Johnbosco

I often find my students' code is littered with dependencies that are loaded and then not used. This is a bad coding practice, but it's also very boring to check.

I updated {psychdsish} to include a function that does this for you.

I'm so glad you provided the code used to produce the Figures. Most repositories don't include code for reproducing the Figures. Thanks 🤝👏

Slide designs that present themselves: The assertion–evidence template Your slides are not your talk.

A simple design framework that will massively improve your slides and your public speaking
clauswilke.substack.com/p/slides-tha...

Anyone have difficulty accessing the Cold Spring Harbor Laboratory site? I haven't been able to access it in a long time! Perhaps I should try using a VPN?

genome.cshlp.org/cgi/doi/10.1...

@cshlnews.bsky.social

GPT-5: It Just Does Stuff Putting the AI in Charge

open.substack.com/pub/oneusefu...

@laurendsnyder.bsky.social thought you might find this interesting.

Just curious, are you able to reproduce this now? I couldn't reproduce it.
Just read this somewhere:
[remember when AI couldn’t count the number of Rs in “strawberry”? that was eight months ago).]

Verified résumés? Or give Bioinformatics tasks on the application call that require at least 6 hours to complete.

New #bioinformatics Scientist opening at @officialatcc.bsky.social ! Love #genomics? Want to help build a digital biology future? We're sequencing our entire collection 😱 Our focus? Authenticated Reference Data. Digital Standards. Reproducibility. Join us! careers-atcc.icims.com/jobs/4000/sc...

www.nature.com/articles/s44...

2. Ten Simple Rules for Reproducible Computational Research
journals.plos.org/ploscompbio...

I love the idea of "micropublications" www.micropublication.org (preparing one now)

What can scientists or the public do when a publication says "data or code available upon reasonable request" - but the author doesn’t respond or refuses to share?

#reproducibility #openscience #opensource #dataaccess #researchintegrity #AcademicSky #EduSky

While authors were extremely or very helpful for 41% of experiments, they were minimally helpful for 9% of experiments, and not at all helpful (or did not respond to us) for 32% of experiments.

#Reproducibility
#CancerResearch

Reproducibility in Cancer Biology: Challenges for assessing replicability in preclinical cancer biology A project to repeat experiments from high-impact papers in cancer biology encountered a series of challenges, many of which were caused by a lack of detail in the original papers.

Moreover, despite contacting the authors of the original papers, we were unable to obtain these data for 68% of the experiments.

elifesciences.org/articles/67995

Reproducibility in Cancer Biology: Challenges for assessing replicability in preclinical cancer biology A project to repeat experiments from high-impact papers in cancer biology encountered a series of challenges, many of which were caused by a lack of detail in the original papers.

Reproducibility Project: Cancer Biology to investigate the replicability of preclinical research in cancer biology.

Conclusion: it is hard to assess whether reported findings are credible.

elifesciences.org/articles/67995

CODECHECK in Practice: How TU Delft and 4TU.ResearchData Are Making Reproducibility Happen How can we make reproducibility a routine part of the publishing process? That question is at the heart of a new pilot bringing together the TU Delft Digital Competence Centre (DCC) and the 4TU.Res…

❓How can we make reproducibility a routine part of the publishing process❓

CODECHECK is a community-led initiative that helps verify the computational reproducibility of #scientific research. Read more on its application on our website:

community.data.4tu.nl/2025/07/09/c...

Why does reproducibility matter and how to achieve it? This session explores the importance of reproducibility in research and how 4TU.ResearchData supports researchers in making their work more transparent and trustworthy. We’ll reflect on how 4TU.Res…

Are #engineering and #design research processes reproducible? Join the lunch session "Why does reproducibility matter and how to achieve it?" at @tue.nl on 17 June! See how 4TU.ResearchData piloted the facilitation of reproducibility checks within the #CODECHECK initiative ⬇️

shorturl.at/qyXkc

x.com/kyleichan/st...

Kyle Chan on X: "China’s scientific progress is real. Citation counts can be gamed. There is some fraud. And Chinese researchers have been incentivized with cash to target top journals. But the Nature Index, which looks at contributors to 145 top international journals, is solid. 1/ 🧵 https://t.co/8jZed6dpQU" / X China’s scientific progress is real. Citation counts can be gamed. There is some fraud. And Chinese researchers have been incentivized with cash to target top journals. But the Nature Index, which looks at contributors to 145 top international journals, is solid. 1/ 🧵 https://t.co/8jZed6dpQU

x.com/kyleichan/st...

Yes, you would think that the norm now sh'd be to run the code to reproduce the figures in the manuscript during review. But alas, the computing environment in which the data was analyzed such as the package versions used are rarely provided hence reproducibility is a nightmare or just impossible!

America’s brain drain

No words

In your experience, having in mind that Air Transport remains the safest means of transport, has there been increase in the frequency of aviation disasters in the last five years or there is increased reporting/coverage?

The Round 1 grants from the R Consortium Infrastructure Steering Committee have been announced. This is one of my favorite things about this working for this org. #rstats
r-consortium.org/posts/r-cons...

A good number of academics Left Twitter/X for good yet on Bluesky or Mastodon there is little to no traction. Twitter was good for making noise. I hope this battle is also happening on Twitter.

Machine learning algorithm brings long-read sequencing to the clinic SAVANA is a new tool designed for accurate detection of structural variations in clinical samples.

Long-read sequencing can reveal hidden cancer mutations, but existing tools often produce false positives.

SAVANA is a machine learning algorithm trained on cancer genomes, built to make analysis faster and clinically reliable.

@isidrolauscher.bsky.social

www.ebi.ac.uk/about/news/r...

#oncosky

Hi Nick, is Mastodon doing any better? Just figured out how to follow people on different servers, took me a while.

Can this work for panel figures like Fig. A-F as required by manuscripts? I have been using GIMP to put the panels together.

I'll be leading a workshop with Justin Landis at useR! in Durham on August 8. It will be a gentle introduction to how we model biological data using tidy data principles

user2025.r-project.org