yourself to the People page is very simple!

1. Upload an image of yourself to images/teampic/ with the format {firstname}_{lastname}.[png|jpg|jpeg]. Please crop your image to a square.
2. Navigate to the _data/ folder and locate the .yml file that matches your position in the group (for instance, if you are a grad student, open grad_students.yml).
3. Add all relevant information in the .yml file.
   • Fill out name and email at minimum, with optional URLs provided in twitter, linkedin, and/or website fields.
   • Add a short biography for the description field.

That's it! Go ahead and make a pull request when you are satisfied.

Adding publications

Some instructions for adding publications and a template are at the top of the (_data/publications.yml) file for your convenience. The main format for a citation is as follows:

• Author list. Linked Title. Journal. Volume(Issue), Pages. (Year) DOI/preprint: DOI/preprint_ID.

The minimum required fields are: title, authors, journal, year, url, themes.

• For journal papers, be sure to at least include doi
• For preprints, be sure to at least include preprint, preprint_url
• For conference papers, be sure to at least include preprint_url

If the preprint_url field is filled out, then the preprint button will appear under the citation.

Further, research themes should be added for each paper and they will appear as tags below the citation. The available themes and their associated colors are found in (_data/research_themes.yml). Currently these themes are:

• molecular representation
• design and optimization
• predictive chemistry
• automation
• metabolomics
• data

Note: There are slight nuances with respect to the doi and preprint fields since the former supercedes the latter.

• For preprints
  • Do NOT include the doi field
  • DO include the preprint and related fields.
• For conference papers
  • Do NOT include doi OR preprint fields.
  • DO include url, preprint_url, preprint_site, preprint_year.

Other changes

The following have been set up to be similarly easy to add new content to. Hopefully it should be simple to extrapolate the editing of .yml files to the following, but ask Kevin or Kento if you need help.

• News (_data/news.yml)
• Group photos (_data/photos.yml, images go in images/grouppic/)
• Open source software (_data/software.yml, logos go in images/logopic)
• Research relevant to Connor's directions on the "Research" page (_data/research.yml)
• WIP: The carousel highlighting recent work still needs to be refactored to be easily editable with .yml files. For now, they are manually declared in _includes/carousel.html with pictures in image/carouselpic)