ASAP Discovery website source

This website is hosted by GitHub Pages at http://asapdiscovery.org . The website content is in the gh-pages branch of this repo.

Making changes

Changes should be contributed as pull requests.

You will primarily want to focus on changing the following Markdown files in content/:

• _index.md: main landing page content (some detail is in themes/kube/layouts/index.html)
• news/: Add new news posts here as separate Markdown files, using a header like

---
date: "2017-04-10T16:42:50+01:00"
draft: false
weight: 180
description: "Smoothly and reliably collapse elements for extra convenience"
title: "Collapse"
bref: "A demo to collapsable elements"
---

with the fields replaced with their equivalents.

• science/_index.md: overview of planned science, timelines, science updates, etc.
• data/publications/publications.yaml: publications and white papers
  • content/publications/img/: thumbnail images for publications and white papers
• consortium/_index.md: information about the Consortium
• faq/_index.md: frequently asked questions

See the Kube for Hugo GitHub repo for more examples of Markdown content.

Adding Science Updates

1. Create a new file in content/science/updates/ using the format YYYY-MM-DD-lastname.md (e.g. 2018-10-11-chodera.md)
2. Populate the file in Markdown with the following header style:

---
date: "2018-10-11T00:00:00+00:00"
title: "Introducing ASAP Discovery Science Updates"
tags: ["general"]
categories: ["science"]
draft: false
description: "ASAP Discovery Science Updates will help you keep track of research and engineering activities from the ASAP Discovery Initiative"
weight: 10
author: "John D. Chodera"
---

3. If you have images to post, create a subdirectory in content/science/updates/ using the format YYYY-MM-DD-lastname/ (e.g. 2018-10-11-chodera/) and put your images there. You can reference them with

![GAFF densities](gaff-densities.jpg "GAFF densities")

where the file gaff-densities.jpg is located in content/science/updates/YYYY-MM-DD-lastname/gaff-densities.jpg

Adding new members

1. Add an image to content/members/img/ (e.g. firstname-lastname.jpg).
2. Add a YAML file firstname-lastname.yaml to data/members/ in the following format:

name: John D. Chodera
role: Primary Investigator
lab: Chodera lab
title: Associate Member
institution: Sloan Kettering Institute
img: john-chodera.jpg
webpage: "http://choderalab.org"
description: Automated Bayesian force field fitting and prediction of systematic error
google_scholar: http://goo.gl/qO0JW
ORCID: 0000-0003-0542-119X
twitter: jchodera
github: jchodera

where role for active members can be Researcher, Advisor, Software Scientist, Primary Investigator, or alum.

Adding new publications

1. Add a thumbnail image to content/publications/img
2. Add an entry to the YAML file data/publications/publications.yaml in the following format:

- title: "Escaping atom types using direct chemical perception"
  authors: "David Mobley, Caitlin C. Bannan, Andrea Rizzi, Christopher I. Bayly, John D. Chodera, Victoria T Lim, Nathan M. Lim, Kyle A. Beauchamp, Michael R. Shirts, Michael K. Gilson, and Peter K. Eastman"
  summary: This paper introduces the SMIRNOFF format in the context of traditional force fields, explains the development and validation of our new small molecule force field smirnoff99Frosst, and highlights some directions the initiative is headed.
  img: smirnoff-v0.1.png
  date: 2018-10-11
  preprint:
    server: bioRxiv
    url: https://doi.org/10.1101/286542
    license: "CC BY 4.0"
    date: 2018-07-13
  published:
    doi: 10.1021/acs.jctc.8b00640
    journal: Journal of Chemical Theory and Computation
    date: 2018-10-11
    volume: 14
    pages: 6076
    year: 2018
    pmcid: PMC6245550
- title: "Toward learned chemical perception of force field typing rules"
  authors: "Camila Zanette, Caitlin C. Bannan, Christopher I. Bayly, Josh Fass, Michael K. Gilson, Michael R. Shirts, John Chodera, and David L. Mobley"
  summary: Here, we introduce a proof of principle for automatically sampling chemical perception compared to traditional atom typed force fields and our SMIRNOFF format.
  img: smarty.jpg
  date: 2018-12-04
  preprint:
    server: chemRxiv
    url: https://chemrxiv.org/articles/Toward_Learned_Chemical_Perception_of_Force_Field_Typing_Rules/6230627
    license: "CC BY 4.0"
    date: 2018-08-06
  published:
    doi: 10.1021/acs.jctc.8b00821
    journal: Journal of Chemical Theory and Computation
    date: 2018-12-04
    volume: 15
    pages: 402
    year: 2019
    nihmsid: 1012523
  github: openforcefield/smarty

• The preprint, published, and github fields are optional, though at least one should be specified.
• For preprints, server can either be bioRxiv or chemRxiv.
• For published papers, the pmcid (PubMed Central PMCID) should be specified. If the article doesn't yet have a PMCID, be sure to submit it to PubMed Central and report the nihmsid instead. Failure to do so will jeopardize our NIH grants.
• Each preprint block should list a url, while published blocks should report a doi (not a URL).

Preview the website locally

0. Download and install Hugo.
1. In the top-level directory, run hugo server -D
2. Copy the Web address from this line (in this example, it is localhost:1313):

Web Server is available at //localhost:1313/ (bind address 127.0.0.1)

3. Paste the Web address into your browser

Making changes

1. Create a new branch with git checkout -b <mybranch>, where <mybranch> is the name of your new branch.
2. Commit the changes (git commit .) and push the repository to your branch (git push origin <mybranch>)
3. Open a PR and request review

Deploying

Deploying is handled by a Github actions (see the .github/workflows/gh-pages.yml file). Commits/PRs into the main branch will trigger a new build. Once built, the action will push the content to the gh-pages branch, which the website is now served from.