Rogue Scholar Digest April 24, 2024


This is a summary of the Rogue Scholar blog posts published April 10 - April 23, 2024.


Martin Fenner

Front Matter


April 14, 2024

import requests
import locale
import re
from typing import Optional
import datetime
from IPython.display import Markdown

locale.setlocale(locale.LC_ALL, "en_US")
baseUrl = ""
published_since = "2024-04-10"
published_until = "2024-04-23"
feature_image = 2
include_fields = "title,authors,published_at,summary,blog_name,blog_slug,doi,url,image"
url = (
    + f"posts?&published_since={published_since}&published_until={published_until}&language=en&sort=published_at&order=asc&per_page=50&include_fields={include_fields}"
response = requests.get(url)
result = response.json()

def get_post(post):
    return post["document"]

def format_post(post):
    doi = post.get("doi", None)
    url = f"[{doi}]({doi})\n<br />" if doi else ""
    title = f"[{post['title']}]({doi})" if doi else f"[{post['title']}]({post['url']})"
    published_at = datetime.datetime.utcfromtimestamp(post["published_at"]).strftime(
        "%B %-d, %Y"
    blog = f"[{post['blog_name']}]({post['blog_slug']})"
    author = ", ".join([f"{x['name']}" for x in post.get("authors", None) or []])
    summary = post["summary"]
    return f"### {title}\n{url}Published {published_at} in {blog}<br />{author}<br />{summary}\n"

posts = [get_post(x) for i, x in enumerate(result["hits"])]
posts_as_string = "\n\n".join([format_post(x) for x in posts])

def doi_from_url(url: str) -> Optional[str]:
    """Return a DOI from a URL"""
    match =
    if match is None:
        return None

images = [x["image"] for x in posts if x.get("image", None) is not None]
image = images[feature_image]
markdown = f"![]({image})\n\n"
markdown += posts_as_string

Rogue Scholar references learn new tricks
Published April 10, 2024 in Front Matter
Martin Fenner
This week the references included in currently 1,123 Rogue Scholar blog posts have become much more powerful, as they now include the full set of scholarly metadata. These metadata are displayed in the Rogue Scholar web pages and can be fetched via an open API. One of my favorite personal blog posts – about the 10th anniversary of PLOS ONE, reference lists, and the X-Files TV series written in 2016 – nicely demonstrates this new functionality.

R-Universe Documentation Gets a Boost from Google Season of Docs
Published April 12, 2024 in rOpenSci - open tools for open science
Noam Ross
We are excited to announce that R-Universe has been awarded a Google Season of Docs grant. R-Universe is rOpenSci’s platform for testing, building, distributing, and discovering R packages, led by Jeroen Ooms.

Research Collaboration Network
Published April 12, 2024 in Stories by Research Graph on Medium
Amir Aryani
Author Amir Aryani: (ORCID: 0000-0002-4259-9774) Definition A research collaboration network is a group of researchers, and practitioners, or both, working together on joint research activities. These networks often span across disciplines, geographic boundaries, and sectors, enabling participants to share resources, expertise, and data to address common research goals more effectively than they could individually.

The Eclipse Experience
Published April 13, 2024 in Triton Station
Stacy McGaugh
We will return to our usual programming shortly. But first, a few words on the eclipse experience last Monday. It. Was. Awesome . That’s a few words, so Mission Accomplished. That’s really all I had planned to say. However, I find I am still giddy from this momentous event, so will share my experience of the day, such as words can humbly convey.

Beautiful movement—the music and beauty of Lissajous(Liss–uh–joo) curves
Published April 15, 2024 in JP’s blog
JP Monteagudo
Lissajous Curves Lissajous curves are created by plotting two oscillations on perpendicular axes and ​​​. These oscillations, represented by sinusoidal functions, intersect to create different patterns. When the ratio of these frequencies is equal to — the oscillations are equally phased— the curve is a straight line.

In Defence of Disease
Published April 15, 2024 in Irish Plants
Jake Dalzell
Disease is something few people love. There are exceptions though, particularly among those who appreciate the diversity and ecological role of plant disease. The early conservationist, Aldo Leopold, described the role of tree diseases in creating food and shelter for the animals on his farm in Wisconsin: I met Chris Preston, a Cambridgeshire botanist, when I was in the first year of my degree.

Sorte e Apostas
Published April 16, 2024 in Risk Taker!
Henrique Costa
Aqui voce pode encontrar a apresentação: Link da Apresentação Aqui você se cadastra para participar do sorteio dos livros: Link para o Formulário You can also reproduce this by choosing the city you want. Check out the complete code on my Github. Hey! 👋, did you find my work useful?

OpenCitations supports the Barcelona Declaration on Open Research Information for a fundamental transformation in the research information landscape
Published April 16, 2024 in OpenCitations blog
Chiara Di Giambattista
Research Information can be defined as an information (sometimes referred to as metadata) relating to the conduct and communication of research.

Fostering Equity and Leadership: the rOpenSci Champions Program Selection Process
Published April 18, 2024 in rOpenSci - open tools for open science
Francisco Cardozo, Yanina Bellini Saibene, Camille Santistevan, Lou Woodley
The goal of the rOpenSci Champions Program is to enable more members of historically excluded groups to participate in, benefit from, and become leaders in the R, research software engineering, and open source and open science communities. This program includes 1-on-1 mentoring for the Champions as they complete a project and perform outreach activities in their local communities.

JOSSCast #8: Deep Learning for 3D Protein Structure Predictions – Giulia Crocioni on DeepRank2
Published April 18, 2024 in Journal of Open Source Software Blog |
Arfon M. Smith
Subscribe Now: Apple, Spotify, YouTube, RSS Giulia Crocioni joins Arfon and Abby to discuss DeepRank2, a deep learning framework for 3D protein structure predictions. Giulia is a Research Software Engineer at the Netherlands eScience Center where she uses different machine learning techniques to develop and contribute to methodologies and applications to answer life sciences research questions.

Animating the Datasaurus dataset as part of the 30 Day Chart Challenge
Published April 19, 2024 in JP’s blog
JP Monteagudo
Visualization & Pearson’s correlation coefficient The 30DayChartChallenge is a data visualization community that hosts daily challenges for April. Today’s challenge involves dinosaurs. I used the Datasaurus package to create an animated visualization to demonstrate the importance of graphing data, and the effects of outliers on statistical properties.

Notes on transforming BHL images
Published April 19, 2024 in iPhylo
Roderic Page
I’ve been down this road before, e.g. BHL, DjVu, and reading the f*cking manual and Demo of full-text indexing of BHL using CouchDB hosted by Cloudant, but I’m revisiting converting BHL page scans to black and white images, partly to clean them up, to make them closer to what a modern reader might expect, and partly to reduce the size of the image. The latter means faster loading times and smaller PDFs for articles.

Forcing a Deterministic View on Probabilistic Phenomena: Implications for the Replication Crisis
Published April 20, 2024 in Critical Metascience
Mark Rubin
By Carol Ting

rOpenSci News Digest, April 2024
Published April 22, 2024 in rOpenSci - open tools for open science
The rOpenSci Team
Dear rOpenSci friends, it’s time for our monthly news roundup! You can read this post on our blog.Now let’s dive into the activity at and around rOpenSci!rOpenSci HQ Coworking Read all about coworking! Join us for social coworking & office hours monthly on first Tuesdays!Hosted by Steffi LaZerte and various community hosts.Everyone welcome.No RSVP needed.Consult our Events page to find your local time and how to join.

Not only Open, but also Diverse and Inclusive: Towards Decentralised and Federated Research Information Sources
Published April 22, 2024 in Leiden Madtrics
Dominique Babini, Arianna Becerril Garcia, Rodrigo Costas, Lautaro Matas, Ismael Rafols, Laura Rovelli
The Barcelona Declaration: a call for openness… but also for diversity and inclusion The launch of the Barcelona Declaration last week aims to mobilise the global research community towards making research information open and accessible.

Dynamic Knowledge Graphs: A Next Step For Data Representation?
Published April 22, 2024 in Stories by Research Graph on Medium

Integrating temporal data into static knowledge graphs Author Amanda Kau (ORCID: 0009–0004–4949–9284 ) Introduction Knowledge graphs (KGs) have proven to be an effective method of data representation that is increasingly popular.

A Deep Dive Into Knowledge Graph Enhanced Pre-trained Language Models
Published April 22, 2024 in Stories by Research Graph on Medium

Techniques to integrate Knowledge Graphs into Language Models Author Amanda Kau (ORCID: 0009–0004–4949–9284 ) Introduction Both knowledge graphs (KGs) and pre-trained language models (PLMs) have gained popularity due to their ability to comprehend world knowledge and their broad applicability.

Find OpenCitations on Infra Finder, a new tool to discover and support Open Infrastructures
Published April 22, 2024 in OpenCitations blog
Chiara Di Giambattista
If you are a leader of a Library or a Research Institution and would like to learn more about the existing open infrastructures that could help your institution to evolve in the research environment, but you don’t know where to look for, you can now use Infra Finder, a brand-new tool aimed at foster discovery, adoption, and investment for open infrastructure services.

Introduction to APOC: Enhancing Neo4j Capabilities
Published April 23, 2024 in Stories by Research Graph on Medium

Neo4j APOC Library Use Case Author Wenyi Pi ( ORCID: 0009–0002–2884–277) Introduction In the realm of Neo4j, the APOC (Awesome Procedures on Cypher) library stands as a powerful tool.

When RAG and LLM Conflict: Who Will AI Listen to?
Published April 23, 2024 in Stories by Research Graph on Medium

Understanding the Balance between Internal Knowledge and External Sources Author Qingqin Fang ( ORCID: 0009–0003–5348–4264) Introduction Previous research often emphasized the limitations of LLM’s information acquisition pathways, focusing on enhancing its capabilities in this regard.

Harnessing Temporal Dynamics: Advanced Reasoning using Temporal Knowledge Graphs
Published April 23, 2024 in Stories by Research Graph on Medium

Exploring the Potential of Temporal Feature-Logic Embedding (TFLEX) in Complex Query Resolution Author · Vaibhav Khobragade ( ORCID: 0009–0009–8807–5982) Introduction Artificial intelligence (AI) and knowledge representation in the field of temporal knowledge graphs are rapidly gaining interest.

Working with Graphs: Pre-training and Application
Published April 23, 2024 in Stories by Research Graph on Medium

Latest findings in pre-training graphs and using them for link recommendation Author · Xuzeng He ( ORCID: 0009–0005–7317–7426) Introduction A graph, in short, is a description of items linked by relations, where the items of a graph are called nodes (or vertices) and their relations are called edges (or links). Examples of graphs can include social networks (e.g. Instagram)

Rogue Scholar is learning a new language
Published April 23, 2024 in Front Matter
Martin Fenner
The Rogue Scholar science blog archive is built with Open Source software, starting with Javascript in June 2023 and adding an API written in Python in October 2023. This week I am releasing the first version of commonmeta written in Go to simplify the Rogue Scholar backend.

Prehistoric: when do authors preprint their papers?
Published April 23, 2024 in quantixed
Stephen Royle
Previously, I took advantage of a dataset that linked preprints to their published counterparts to look at the fraction of papers in a journal that are preprinted. This linkage can be used to answer other interesting questions. Such as: when do authors preprint their papers relative to submission? And does this differ by journal? There’s a bit of preamble. If you just want to know the answer, click here.

Open Publishing Fest Lifetime Achievement Award: Interview with Lars Bjørnshauge
Published April 23, 2024 in Upstream
Joanna Ball
Lars Bjørnshauge is the visionary founder of the Directory of Open Access Journals (DOAJ). His transformation of a simple idea into a globally trusted directory revolutionized the accessibility and credibility of open access publishing. Under his leadership, DOAJ became a critical resource, supporting the dissemination of scholarly work worldwide and setting high standards for transparency in publishing.

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