Fernando Pérez
LightNews LightNews
banner
fernandoperez.org
Fernando Pérez
@fernandoperez.org
1.6K followers 600 following 120 posts
Open source, open science, AI in science for earth/ice and healthcare. IPython creator, @projectjupyter.bsky.social and 2i2c.org co-founder.

Prof @ UC Berkeley Stats, director of @ucbids.bsky.social, co-director @schmidtdse.bsky.social; LBL scientist.
Posts Replies Media Videos
Pinned
fernandoperez.org
Fernando Pérez @fernandoperez.org · Nov 7
Well, time to start setting up shop for real away from Twitter - used to be fperez_org there, used it a lot as a science feed and community building tool, til the Musk purchase.

Went quiet since but hadn't fully moved on; the election seems like a good time to shut the curtains and move.
Reposted by Fernando Pérez
iansociologo.bsky.social
If you haven't joined your local AAUP, now is a great time to do so.
veenadubal.bsky.social Veena Dubal @veenadubal.bsky.social · 5h
BREAKING: In AAUP et al v. Trump (wall-to-wall union lawsuit challenging the administration’s unlawful use of TItle VI to reshape the University of California system), the faculty and staff of the UC system WON!!!

We were granted our preliminary injunction! @aaup.org
November 15, 2025 at 12:51 AM
fernandoperez.org
Using this excellent thread and the related papers tomorrow in my class on open science, stat159.berkeley.edu.

I will also include some choice examples from my inbox full of "invitations to publish" where my "expertise" (in fields I know exactly nothing about) is welcome by these "editors".
November 12, 2025 at 8:48 AM
Reposted by Fernando Pérez
benbraun.bsky.social
The central argument in this excellent paper & thread is that the open-access turn has neglected profit; indeed, it turbo-charged publishers’ margins. As political economists who know a thing or two about profit and power we should speak up a lot more. As it says below: What we’re doing is crazy.
hansonmark.bsky.social Mark A. Hanson @hansonmark.bsky.social · 3d
We wrote the Strain on scientific publishing to highlight the problems of time & trust. With a fantastic group of co-authors, we present The Drain of Scientific Publishing:

a 🧵 1/n

Drain: arxiv.org/abs/2511.04820
Strain: direct.mit.edu/qss/article/...
Oligopoly: direct.mit.edu/qss/article/...
A table showing profit margins of major publishers. A snippet of text related to this table is below. 1. The four-fold drain 1.1 Money Currently, academic publishing is dominated by profit-oriented, multinational companies for whom scientific knowledge is a commodity to be sold back to the academic community who created it. The dominant four are Elsevier, Springer Nature, Wiley and Taylor & Francis, which collectively generated over US$7.1 billion in revenue from journal publishing in 2024 alone, and over US$12 billion in profits between 2019 and 2024 (Table 1A). Their profit margins have always been over 30% in the last five years, and for the largest publisher (Elsevier) always over 37%. Against many comparators, across many sectors, scientific publishing is one of the most consistently profitable industries (Table S1). These financial arrangements make a substantial difference to science budgets. In 2024, 46% of Elsevier revenues and 53% of Taylor & Francis revenues were generated in North America, meaning that North American researchers were charged over US$2.27 billion by just two for-profit publishers. The Canadian research councils and the US National Science Foundation were allocated US$9.3 billion in that year. A figure detailing the drain on researcher time. 1. The four-fold drain 1.2 Time The number of papers published each year is growing faster than the scientific workforce, with the number of papers per researcher almost doubling between 1996 and 2022 (Figure 1A). This reflects the fact that publishers’ commercial desire to publish (sell) more material has aligned well with the competitive prestige culture in which publications help secure jobs, grants, promotions, and awards. To the extent that this growth is driven by a pressure for profit, rather than scholarly imperatives, it distorts the way researchers spend their time. The publishing system depends on unpaid reviewer labour, estimated to be over 130 million unpaid hours annually in 2020 alone (9). Researchers have complained about the demands of peer-review for decades, but the scale of the problem is now worse, with editors reporting widespread difficulties recruiting reviewers. The growth in publications involves not only the authors’ time, but that of academic editors and reviewers who are dealing with so many review demands. Even more seriously, the imperative to produce ever more articles reshapes the nature of scientific inquiry. Evidence across multiple fields shows that more papers result in ‘ossification’, not new ideas (10). It may seem paradoxical that more papers can slow progress until one considers how it affects researchers’ time. While rewards remain tied to volume, prestige, and impact of publications, researchers will be nudged away from riskier, local, interdisciplinary, and long-term work. The result is a treadmill of constant activity with limited progress whereas core scholarly practices – such as reading, reflecting and engaging with others’ contributions – is de-prioritized. What looks like productivity often masks intellectual exhaustion built on a demoralizing, narrowing scientific vision. A table of profit margins across industries. The section of text related to this table is below: 1. The four-fold drain 1.1 Money Currently, academic publishing is dominated by profit-oriented, multinational companies for whom scientific knowledge is a commodity to be sold back to the academic community who created it. The dominant four are Elsevier, Springer Nature, Wiley and Taylor & Francis, which collectively generated over US$7.1 billion in revenue from journal publishing in 2024 alone, and over US$12 billion in profits between 2019 and 2024 (Table 1A). Their profit margins have always been over 30% in the last five years, and for the largest publisher (Elsevier) always over 37%. Against many comparators, across many sectors, scientific publishing is one of the most consistently profitable industries (Table S1). These financial arrangements make a substantial difference to science budgets. In 2024, 46% of Elsevier revenues and 53% of Taylor & Francis revenues were generated in North America, meaning that North American researchers were charged over US$2.27 billion by just two for-profit publishers. The Canadian research councils and the US National Science Foundation were allocated US$9.3 billion in that year. The costs of inaction are plain: wasted public funds, lost researcher time, compromised scientific integrity and eroded public trust. Today, the system rewards commercial publishers first, and science second. Without bold action from the funders we risk continuing to pour resources into a system that prioritizes profit over the advancement of scientific knowledge.
November 12, 2025 at 8:30 AM
Reposted by Fernando Pérez
matti.vuorre.com
Everyone involved in scientific publishing should take a look at these papers.

>"The domination of scientific publishing in the Global North by major commercial publishers is harmful to science; we need [...] to re-communalise publishing to serve science not the market."
hansonmark.bsky.social Mark A. Hanson @hansonmark.bsky.social · 3d
We wrote the Strain on scientific publishing to highlight the problems of time & trust. With a fantastic group of co-authors, we present The Drain of Scientific Publishing:

a 🧵 1/n

Drain: arxiv.org/abs/2511.04820
Strain: direct.mit.edu/qss/article/...
Oligopoly: direct.mit.edu/qss/article/...
A table showing profit margins of major publishers. A snippet of text related to this table is below. 1. The four-fold drain 1.1 Money Currently, academic publishing is dominated by profit-oriented, multinational companies for whom scientific knowledge is a commodity to be sold back to the academic community who created it. The dominant four are Elsevier, Springer Nature, Wiley and Taylor & Francis, which collectively generated over US$7.1 billion in revenue from journal publishing in 2024 alone, and over US$12 billion in profits between 2019 and 2024 (Table 1A). Their profit margins have always been over 30% in the last five years, and for the largest publisher (Elsevier) always over 37%. Against many comparators, across many sectors, scientific publishing is one of the most consistently profitable industries (Table S1). These financial arrangements make a substantial difference to science budgets. In 2024, 46% of Elsevier revenues and 53% of Taylor & Francis revenues were generated in North America, meaning that North American researchers were charged over US$2.27 billion by just two for-profit publishers. The Canadian research councils and the US National Science Foundation were allocated US$9.3 billion in that year. A figure detailing the drain on researcher time. 1. The four-fold drain 1.2 Time The number of papers published each year is growing faster than the scientific workforce, with the number of papers per researcher almost doubling between 1996 and 2022 (Figure 1A). This reflects the fact that publishers’ commercial desire to publish (sell) more material has aligned well with the competitive prestige culture in which publications help secure jobs, grants, promotions, and awards. To the extent that this growth is driven by a pressure for profit, rather than scholarly imperatives, it distorts the way researchers spend their time. The publishing system depends on unpaid reviewer labour, estimated to be over 130 million unpaid hours annually in 2020 alone (9). Researchers have complained about the demands of peer-review for decades, but the scale of the problem is now worse, with editors reporting widespread difficulties recruiting reviewers. The growth in publications involves not only the authors’ time, but that of academic editors and reviewers who are dealing with so many review demands. Even more seriously, the imperative to produce ever more articles reshapes the nature of scientific inquiry. Evidence across multiple fields shows that more papers result in ‘ossification’, not new ideas (10). It may seem paradoxical that more papers can slow progress until one considers how it affects researchers’ time. While rewards remain tied to volume, prestige, and impact of publications, researchers will be nudged away from riskier, local, interdisciplinary, and long-term work. The result is a treadmill of constant activity with limited progress whereas core scholarly practices – such as reading, reflecting and engaging with others’ contributions – is de-prioritized. What looks like productivity often masks intellectual exhaustion built on a demoralizing, narrowing scientific vision. A table of profit margins across industries. The section of text related to this table is below: 1. The four-fold drain 1.1 Money Currently, academic publishing is dominated by profit-oriented, multinational companies for whom scientific knowledge is a commodity to be sold back to the academic community who created it. The dominant four are Elsevier, Springer Nature, Wiley and Taylor & Francis, which collectively generated over US$7.1 billion in revenue from journal publishing in 2024 alone, and over US$12 billion in profits between 2019 and 2024 (Table 1A). Their profit margins have always been over 30% in the last five years, and for the largest publisher (Elsevier) always over 37%. Against many comparators, across many sectors, scientific publishing is one of the most consistently profitable industries (Table S1). These financial arrangements make a substantial difference to science budgets. In 2024, 46% of Elsevier revenues and 53% of Taylor & Francis revenues were generated in North America, meaning that North American researchers were charged over US$2.27 billion by just two for-profit publishers. The Canadian research councils and the US National Science Foundation were allocated US$9.3 billion in that year. The costs of inaction are plain: wasted public funds, lost researcher time, compromised scientific integrity and eroded public trust. Today, the system rewards commercial publishers first, and science second. Without bold action from the funders we risk continuing to pour resources into a system that prioritizes profit over the advancement of scientific knowledge.
November 12, 2025 at 8:15 AM
Reposted by Fernando Pérez
dsi-uchicago.bsky.social
🎉 Congratulations to kylecranmer.bsky.social, inaugural recipient of the Margot and Tom Pritzker Prize for AI in Science Research Excellence!

Read more: bit.ly/47Sku5N

#AIinScience #ParticlePhysics
November 11, 2025 at 8:10 PM
Reposted by Fernando Pérez
mystmd.org
We recently pushed Jupyter Book 2, which was a breaking change for many of our users! We considered publishing a completely different package (e.g., `jupyter-book2`) but decided against it. Here's a quick rationale why:
Why we made a major release for Jupyter Book 2 instead of creating a new package - Jupyter Book: Blog
Updates from the Jupyter Book subproject.
blog.jupyterbook.org
November 7, 2025 at 6:16 PM
Reposted by Fernando Pérez
dsi-uchicago.bsky.social
Job Opportunity Alert

Instructional Professor (open rank) in Data Science: apply.interfolio.com/176416

EOE/Vet/Disability
Apply - Interfolio {{$ctrl.$state.data.pageTitle}} - Apply - Interfolio
apply.interfolio.com
November 7, 2025 at 3:00 PM
Reposted by Fernando Pérez
gadom.ski
Slides for my @foss4gna.bsky.social NA talk, "Cloud-Native Geospatial Metadata with stac-geoparquet" are at www.gadom.ski/presentation...

I subtitled the talk "Practical STAC", because #stac-geoparquet was motivated by real-world problems found while managing large @stacspec.bsky.social systems
stac-geoparquet
www.gadom.ski
November 5, 2025 at 10:44 AM
Reposted by Fernando Pérez
dianarycai.bsky.social
I'm on the academic job market!

I design and analyze probabilistic machine-learning methods---motivated by real-world scientific constraints, and developed in collaboration with scientists in biology, chemistry, and physics.

A few highlights of my research areas are:
Probabilistic ML in scientific pipelines
November 7, 2025 at 2:47 PM
Reposted by Fernando Pérez
jnywong.github.io
Shravan Achar and Zach Sailor demonstrating a simple sharing service for Jupyter Notebooks #jupytercon
November 5, 2025 at 10:32 PM
Reposted by Fernando Pérez
ucbids.bsky.social
So much activity at #JupyterCon 2025 -> tutorials 🧠, meetups 🤝, talks 🎤! Thankfully, Silas Santini captured some highlights and shared some valuable resources!

Read "Themes of Day 1, JupyterCon 2025: Collaboration and Modularity" for details:
bids.berkeley.edu/news/themes-...
group of about 50 people pose for the camera in a large room, with the JupyterCon logo on the side of the photo
November 6, 2025 at 12:46 AM
Reposted by Fernando Pérez
schmidtdse.bsky.social
We're live at #JupyterCon! Here's @mfisher87.bsky.social walking attendees through #GeoJupyter with @fernandoperez.org 🧑🏻‍💻

🌏 GeoJupyter is an open and community-driven effort to reimagine #geospatial interactive #computing experiences for education, research, & industry: bit.ly/49CMRY1 #GIS #Jupyter
matt fisher presenting at a data science conference behind a podium
November 4, 2025 at 7:40 PM
Reposted by Fernando Pérez
altagliabue.bsky.social
Seeking a three year postdoc in the field of ocean biogeochemistry and productivity using mechanistic models and synthesis of observations. Note the short fuse for applications. Please help distribute. All nationalities welcome to apply! 🌊

www.jobs.ac.uk/job/DPG117/p...
Postdoctoral Research Associate at University of Liverpool
Looking for a new job opportunity in academia? Check out this job opening for a Postdoctoral Research Associate on jobs.ac.uk!
www.jobs.ac.uk
October 29, 2025 at 5:38 PM
Reposted by Fernando Pérez
earthmover.io
Today, napari users can’t fully leverage Xarray’s labeled metadata, as slider names, units & dimensions often get out of sync. That’s changing. At SciPy 2025, napari, Xarray & CellProfiler devs began a collab to build true metadata-aware visualization across sciences.
earthmover.io/blog/scienti...
Scientific Data Visualization with Xarray and Napari - Earthmover
Ian Hunt-Isaak Xarray Community Developer Tim Monko Neuroscience PhD & napari community manager This blog was also published on the xarray blog and the napari blog. TL;DR Making Napari and Xarray work...
earthmover.io
October 29, 2025 at 5:53 PM
Reposted by Fernando Pérez
python.org
TLDR; The PSF has made the decision to put our community and our shared diversity, equity, and inclusion values ahead of seeking $1.5M in new revenue. Please read and share. pyfound.blogspot.com/2025/10/NSF-...
🧵
The official home of the Python Programming Language
www.python.org
October 27, 2025 at 2:47 PM
Reposted by Fernando Pérez
flipperpa.bsky.social
You can thank our idiotic governmental leadership for making us all less secure. I'm incredibly proud to be a PSF member. www.theregister.com/2025/10/27/p...
Python Foundation rejects $1.5M grant with no-DEI strings
: Foundation says it won't compromise policy of inclusivity even if that cash would've really helped
www.theregister.com
October 29, 2025 at 1:32 AM
Reposted by Fernando Pérez
ingoboltz.bsky.social
Very well said. Short and to the point and worth every one of the 5 minutes it will take you to read it.

The Majority AI View - Anil Dash
The Majority AI View - Anil Dash
A blog about making culture. Since 1999.
www.anildash.com
October 25, 2025 at 12:42 PM
Reposted by Fernando Pérez
richardsever.bsky.social
That merely being “under review” by a Nature family journal is offered as a quality proxy for a paper is a tragic illustration of the extent to which academia is addicted to brands and outsources evaluation
October 25, 2025 at 6:37 PM
Reposted by Fernando Pérez
phildini.net
Inspired by a chat with @bajoran.engineer at #PyTorchCon, I wrote up my thoughts about #Python as a scripting engine for apps.

phildini.dev/python-in-ev...

Shares appreciated, commentary welcome but if you're a jerk I'll block you 😇

Maybe of interest to @anacondainc.bsky.social as well ✨
Python should be in every application - phildini.dev
The best in-app scripting engine is within reach
phildini.dev
October 24, 2025 at 8:55 PM
Reposted by Fernando Pérez
cboettig.bsky.social
Really thrilled to see the renewed momentum from @ucbids.bsky.social on open source infrastructure! A new partnership with @2i2c.org puts supporting tools, their developers, and their community at the center. cdss.berkeley.edu/news/berkele...
Berkeley Institute for Data Science partners with 2i2c on open source infrastructure
The Berkeley Institute for Data Science (BIDS) has formally partnered with 2i2c, a nonprofit that provides open source support services with shared digital tools and resources for researchers and educ...
cdss.berkeley.edu
October 23, 2025 at 4:29 AM
Reposted by Fernando Pérez
beninquiring.bsky.social
It’s hard to explain how much George Norlin’s name being on my college’s beloved library means to me.
yellowscenemag.bsky.social yellowscenemag @yellowscenemag.bsky.social · 24d
When CU Boulder’s president George Norlin stood up to the Klan in the 1920s, he risked funding to defend academic freedom.

Nearly a century later, Texas A&M faces its own test and the question remains the same: who has the courage to say no?

yellowscene.com/2025/10/10/w...
What Texas A&M Can Learn From CU Boulder’s Darkest Hour
Texas A&M’s recent controversy echoes a moment in Colorado’s past, when CU Boulder’s George Norlin stood firm for academic freedom.
yellowscene.com
October 21, 2025 at 10:46 PM
Reposted by Fernando Pérez
anildash.com
I don't ever ask this, but if you have a LinkedIn account, I am actually finding some success with the "please try to be normal about AI! Don't listen to the tycoons who are lying to you!" message, so if you're up for amplifying a link, I'd appreciate it: www.linkedin.com/posts/anilda...
The Majority AI View - Anil Dash | Anil Dash | 91 comments
Here's something remarkable: You almost *never* hear the most popular view of AI that the majority of people who work in tech have about technologies like LLMs. By popular request, I've tried to sum u...
www.linkedin.com
October 21, 2025 at 6:43 PM
fernandoperez.org
Interested in a sustainable future for open source communities in research and education?

@kirstiejane.bsky.social @ucbids.bsky.social are hosting @2i2c.org leads @choldgraf.com and Yuvi Panda, w/ Jarrod Millman at the AI Futrues Lab-supported by UC Investments:

events.berkeley.edu/BIDS/event/3...
OSPO Monthly Meetup: Launching the BIDS membership of 2i2c
Join us in shaping the future of open source at UC Berkeley, building on its rich legacy of leadership in open source software development. There w...
events.berkeley.edu
October 16, 2025 at 4:50 PM
fernandoperez.org
The interactive demos that @geostatsguy.bsky.social (Michael Pyrcz, prof @ UT Austin and prolific creator of open educational content) creates are an incredible collection for learning stats/geospatial data with Python, and a great showcase of using @jupyter.org widgets for exploring concepts.
geostatsguy.bsky.social GeostatsGuy @geostatsguy.bsky.social · Dec 21
I’ve spent the past week refining my free e-book, Applied Geostatistics in Python 📚💻

glossary 📖, illustrations 🎨, & descriptions, 32 chapters, downloadable Python workflows 🐍!

My university content in a more accessible format to reach a broader audience 🌍 🚀

geostatsguy.github.io/GeostatsPyDe...
October 15, 2025 at 2:02 AM
Reposted by Fernando Pérez
russpoldrack.org
OpenNeuro @openneuro.bsky.social just hit a huge milestone: 1500 datasets! Congrats to the team on making this project so successful over the last 7 years.
October 13, 2025 at 11:35 PM