Johnbosco

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

A grade 9 prostate tumor

IS NOT

stage 9 cancer

Cancer stages range from I to IV & are used for all cancers.
Gleason grades: specific to prostate cancer, range from 6 to 10.

They tell us different things.

IF anyone confuses them, they have NO business talking about cancer in ANY capacity.

Cancer: hundreds of complex diseases that are plagued with misinformation Lack of understanding of cancer underlies harmful pseudoscience that circulates rampantly

If you want to learn some basics on cancer biology, read this article:

news.immunologic.org/p/cancer-hun...

It’s time: @benjamingvincent.bsky.social and I are going to do a cancer immunotherapy / cool research / accelerating future medicine podcast.

Any tips for getting started?

A graphic for the Marie Skłodowska-Curie Actions (MSCA), showing a historical portrait of Marie Skłodowska-Curie overlaid with an image of four young researchers walking down a hallway. The European Commission logo is in the top left. Text reads: "Marie Skłodowska-Curie Actions – €404.3 million to support postdoctoral researchers”

Choose Science. Choose Europe.

A new Marie Skłodowska-Curie Actions Postdoctoral Fellowships 2025 call is now open.

With a budget of €404.3 million, it will support around 1,650 researchers from Europe and beyond.

Apply by 10 September → europa.eu/!fBTMgF

Hello, I noticed that Notification of acceptance was today May 15th, 2025.
Will you be communicating your decisions to all the applicants that submitted applications or only the successful applicants? Thanks.

I had a 26GB TSV file. R choked. So I turned to UNIX. And it worked.
1/
You only need 500 columns.
But the file is 26GB.
R freezes. Memory bleeds.
You need the data—but you don’t need the pain.
Here’s what I did.

Merging large TCGA .tsv files in a memory-efficient way on Posit Cloud (formerly RStudio) I have 448 .tsv files that contain gene expression data (RNAseq) that were downloaded from The Cancer Genome Atlas Genomic Data Commons (GDC) Portal. These files have 60666 rows and 9 columns. Then...

On stackoverflow, the accepted answer for a very similar problem used
`data.table::fread()` and `dcast`

stackoverflow.com/questions/75...

Hi Tommy, do you know of any great publicly available single-cell RNA-seq data? Thanks for your resourceful threads.

Rethinking the production and publication of machine-readable expressions of research findings - Scientific Data Scientific Data - Rethinking the production and publication of machine-readable expressions of research findings

📢New article alert. Open-source approach transforms the production of scientific results by making them machine-readable. Published in Scientific Data from @natureportfolio.nature.com

Open access article: doi.org/10.1038/s415...

Press release: bit.ly/4iKb6Vj

#FAIRScience #pressrelease