This website is hosted by GitHub Pages at http://asapdiscovery.org . The website content is in the gh-pages
branch of this repo.
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 papersconsortium/_index.md
: information about the Consortiumfaq/_index.md
: frequently asked questionsSee the Kube for Hugo GitHub repo for more examples of Markdown content.
content/science/updates/
using the format YYYY-MM-DD-lastname.md
(e.g. 2018-10-11-chodera.md
)---
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"
---
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
content/members/img/
(e.g. firstname-lastname.jpg
).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
.
content/publications/img
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
preprint
, published
, and github
fields are optional, though at least one should be specified.server
can either be bioRxiv
or chemRxiv
.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.preprint
block should list a url
, while published
blocks should report a doi
(not a URL).hugo server -D
localhost:1313
):
Web Server is available at //localhost:1313/ (bind address 127.0.0.1)
git checkout -b <mybranch>
, where <mybranch>
is the name of your new branch.git commit .
) and push the repository to your branch (git push origin <mybranch>
)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.