Publications Management

TL;DR

1. Add new publication to the _data/pubs.json array
2. Optionally add details to the _data/pubs_info.json array using the same DOI
3. Run ./pubs_update.sh (while in pubs/) to generate the publications page

This directory contains the scripts to manage the publications section of the website. The publication data itself lives in _data/ (so it is also readable by Jekyll as site.data.pubs — the Projects page links its publications to these entries by DOI, avoiding any duplication).

Files

• pubs.py: Python script that generates the publications page markdown
• pubs_update.sh: Shell script to run the publication update process
• ../_data/pubs.json: JSON file containing publication data
• ../_data/pubs_info.json: JSON file containing additional publication information

How to Add a New Publication

Step 1: Add Publication to pubs.json

The pubs.json file contains an array of publication objects with the following required fields:

• Authors: List of authors separated by semicolons, in “LastName, FirstName” format
  • For co-first authors, add an asterisk (*) after their name
  • For co-senior authors, add a plus (+) after their name
• Title: Publication title
• Publication: Journal name
• Volume: Volume number
• Number: Issue number (can be empty)
• Pages: Page range
• Year: Publication year
• doi: DOI identifier (this is used as the unique key)

Example entry:

{
  "Authors": "Kiefl, Evan; Delmont, Tom O; Eren, A Murat;",
  "Title": "Using microbial genomics to track antibiotic resistance",
  "Publication": "Nature Microbiology",
  "Volume": "5",
  "Number": "8",
  "Pages": "1028-1030",
  "Year": "2020",
  "doi": "10.1038/s41564-020-0756-3"
}

Step 2: Add Optional Publication Info

If you want to add highlights or a featured image for your publication, add an entry to the array in pubs_info.json with the following fields:

• doi: The DOI that matches an entry in pubs.json
• highlights: Array of brief bullet points about the work
• featured_image: Path to an image to feature with the publication

Example entry:

{
  "doi": "10.1038/s41564-020-0756-3",
  "highlights": [
    "First study to use sequence variants for tracking ARGs",
    "Created a framework for tracking mobile genetic elements"
  ],
  "featured_image": "../images/pubs/antibiotic-resistance.png"
}

Step 3: Run the Update Script

After adding your publication, run the update script:

cd pubs
./pubs_update.sh

This will:

1. Run the pubs.py script to process the JSON files
2. Generate the publications markdown page

Creating and Updating Publications Page

The Python script generates /publications/index.md which is used to build the publications page.