Education, Programming, and Standards

posted by Roy Schestowitz on Sep 25, 2024

• Open Access/Content

  • Rlang ☛ Exploding, Impacting: looking at bioRxiv preprint view dynamics with R

    We posted a preprint recently and it clocked up over 1,000 views in the first day or so. This made me wonder: is that a lot of views or not? How does it compare to other preprints in our category? I wrote some code to find out. It turns out our paper was the third most viewed cell biology preprint in September. My co-authors and I were very grateful for the interest!

    Anyway, this post is about the code and how to get the necessary data to look at preprint view metrics. I’ll use it to look at the more interesting question of preprint view dynamics in our category “Cell Biology” this year. Read on for the R stuff, or skip to the findings.

    tl;dr a cell biology preprint gets 50% of its lifetime views in the first 4-5 days.

• Education

  • Raspberry Pi ☛ OUT NOW: The Official Raspberry Pi Handbook 2025 has landed

    Our annual bumper book is lovingly made by us folks from The MagPi, the official Raspberry Pi magazine, and we’ve got another fantastic edition for you to read.

  • APNIC ☛ Event Wrap: ITCN Expo 2024

    APNIC participated in the ITCN Expo 2024, held from 27 to 29 August in Karachi, Pakistan.

    The three-day expo welcomed delegates from all over Pakistan and the region to network and share knowledge on topics including cloud, data centres, Artificial Intelligence (AI), and much more.

  • Undeadly ☛ EuroBSDCon 2024 presentations

    Video of the individual presentations can be expected somewhat later. In the meantime, OpenBSD-related presentations [including those from non-developers] can be found in the recordings of the "Foyer B" streams.

• Programming/Development

  • Scott Dubinsky ☛ Installing Sway From Source

    I wanted to use the new explicit sync code in sway master, and got bored waiting for a release. So I decided to compile and install sway myself. Here’s all the problems I had that aren’t listed in the readme, and how I got past them.

  • Rlang ☛ How to Remove Outliers from Multiple Columns in R: A Comprehensive Guide

    Outliers can significantly skew your data analysis results, leading to inaccurate conclusions. For R programmers, effectively identifying and removing outliers is crucial for maintaining data integrity. This guide will walk you through various methods to handle outliers in R, focusing on multiple columns, using a synthetic dataset for demonstration.

  • Jason Becker ☛ Thinking about software rewrites and domain models

    A huge part of software change management involves being clear how the application models the domain. How do we think about these concepts? How can we teach people the appropriate amount to lead them to “pits of success”. Preferably, how do we make using the application just “feel right” without having to do a ton of work expressing our intent and design?

  • Python

    • Modus Create LLC ☛ Python Packaging in the Real World: Biomedical projects vs. PyPI

      The Python programming language, and its huge ecosystem (there are more than 500,000 projects hosted on the main Python repository, PyPI), is used both for software engineering and scientific research. Both have similar requirements for reproducibility. But, as we will see, the practices are quite different.

      In fact, the Python ecosystem and community is notorious for the countless ways it uses to declare dependencies. As we were developping FawltyDeps1, a tool to ensure that declared dependencies match the actual imports in the code, we had to accommodate many of these ways. This got us thinking: Could FawltyDeps be used to gain insights into how packaging is done across Python ecosystems?

      In this blog post, we look at project structures and dependency declarations across Python projects, both from biomedical scientific papers (as an example of scientific usage of Python) as well as from more general and widely used Python packages. We’ll try to answer the following questions: [...]

    • Trickster Dev ☛ Lesser known parts of Python standard library – Trickster Dev

      In this article we will explore some lesser known, but interesting and useful corners of Python standard library.

  • Shell/Bash/Zsh/Ksh

    • Undeadly ☛ OpenBSD now enforcing no invalid NUL characters in shell scripts

      Our favorite operating system is now changing the default shell (ksh) to enforce not allowing invalid NUL characters in input that will be parsed as parts of the script.

• Standards/Consortia

  • Ruben Schade ☛ I now refer to RSS et.al. as web feeds

    I also think the Mozilla feed icon is the closest we’ve come to a universal symbol for these technologies, so I’m using it again.

  • Terence Eden ☛ http:, ftp:, and … dict:?

    It turns out that, lurking on the Internet are Dictionary Servers! They exist to allow you to query dictionaries over a network.

  • [Old] IETF ☛ A Dictionary Server Protocol

    The Dictionary Server Protocol (DICT) is a TCP transaction based query/response protocol that allows a client to access dictionary definitions from a set of natural language dictionary databases.