Staying Current with the Journals

Capture Current Literature of a Scientific domain with RSS

Colton Baumler

ccbaumler@ucdavis.edu

University of California, Davis

Bryshal Moore

brymoore@ucdavis.edu

University of California, Davis

Wednesday, the 29^th of January, 2025

Customized Agg. of Current Scientific Literature

Log in talk about: - folder and journal feeds - navigate with hotkeys - use v to load a new tab

What does a completed setup look like?

Overview

Add google scholar alerts, pubmed alerts, arxiv alerts with killthenewsletter https://scholar.google.com/scholar_alerts?view_op=list_alerts&hl=en

Backward design for teaching - “What do you want the audience to take away?”

• Basics of RSS
  • Understand the basics of what RSS is
  • How to find RSS feeds and add to a reader
  • Functionality of a RSS reader I like
  • Techniques I like with RSS readers

• Background

• Install and Set Up

• Suggested Usage

• Techniques for Success

Background

• The fundamentals of RSS
  • What is RSS?
  • Why use RSS?
  • Which RSS to use?

WoS query: (“RDF Site Summary”) OR (“Really Simple Syndication”) OR (“RSS FEEDS”) OR (“Rich Site Summary”) Keywords: https://en.wikipedia.org/wiki/RSS

RSS is a web-based aggregation tool

Background

• What does RSS stand for?

  • Conflicting accounts!
    • Really Simple Syndication
    • Rich Site Summary
    • RDF Site Summary
  • RSS \(\equiv\) a website feed aggregator

• What is RSS though?

  • Set of technical standards
    • A standard, computer-readable format
  • Written in extensible mark-up language (XML)
  • For storing and sending data through the internet

A self-updating scientific journal website aggregation system

What is RSS good for?

Quick Write

In one or two sentences,

how can RSS be applied to your scientific or scholarly work?

01:00

Academia is impacted by politics

Background

It is not always as heavily publisized as the NIH freeze

Big Think Article

An RSS aggregator will centralize all feeds across devices

Background

The day an important article is published you will be able to find it!

• Single concentrated reference point
  • Track many different websites
  • Regular updates (~1-6hrs)
  • Convenient
    • Desktop
    • Mobile
    • Browser

Too many software options!!!

Background

The goal is not to become a poweruser!!!

This serves a focused purpose and it does that well.

There are dozens of notable RSS readers.

Most have a pay-tiered system.

• I suggest Inoreader… currently

  • Most useful options at unpaid subscription level are:
    • Compatible with IOS, Andriod, and the Web
    • Organizing with folders and tags
    • Highlighting keywords
    • Ability to search

Install and Set Up

• Install Inoreader
• Find academic journal feeds
• Organize feeds

Create an account

Install and Set Up

1. Go to Inoreader

Create an account

Install and Set Up

1. Go to Inoreader
2. Select Create account

Create an account

Install and Set Up

1. Go to Inoreader
2. Select Create account
3. Fill in email and password
4. Select Create account

Optionally, download the mobile app

Install and Set Up

for local image as badges

• Benefits
  • Portability
  • Interoperability
  • Make doom scrolling productive

Click your system below:

Optionally, install a browser extension

Install and Set Up

05:00

• Benefits
  • Portability
  • Interoperability
  • Make doom scrolling productive

Click your system below:

Quick guide to curate feeds in Inoreader

Install and Set Up

1. Select Add new

Quick guide to curate feeds in Inoreader

Install and Set Up

1. Select Add new
2. Search a topic, website, or journal

Quick guide to curate feeds in Inoreader

Install and Set Up

1. Select Add new
2. Search a topic, website, or journal
3. Select Follow from the feed suggestions

Gather feeds to fit your research interests

Install and Set Up

go to science.com and scroll to the bottom

click the rss symbol

copy url of rss xml site and paste into inoreader

wsj:thejournal (rss symbol)

Use nature (rss feed), science (rss symbol), and biorxiv (specific set up) as examples

document.getElementById("userInput").addEventListener("input", function() {
  let userInput = this.value;
  let words = userInput.split("-");
  
  let output = "";
  words.forEach(word => {
    output += `<li>${word}</li>`;
  });
  
  document.getElementById("outputText").innerHTML = `<ul>${output}</ul>`;
});

08:00

• Journal options

  • Wiki of Journals
  • Scopus Journals
  • The NIH Library of Journals
  • ChatGPT: “what are the best journals for [bioinformatics] research?”
  • Find RSS Links on a Website Supp.

Organize feeds by creating folders

Install and Set Up

Create new folder

1. Select 📁 icon

Organize feeds by creating folders

Install and Set Up

Create new folder

1. Select 📁 icon
2. Write Folder name

Organize feeds by creating folders

Install and Set Up

Create new folder

1. Select 📁 icon
2. Write Folder name
3. Begin searching for feeds

Organize feeds by creating folders

Install and Set Up

Create new folder

1. Select 📁 icon
2. Write Folder name
3. Begin searching for feeds
4. Select feeds to add

Organize feeds by adding to existing folders

Install and Set Up

Add to existing

1. Select ⚙️ icon

Organize feeds by adding to existing folders

Install and Set Up

Add to existing

1. Select ⚙️ icon
2. Select folders dropdown

Organize feeds by adding to existing folders

Install and Set Up

Add to existing

1. Select ⚙️
2. Select folders dropdown
3. Select Without folder

Organize feeds by adding to existing folders

Install and Set Up

Add to existing

1. Select ⚙️
2. Select folders dropdown
3. Select Without folder
4. Select feeds

Organize feeds by adding to existing folders

Install and Set Up

Add to existing

1. Select ⚙️
2. Select folders dropdown
3. Select Without folder
4. Select feeds
5. Select option from dropdown

Make your folders for your feeds

Install and Set Up

05:00

• Consider grouping journals categories:

  • Broad
    • interdisciplinary, high-impact factor
  • Topics
    • Molecular Biology, Genetics, Bioinformatics
  • Time span they publish or you want to check
    • Continuous, Weekly, Monthly, Quarterly, Annually
    • “Nature is a weekly international journal”
  • Access
    • Open access, Publisher, Preprints

document.getElementById("userInput2").addEventListener("input", function() {
  let userInput2 = this.value;
  let words = userInput2.split("-");
  
  let output = "";
  words.forEach(word => {
    output += `<li>${word}</li>`;
  });
  
  document.getElementById("outputText2").innerHTML = `<ul>${output}</ul>`;
});

Suggested Usage

• The functionality of Inoreader
  • Highlighting keywords
  • Tagging system
  • Rapid navigation
  • Search the feeds

Highlighting keywords for efficient literature discovery

Suggested Usage

05:00

Assign color to keywords

• Trouble? Try asking ChatGPT for a list:
  • What are keywords for [microbial metagenomic metabolomic metabolite cancer] research?
  • Please expand this list further. (Generic or with direction…)

Tags articles to organize and recall

Suggested Usage

• Like the Read later category

Library

• Tag with keywords like:
  • Topics: ProjectName, QE, Grant
  • Content: Video, peer, opinion, review
  • Resources: Github, scripts, references
  • Priority: High, medium, low

Navigating literature blazingly fast with keybindings

Suggested Usage

h or ? for keybindings

Navigating literature blazingly fast with keybindings

Suggested Usage

05:00

Below are some suggestions to speed-up your usage:

• n, p or with shift: navigate the articles or side-bar
• j, k : navigate the Article view or space: to scroll through the abstract
• m, f: mark the articles as read or read later
• 1, 3: change views from list to cards
• use v to load a new tab or w to load the content

document.getElementById("userInput3").addEventListener("input", function() {
  let userInput3 = this.value;
  let words = userInput3.split(" ");
  
  let output = "";
  words.forEach(word => {
    output += `<li>${word}</li>`;
  });
  
  document.getElementById("outputText3").innerHTML = `<ul>${output}</ul>`;
});

Search the feeds for rapid re/discovery

Suggested Usage

Located at:

• Upper right 🢖 🔍
• Left-hand 🢖 🔍
• Add feed 🢖 Monitor feed

Straight-forward operation:

• Search articles in feeds, folder, or tags

• Use boolean operators
  • AND
  • OR
  • NOT
  • ""
  • ()

Boolean operators are terms used to combine or exclude keywords in search queries to narrow down or broaden search results in a search engine. They are words like “AND,” “OR,” and “NOT” that help refine the search by specifying relationships between keywords.

AND: Narrows down the search by requiring both terms to be present in the results. For example, searching for "cats AND dogs" will return results that mention both cats and dogs.

OR: Broadens the search, returning results that include either one or both of the specified terms. Searching for "cats OR dogs" will retrieve results mentioning either cats or dogs or both.

NOT: Excludes specific terms from the search results. For instance, searching for "cats NOT dogs" will display results related to cats but exclude any that mention dogs.

These operators are useful for making searches more precise and tailored to your needs by including, excluding, or combining keywords in various ways.

Techniques for Success

• Quickly sort articles from feeds
• Time management and blocking

The 80:20 method is ideal to filter papers

Techniques for Success

• 80:20?
  • Remove 20% each step
• Remember IMRaD?
  • RSS reader focus on Title and Abstract! f
  • Import f into reference manager
  • “I’D MembeR” better

https://github.com/quarto-dev/quarto-cli/issues/2165

https://stackoverflow.com/questions/63082398/change-font-of-text-on-links-in-graph-mermaid

Mindfully approach time management for best results!

Techniques for Success

• Consider time blocking
  • When do you work best?
  • 3-2-1 method

Summary

You have learned:

• RSS and Readers
  • The fundamentals of RSS
  • The application to use
• Inoreader
  • Install Inoreader
  • Find academic journal feeds
  • Organize feeds
  • The functionality of Inoreader
• Skills to rapidly consume literature
  • Quickly sort articles from feeds
  • Time management and blocking

Acknowledgments

“The next best thing to being wise oneself is to live in a circle of those who are.” 👤 C.S. Lewis

• C. Titus Brown
• Pamela Reynolds
• Bryshal Moore
• Luiz Irber
• The DataLab
• Professors For The Future
• NSF GRFP
• IMSD

Supplementary

Finding the RSS link to a website

Click Here to Go Back to Gathering Feeds

• RSS Validator
• Navigate to the website:
  • Right click page
  • Select Page Source
  • Press ctrl+f or cmd+f
  • Type rss
• No RSS found?