iiinova — where your digital self keeps evolving

Jim Brody @jpbrody.bsky.social · 17/07/2025

It's gone from 3-1 in favor to about an even split over the past 20 years. We need more scientists to speak to the general public about the importance of animal research, or there's going to be a major change in policies in the next decade or so.

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Jim Brody @jpbrody.bsky.social · 17/07/2025

I teach a large general education class, with lots of non-STEM majors. I was amazed how many students were just against the use of animals in research. I thought it was a niche view, like the earth is flat, but nope. Gallup has an annual poll where they ask people about animal research.

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Jim Brody @jpbrody.bsky.social · 16/07/2025

No, never published. I made it as part of a review article that I couldn't get any editors interested in. I was contrasting the above figure with this one, from doi.org/10.1038/s435... Same data source, but a different presentation tells a very different story.

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Jim Brody @jpbrody.bsky.social · 16/07/2025

The belief that it's a continuous rise might be an illusion created by data censoring. If a cancer's true peak is at age 95, we'll rarely see the full curve because most people have already died from other causes by then.

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Jim Brody @jpbrody.bsky.social · 16/07/2025

I made this graph from SEER data to illustrate it might be more accurate to say that specific cancers peak at specific ages, rather than incidence simply increases forever.

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Jim Brody @jpbrody.bsky.social · 30/05/2025

There's the Flexner report from 1910, but it's really about medical research/education before biomedical research existed. archive.carnegiefoundation.org/publications/pdfs/elibrary/Carnegie_Flexner_Report.pdf

archive.carnegiefoundation.org

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Jim Brody @jpbrody.bsky.social · 24/05/2025

I've noticed two other universities that weren't reimbursed during those three weeks: University of Michigan, University of California, Davis.

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Jim Brody @jpbrody.bsky.social · 24/05/2025

Check here for schools that have been paid (reimbursed) by NIH between April 21 - May 13. (That's all the data DOGE has published.) uci-bme-jpbrody.shinyapps.io/DogeFreeze/

uci-bme-jpbrody.shinyapps.io

Doge Payments Explorer: HHS-NATIONAL INSTITUTES OF HEALTH

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Jim Brody @jpbrody.bsky.social · 21/05/2025

My understanding is that reimbursement can be requested any time after expenses are incurred. So, there's no set schedule.

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Jim Brody @jpbrody.bsky.social · 21/05/2025

Irvine and UCSD are getting paid. Davis, Berkeley, and UCLA are mostly missing, but maybe "University of California" and "Regents, University of California" refers to Berkeley?

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Jim Brody @jpbrody.bsky.social · 21/05/2025

University of California system is interesting

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Jim Brody @jpbrody.bsky.social · 21/05/2025

Harvard got one payment of $7k on April 22. Northwestern University is not listed.

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Jim Brody @jpbrody.bsky.social · 21/05/2025

The DOGE data for HHS/NIH payments starts 21 April and is currently through 13 May. (They say it's updated weekly, but will switch to realtime in the future.) If you university received any payments in that time frame, this app will tell you how much and when was the last payment.

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Jim Brody @jpbrody.bsky.social · 21/05/2025

DOGE is publishing all payments made by the Payment Management System. My tool just uses the API to grab all of the recorded payments and organizes them a bit better. doge.gov/payments

doge.gov

DOGE: Department of Government Efficiency

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Jim Brody @jpbrody.bsky.social · 21/05/2025

I made a tool where you can check to see if a university is being frozen out of NIH payments #academicsky #science 🧪 #NSF #NIH #MedicalResearch uci-bme-jpbrody.shinyapps.io/DogeFreeze/

uci-bme-jpbrody.shinyapps.io

Doge Payments Explorer: HHS-NATIONAL INSTITUTES OF HEALTH

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Jim Brody @jpbrody.bsky.social · 16/05/2025

They also have a Department of Energy cancellation. It only lists one grant. storage.courtlistener.com/recap/gov.us...

storage.courtlistener.com

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Jim Brody @jpbrody.bsky.social · 15/05/2025

That should say Department of Defense (DoD), not DOE.

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Jim Brody @jpbrody.bsky.social · 15/05/2025

The list of terminated DOE grants at Harvard are here: storage.courtlistener.com/recap/gov.us... They total $105 million.

storage.courtlistener.com

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Jim Brody @jpbrody.bsky.social · 02/05/2025

I've learned that this is known as Vibe coding en.wikipedia.org/wiki/Vibe_co...

en.wikipedia.org

Vibe coding - Wikipedia

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Jim Brody @jpbrody.bsky.social · 02/05/2025

I had a separate prompt to generate python code that took a directory full of json files (those are directly from NSF) to the csv files.

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Jim Brody @jpbrody.bsky.social · 02/05/2025

After that prompt there were a few iterations of me asking for specific modifications, like: "A division is within a directorate. Can you make it so that if I select a diretorate, then the only choices in "Filter by division" are divisions that are within that directorate?"

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Jim Brody @jpbrody.bsky.social · 02/05/2025

I'd like to make a shiny app to do this online, with the two datafiles called, "2024combined_awards.csv" and "2025combined_awards.csv" already loaded into the shiny app. Tell me how to do this

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Jim Brody @jpbrody.bsky.social · 02/05/2025

I want to visualize the difference between award data in 2024 and 2025, as a function of the date of the year. I would like to see this difference overall, and also broken down by different "org_dir_long_name" and "org_div_long_name".

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Jim Brody @jpbrody.bsky.social · 02/05/2025

Here is my prompt: I have two files. One for 2024 award data and the other for 2025 award data. Each file is a csv file. These files are formatted as follows. Each row is a different award. the columns include, "awd_eff_date", "awd_amount", "org_dir_long_name", and "org_div_long_name".

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Jim Brody @jpbrody.bsky.social · 02/05/2025

I'll try to this the next time I update it. By the way, this would take me way too long to code by myself. I did it quickly using an LLM (Gemini 2.5 pro).

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Jim Brody @jpbrody.bsky.social · 02/05/2025

I made a dashboard to compare NSF funding by division/directorate during FY 24 vs FY 25. #academicsky #science 🧪 #NSF uci-bme-jpbrody.shinyapps.io/NSFAwardData/

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Jim Brody @jpbrody.bsky.social · 28/03/2025

Wow, you should do more mechanism breakdowns! (R/T/P/U/etc). It looks like this T32 is the only non competitive one that has been approved: reporter.nih.gov/project-deta...

reporter.nih.gov

RePORT ⟩ RePORTER

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Jim Brody @jpbrody.bsky.social · 23/02/2025

This Heritage Foundation report lays out the reasoning behind the 15% cap much better then the NIH notice. It would be nice to see a reasoned response. www.heritage.org/sites/defaul...

heritage.org

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Jim Brody @jpbrody.bsky.social · 18/02/2025

The "view on PPDS" links to this page: www.fpds.gov/common/jsp/L... which is not the COPD gene study. It's the Strong Heart Study. It's a large long term (since the 80's) study of "cardiovascular disease and its risk factors among American Indian men and women."

fpds.gov

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Jim Brody @jpbrody.bsky.social · 18/02/2025

It's not clear whether this is cancelled ($0 savings), and why they would want to cancel it. The COPD gene study even has it's own website copdgene.org

copdgene.org

COPD Gene Study – The COPDGene® Study investigates the underlying genetic factors of Chronic Obstructive Pulmonary Disease or COPD

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Jim Brody @jpbrody.bsky.social · 18/02/2025

The doge.gov site lists this project, which is concerning. It's a large project that among other things will provide a GWAS of COPD. #MedSky #EpiSky 🧪🛟

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Jim Brody @jpbrody.bsky.social · 18/02/2025

The main pubmed page has a message: "Some NLM-NCBI services and products are experiencing heavy traffic, which may affect performance and availability. We apologize for the inconvenience and appreciate your patience. For assistance, please contact our Help Desk at info@ncbi.nlm.nih.gov."

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Jim Brody @jpbrody.bsky.social · 13/02/2025

This is the HHS office that negotiates indirect cost rates www.hhs.gov/about/agenci...

hhs.gov

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Jim Brody @jpbrody.bsky.social · 13/02/2025

New: "Certain differences—such as many of the differences which characterize groups that have historically been underrepresented in biomedical and health research—are considerably more prone to stigma than others."

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Jim Brody @jpbrody.bsky.social · 13/02/2025

Old: "Certain differences—such as differences in skin color, ethnicity, country of origin, ancestry, sex, gender, sexual orientation, socioeconomic status, educational attainment, disability status, and body type—are considerably more prone to stigma than others."

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Jim Brody @jpbrody.bsky.social · 13/02/2025

Primary difference according to gemini,

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Jim Brody @jpbrody.bsky.social · 13/02/2025

I found a separate link to another copy of the policy. Wayback machine did archive this copy. www.researchallofus.org/faq/policy-o...

researchallofus.org

Policy on Stigmatizing Research – All of Us Research Hub

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Jim Brody @jpbrody.bsky.social · 12/02/2025

I did try that. It didn't capture the pdf document.

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Jim Brody @jpbrody.bsky.social · 11/02/2025

Once Walden and Eli Lilly perfected the process there was plenty of insulin for everyone who needed it.

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Jim Brody @jpbrody.bsky.social · 11/02/2025

George Walden, an engineer at Lilly, figured out that insulin solubility depended even more strongly on pH. When Collip scaled up his process the pH changed and the insulin's alcohol solubility changed. pH was a new concept in chemistry then. The first pH meter was invented by Beckman in 1934.

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Jim Brody @jpbrody.bsky.social · 11/02/2025

Collip tried to scale up his purification process, but it just didn't work. They went through the process and everything was exactly the same. Collip eventually gave up. People were dying. The Toronto group turned to Eli Lilly.

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Jim Brody @jpbrody.bsky.social · 11/02/2025

This surgical method worked at first in animals, but was cumbersome and never worked in humans. Collip was the biochemist. He perfected a way of purifying insulin based on alcohol precipitation. This was the insulin first used in humans. After this paper came out, demand went way up.

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Jim Brody @jpbrody.bsky.social · 11/02/2025

I teach a class based on this story. Here's some more interesting facts. Banting first isolated insulin. He was a surgeon, and had a really crazy way to purify insulin that involved tying off tubes in a dog, then sewing the dog back up, waiting a month, then taking out the pancreas.

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Jim Brody @jpbrody.bsky.social · 11/02/2025

I noticed the #NIH #AllofUs "Policy on Stigmatizing Research" was updated Jan 31, 2025. I'm wondering what changed. Does anyone have an old version of the policy? #MedSky #EpiSky 🧪🛟 www.researchallofus.org/faq/policy-o...

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Jim Brody @jpbrody.bsky.social · 08/02/2025

Organizations that get federal grants have to submit annual audits. You can find the audits here app.fac.gov/disseminatio...

app.fac.gov

Federal Audit ClearinghouseLock

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Jim Brody @jpbrody.bsky.social · 08/02/2025

Some small research institutes that are wholly dependent on NIH funds, like this one, will probably have to close.

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Jim Brody @jpbrody.bsky.social · 08/02/2025

when you look at their balance sheet, $100 million is a lot, but it doesn't look like it would bankrupt them.

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Jim Brody @jpbrody.bsky.social · 08/01/2025

#Sentinel-2 caught the start of the #palisadesfire. Photo was taken 10:45 am this morning. Second photo is a closeup using false color (IR bands). It looks like the fire started right along Temescal Ridge Trail

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Jim Brody @jpbrody.bsky.social · 15/11/2024

Here's the command to run. It uses the rocker project's docker container. docker run -d --name rstudio -v $HOME:/home/'whoami' -e PASSWORD=secret -e ROOT=true -p 8787:8787 -p 54321:54321 rocker/tidyverse (I sped up the docker container pull for the video, so it will take you a bit longer.)

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