Johnbosco
@biocodebreaker.bsky.social
Bioinformatician | Cancer Omics | Health informatics | FAIR Principles | Reproducible Research
https://orcid.org/0000-0002-2355-8475
https://orcid.org/0000-0002-2355-8475
Pinned
Johnbosco
@biocodebreaker.bsky.social
· Oct 24
Meet the 2025 #ORKGreborn curation grantees who are helping us grow our #openscience digital library! Over the next few weeks, they’ll share why they’re invested in a future where all scientific knowledge is represented in open digital libraries like ORKG reborn: reborn.orkg.org/pages/submit
Meet the 2025 #ORKGreborn curation grantees who are helping us grow our #openscience digital library! Over the next few weeks, they’ll share why they’re invested in a future where all scientific knowledge is represented in open digital libraries like ORKG reborn: reborn.orkg.org/pages/submit
October 24, 2025 at 11:20 AM
Reposted by Johnbosco
Meet Johnbosco (@biocodebreaker.bsky.social), our new #ORKGreborn curation grantee! As a bioinformatics researcher, he is helping us expand our open-source digital library into medical research. He shares his motivation for contributing to this initiative.
Visit the library here: reborn.orkg.org
Visit the library here: reborn.orkg.org
October 23, 2025 at 1:22 PM
Meet Johnbosco (@biocodebreaker.bsky.social), our new #ORKGreborn curation grantee! As a bioinformatics researcher, he is helping us expand our open-source digital library into medical research. He shares his motivation for contributing to this initiative.
Visit the library here: reborn.orkg.org
Visit the library here: reborn.orkg.org
Reposted by Johnbosco
Meet the 2025 #ORKGreborn curation grantees who are helping us grow our #openscience digital library! Over the next few weeks, they’ll share why they’re invested in a future where all scientific knowledge is represented in open digital libraries like ORKG reborn: reborn.orkg.org/pages/submit
October 1, 2025 at 7:49 AM
Meet the 2025 #ORKGreborn curation grantees who are helping us grow our #openscience digital library! Over the next few weeks, they’ll share why they’re invested in a future where all scientific knowledge is represented in open digital libraries like ORKG reborn: reborn.orkg.org/pages/submit
Reposted by 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 updated {psychdsish} to include a function that does this for you.
August 23, 2025 at 8:43 AM
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 updated {psychdsish} to include a function that does this for you.
Reposted by Johnbosco
A simple design framework that will massively improve your slides and your public speaking
clauswilke.substack.com/p/slides-tha...
clauswilke.substack.com/p/slides-tha...
Slide designs that present themselves: The assertion–evidence template
Your slides are not your talk.
clauswilke.substack.com
August 15, 2025 at 11:10 AM
A simple design framework that will massively improve your slides and your public speaking
clauswilke.substack.com/p/slides-tha...
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
genome.cshlp.org/cgi/doi/10.1...
@cshlnews.bsky.social
Highly accurate assembly polishing with DeepPolisher
An international, peer-reviewed genome sciences journal featuring outstanding original research that offers novel insights into the biology of all organisms
genome.cshlp.org
August 13, 2025 at 9:26 AM
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
genome.cshlp.org/cgi/doi/10.1...
@cshlnews.bsky.social
Reposted by Johnbosco
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...
careers-atcc.icims.com
August 4, 2025 at 8:01 PM
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...
July 20, 2025 at 5:40 PM
Reposted by Johnbosco
2. Ten Simple Rules for Reproducible Computational Research
journals.plos.org/ploscompbio...
journals.plos.org/ploscompbio...
Ten Simple Rules for Reproducible Computational Research
journals.plos.org
July 12, 2025 at 1:15 PM
2. Ten Simple Rules for Reproducible Computational Research
journals.plos.org/ploscompbio...
journals.plos.org/ploscompbio...
Reposted by Johnbosco
I love the idea of "micropublications" www.micropublication.org (preparing one now)
microPublication - Get Your Data Out, Be Cited
www.micropublication.org
July 14, 2025 at 8:29 AM
I love the idea of "micropublications" www.micropublication.org (preparing one now)
Reposted by Johnbosco
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
#reproducibility #openscience #opensource #dataaccess #researchintegrity #AcademicSky #EduSky
July 11, 2025 at 6:58 PM
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
#reproducibility #openscience #opensource #dataaccess #researchintegrity #AcademicSky #EduSky
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
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.
elifesciences.org
July 12, 2025 at 6:45 PM
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
elifesciences.org/articles/67995
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
Conclusion: it is hard to assess whether reported findings are credible.
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.
elifesciences.org
July 12, 2025 at 6:40 PM
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
Conclusion: it is hard to assess whether reported findings are credible.
elifesciences.org/articles/67995
Reposted by Johnbosco
❓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...
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...
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…
community.data.4tu.nl
July 9, 2025 at 1:32 PM
❓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...
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...
Reposted by Johnbosco
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
shorturl.at/qyXkc
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…
shorturl.at
June 11, 2025 at 12:55 PM
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
shorturl.at/qyXkc
July 10, 2025 at 4:55 PM
Reposted by Johnbosco
No words
May 30, 2025 at 12:23 PM
No words
Reposted by Johnbosco
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...
r-consortium.org/posts/r-cons...
R Consortium Awards First Round of 2025 ISC Grants – R Consortium
The R Consortium’s Infrastructure Steering Committee (ISC) is proud to announce the first round of 2025 grant recipients. These seven projects are receiving support to enhance and expand the capabilit...
r-consortium.org
May 29, 2025 at 4:32 PM
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...
r-consortium.org/posts/r-cons...
Reposted by Johnbosco
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
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
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.
www.ebi.ac.uk
May 29, 2025 at 8:54 AM
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
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
Reposted by Johnbosco
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
user2025.r-project.org
useR! 2025
user2025.r-project.org
May 20, 2025 at 12:05 PM
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
user2025.r-project.org
Reposted by Johnbosco
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.
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.
May 20, 2025 at 6:40 PM
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.
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.
Reposted by Johnbosco
If you want to learn some basics on cancer biology, read this article:
news.immunologic.org/p/cancer-hun...
news.immunologic.org/p/cancer-hun...
Cancer: hundreds of complex diseases that are plagued with misinformation
Lack of understanding of cancer underlies harmful pseudoscience that circulates rampantly
news.immunologic.org
May 20, 2025 at 12:44 AM
If you want to learn some basics on cancer biology, read this article:
news.immunologic.org/p/cancer-hun...
news.immunologic.org/p/cancer-hun...
Reposted by Johnbosco
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?
Any tips for getting started?
May 17, 2025 at 4:12 PM
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?
Any tips for getting started?