Nicola Romanò @nicolaromano@qoto.org

Batch effects correction with ComBat or ComBat-Seq... but in Python? Glad to see the pyComBat paper finally out https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-023-05578-5

#bioinformatics #batchEffects

W3C has posted that we are no longer active on X/Twitter and have directed all our followers here to Mastodon.

We are encouraging all W3C-related accounts to do the same.

Encourage your friends to follow us here!

A few weeks ago, I decided to make my first ever science comic about some of our research. I hope you love these lil blobs as much as I do! The comic continues in the comments :) #developers #DeveloperThriving #SoftwareEngineering @seresearchers

This is a nice tutorial if you are interested in how and why overfitting (etc) happens, how/why regularization helps to alleviate overfitting, ...

"The Theory Behind Overfitting, Cross Validation, Regularization, Bagging, and Boosting: Tutorial", Benyamin Ghojogh, Mark Crowley

#machinelearning #overfitting

https://arxiv.org/abs/1905.12787

#bioawk is a command-line gem; it’s an extension of awk that auto-assigns variables for BED, SAM, VCF, GFF, and FASTX[AQ] format files, speeding up routine tasks.

For FASTX:
$1:name
$2:seq
$3:qual (FASTQ only)
$4:comment

Found in @vsbuffalo’s great #Bioinformatics Data Skills.

I am actively recruiting students for my lab at UMass Dartmouth!

Are you interested in a project on actin, amoebae, cell migration, and/or pathogenesis? Send me an email & apply to the Integrative Biology PhD program by Jan 15!

Please RT
More info: https://katrinavelle.wixsite.com/science

What does a #scientist look like? Children are drawing women more than ever before.

https://www.science.org/content/article/what-does-scientist-look-children-are-drawing-women-more-ever

@nicolaromano @tomstafford
I'd agree. But that's why I voted C. It's past the time where these self serving bad practices can be called "inadvertent".

Researchers! Please complete my poll with uneven response options (and boost for reach)

How much of a problem is deliberate research fraud?

meetings today? zero should be the goal https://blog.codinghorror.com/meetings-where-work-goes-to-die/

Even this very, very simple lesson is lost on most large companies, even today

"We must not forget that when radium was discovered no one knew that it would prove useful in hospitals. The work was one of pure science. And this is a proof that scientific work must not be considered from the point of view of the direct usefulness of it. It must be done for itself, for the beauty of science, and then there is always the chance that a scientific discovery may become like the radium a benefit for humanity."
Lecture at Vassar College

~Marie Curie (7 November 1867 – 4 July 1934)

Tonight a dear friend sent me this photo of my lab circa 2007. A coffee bar, shelves of books, and off-camera a 12' long table in a massive room surrounded by whiteboards.

Now? My department has moved to a sleek new building. I don't have a lab, just a 120 square foot office. Theorists don't need space; all they do is think. If they need to talk to one another, they can reserve departmental conference rooms so long as they remember to do so six weeks in advance.

Progress marches on.

Last time I brought this up on a UK-based technical mailing list, an entrepreneur—themself from a historically persecuted ethnic group—told me that, "no one cares".
Well, I can't make anyone care but if you are in the position to advise on or choose a domain name you should maybe at least know some of the history behind .IO before buying one.
https://www.beep.blog/io/

"He was doing physical therapy, spending time with family members, and playing cards with his wife, according to the university. But in the days leading up to his death, his heart began to show signs of organ rejection; in other words, his immune system recognized the pig heart as foreign and attacked it. "

https://www.wired.com/story/pig-heart-transplant-lawrence-faucette-death/