Nicola Romanò @nicolaromano@qoto.org

Tis the season to be marking

Falalalalaaaa la la la laaa

@mcaleerp and I collected together all our ideas for making feedback and engaging students in using that feedback to make some tools that we and others can use go make better and useful feedback, but also tools to help student to use that feedback.

Access our article here:
https://osotl.org/index.php/osotl/article/view/42

#sotl #feedback #assessment #teaching

Wow, this paper on #scRNAseq and differential expression methods is an eye opener. https://www.nature.com/articles/s41467-021-25960-2

Nice overview of methods and relatively easy to understand explanation of what is wrong with certain, especially single-cell-specific, methods.

Of great help in my own scRNA-seq efforts. Should probably have read this earlier. Now, back to R I go. 😅

#statistics #rnaseq #limma #edgeR #DESeq2

As a blind individual, I have to say that #Caturday on #Mastodon is far far more enjoyable then at #Twitter, where the vast majority of cat photos are not described.

It is also been fascinating for me to hear descriptions written by those who sent the image, immediately followed by Apple image recognition’s attempts to describe the same image. Only rarely does that add anything to the ALT, & often directly contradicts it.

There is no auto magical solution to image description. It is something best done by a human, for only that human can explain the “why” of the image: the reason that image was chosen to speak so eloquently without words for those who can see it. ALT allows you to provide those words.

Pride in history can be detrimental to progress. It can make people delusional that they’re special relating to times they didn’t exist in. The reality of those times is often translated to them as one-sided stories where they imagine themselves to be the heroes. They get stuck.

"More than our rank".
This is an initiative that every university would do well to join, regardless of its ranking.
Indeed, each institution, for various reasons, many of which are its own, is worth much more than the rank assigned to it by a limited, indigent and ideologically connoted system of indicators.
https://inorms.net/more-than-our-rank/

It only takes a few lines of #python code to gain insights from scientific images.

They are just a click away if you are not into coding - ask me about it.
#deeplearning #bioimageanalysis #microscopy

Why? I really started believing in federated platforms (again). That’s what the internet was and should be. I must take the sacrifice for this belief, despite loving the Twitter community.

The slides for my recent intro to open science (OS) talk, including 5 things about OS that everyone should know

➡️ https://osf.io/zy2pc ⬅️

1. OS practices accelerate scientific discovery
2. Adopting OS practices can make you a more competitive job/grant applicant
3. Data sharing is on a continuum (it doesn’t have to be either fully open or fully closed)
4. Take it one step at a time, you don’t have to learn every skill at once
5. Your future self will thank you for adopting OS practices

Move to #Mastodon is going well, but raises an important question: how and when do I get rid of #Twitter altogether?!?
Whats a reasonable timeline and strategy?!? 6 month? When 50% of my contacts moved? Opinions???

🔖 Statistical code in a high-impact medical journal

A journal started asking authors to submit code with their manuscripts. They then analysed the next 314 papers accepted

87% denied using code, even when publishing substantial statistical analysis

10% used code but refused to share it with the journal

For the few that provided code, none scored even moderately on basic quality criteria

Assel & Vickers
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6705117/

#MedMastodon
#OpenScience
#ResearchWaste
#doi:10.7326/M17-2863

Thanks to a toot from @DavidKnuffke that I saw this morning, I tried another #AI tool - Elicit https://elicit.org/
"This workflow tries to answer your research question with information from published papers."
My example is shown here with my initial question in the red box. Wow.
#EdTech #EduTooter #Education #GoogleEDU

Just making sure that the Mastodon #rstats community is aware of the {dadjoke} package. And if you need it, add this to your .Rprofile for a dadjoke on startup:

# Dadjoke on start up
if (interactive())
dadjokeapi::groan(sting = FALSE)

🔖 Do cancer researchers make their data and code available?

306 cancer studies:

16% shared data

4% shared analysis code

1% of data were FAIR (posted to a recognised repository, in a non-proprietary format, with an identifier and a license)

Cancer research transparency was this bad despite many journals having policies mandating openness.

Daniel Hamilton et al
https://bmcmedicine.biomedcentral.com/articles/10.1186/s12916-022-02644-2

#MedMastodon
#OpenScience
#ResearchIntegrity
#ResearchWaste
#doi:10.1186/s12916-022-02644-2

@Sheril
Im in my 50s. When i was in school, i wanted to study sharks. I was told no women made contributions to science (cept Currie, who they could not ignore, though they tried!). And it was because THERE WERE NO WOMEN IN SCIENCE, and not because “women were there, but we dont learn about them!”

I hope no other 10 year old decides to go into a field she doesnt want, because aomone says she cant do what she really wants to do.

In 1925, Dr. Cecilia Payne completed her PhD thesis, described as “the most brilliant ever written in astronomy.” At a time when few #women entered academia, Payne discovered what the universe is made of. Her work began a revolution in astrophysics.

Dr. Payne-Gaposchkin became the 1st female professor & 1st female department chair at Harvard. Given most of us remember names like Darwin & Newton, we should also celebrate Payne. #science #space

Read more at https://www.aps.org/publications/apsnews/201501/physicshistory.cfm

Using ALT to describe pictures and photos is actually much more tricky than it sounds - it’s not about making a jokey comment but trying to use words to reflect an image. Sometimes you discover new aspects to the image and why you. chose it, too

Expansion microscopy is one of the best things to come along in #cellbiology. A new preprint from Ons M’Saad in the Bewersdorf lab at Yale describes methods for ~8000-fold volumetric expansion and labeling that deals with the dilution problem associated with such huge expansion. Cell-level details can be observed with a cell phone camera!

https://www.biorxiv.org/content/10.1101/2022.11.29.518361v1

Fellow academics:

Strongly consider changing your syllabi now, and designing assignments that can't be fulfilled by #AI chatbots. Even better, consider only assigning work that students will actually be excited to do themselves (for instance, autobiographical essays).

I just got OpenAI to write a better essay on #minstrelsy & US #popmusic than most of my UG students could muster, in about 1 second.