Sign in

Naupaka Zimmerman

@phytobio.me
2.3K followers 8.9K following 22 posts

Assistant Prof at University of Kansas. Microbial Ecology, Bioinformatics, Environmental Data Science, Open Science, R, emacs. he/him 🌱 🍄 🔬 🧬 📈 👨‍💻

PostsRepliesMedia
Reposted by Naupaka Zimmerman
Jeremy Van Cleve @vancleve.theoretical.bio · 29/09/2026
My group is recruiting a Ph.D student for Fall 2027! We're a friendly group of mathematically-minded and computationally-inspired biologists studying topics including social evolution, host-pathogen interactions, genetics, and demography. See vancleve.theoretical.bio for more info!
vancleve.theoretical.bio
van cleve research group
Van Cleve Research Group – theoretical evolution & ecology at the University of Kentucky
04965
Reposted by Naupaka Zimmerman
Sophien Kamoun @kamounlab.bsky.social · 27/09/2026
I just published: How do we recognize world-class science? Not by the journal it appeared in What I told early-career researchers about prediction, rigour, failure, priors — and the tyranny of bar graphs. kamounlab.medium.com/how-do-we-re...
kamounlab.medium.com
How do we recognize world-class science? Not by the journal it appeared in
What I told early-career researchers about prediction, rigour, failure, priors — and the tyranny of bar graphs.
27638
Reposted by Naupaka Zimmerman
SORTEE @sortee.bsky.social · 17/09/2026
Interested in helping make science a better place? Nominations for 2027 #SORTEE volunteer positions are open now! With 10 committees to choose from and so many ways to get involved, we welcome everyone to volunteer with us! Nominations close 31st Oct. sortee.org/join/ #openscience
01319
Reposted by Naupaka Zimmerman
EUMETSAT @eumetsat.int · 15/09/2026
We have LIFTOFF! 🚀 #Copernicus Sentinel-3C is on its way to orbit having successfully lifted off aboard a Vega C rocket alongside ESA's FLEX mission from Europe’s Spaceport in Kourou! Next milestone: Spacecraft separation in ~1 hour. stay tuned 🛰️
2102
Naupaka Zimmerman @phytobio.me · 15/09/2026
Happy to see this. Will make it much easier to use in classes #rstats posit.co/blog/positro...
posit.co
Positron is now available on Posit Cloud in preview
Since we la
030
Reposted by Naupaka Zimmerman
Lydia Jennings, PhD @1nativesoilnerd.bsky.social · 03/09/2026
Proud of this feature in @nativenewsonline.bsky.social about our recently (as of yesterday!) released Guidelines for the Publishing of Indigenous Data. Check it out!
nativenewsonline.net
Indigenous Scholars Establish Guidelines for Governance of Indigenous Data in Scholarly Publishing
Overview: Indigenous scholars led by Lydia Jennings have developed new guidelines to help ensure Indigenous peoples’ rights, knowledge and data sovereignty are respected in scientific research and sch...
35633
Reposted by Naupaka Zimmerman
Crystal Lewis @cghlewis.bsky.social · 02/09/2026
Why have I been using \\ all these years to escape regex patterns, rather than just wrapping text in fixed()? 😜 #rstats
library(tidyverse)

# A tibble: 5 × 2
  name  pizza_toppings     
  <chr> <chr>              
1 Bear  pepperoni, cheese  
2 Rosie cheese             
3 Frank pepperoni, onion   
4 Rudy  sausage (ground)   
5 Baloo pineapple, with ham

# I want to replace the words in the "select all" variable, with numeric values from a key

codes <- c("pepperoni" = "1", "cheese" = "2", "onion" = "3", "sausage (ground)" = "4", "pineapple, with ham" = "5")

# Can't just replace because of () issue

# A tibble: 5 × 2
  name  pizza_toppings  
  <chr> <chr>           
1 Bear  1, 2            
2 Rosie 2               
3 Frank 1, 3            
4 Rudy  sausage (ground)
5 Baloo 5    

# (01) Using \\ to escape () in sausage (ground)

codes_escape <- c("pepperoni" = "1", "cheese" = "2", "onion" = "3", "sausage \\(ground\\)" = "4", "pineapple, with ham" = "5")

df |> 
	mutate(pizza_toppings = str_replace_all(pizza_toppings, codes_escape))

# (02) Using fixed()

codes <- c("pepperoni" = "1", "cheese" = "2", "onion" = "3", "sausage (ground)" = "4", "pineapple, with ham" = "5")

df |> 
	mutate(pizza_toppings = str_replace_all(pizza_toppings, fixed(codes)))

# A tibble: 5 × 2
  name  pizza_toppings
  <chr> <chr>         
1 Bear  1, 2          
2 Rosie 2             
3 Frank 1, 3          
4 Rudy  4             
5 Baloo 5
4372
Reposted by Naupaka Zimmerman
Moi Expósito-Alonso (MOILAB) @mexpositoalonso.bsky.social · 28/07/2026
The prestigious Miller Research Postdoctoral Fellowship is open! University of California, Berkeley This is a postdoc fellowship with substantial support and independence to be hosted at a lab at Berkeley, reach out with interests! miller.berkeley.edu/nominate-app...
miller.berkeley.edu
Miller Research Fellowship | Miller Institute for Basic Research in Science
04761
Reposted by Naupaka Zimmerman
Jacquelyn Gill @jacquelyngill.bsky.social · 28/07/2026
My alma mater (College of the Atlantic) is hiring faculty in Field Ecology, Agroecology, and Chemistry. If you're looking for a very cool small liberal arts college on the coast of Maine with a strong environmental focus, check it out (happy to answer questions!): www.coa.edu/human-resour...
coa.edu
Career Opportunities | College of the Atlantic
Career opportunities at the College of the Atlantic in Bar Harbor Maine.
47774
Naupaka Zimmerman @phytobio.me · 16/07/2026
Great list! US and many other countries too
020
Reposted by Naupaka Zimmerman
Tiffany Timbers @tiffanytimbers.bsky.social · 11/06/2026
Thrilled to share that @minecr.bsky.social and my paper on Ten simple rules for teaching data science is now available from @plos.org Computational Biology! journals.plos.org/ploscompbiol...
journals.plos.org
Ten simple rules for teaching data science
16724
Naupaka Zimmerman @phytobio.me · 11/06/2026
Congrats!! 🎉 I'll make a note and maybe we can get you up to Lawrence some time for a seminar
000
Reposted by Naupaka Zimmerman
Shelly Gaynor @shellygaynor.bsky.social · 10/06/2026
Just got an alert that views for the Biology PhD Stipends database spiked over the past weekend! Lets keep this database up-to-date, if your program increased their EEB PhD stipend, submit an update: mlgaynor.com/BiologyPhDSt...
mlgaynor.com
Biology PhD Stipends
Biology Ph.D. stipend database with live summaries from the shared Google Sheet.
01918
Reposted by Naupaka Zimmerman
Dr. Carly Kenkel @drcarl.bsky.social · 03/06/2026
The list of Ecology/Evolution/Marine Bio Labs recruiting grad students for Fall 2027 is live! PIs enter your position info here: forms.gle/MAGd4ohyPeoY... students (and PIs not recruiting) share the composite list: docs.google.com/spreadsheets... Please share widely! 🧪
forms.gle
Ecology/Evolution/Marine Biology labs recruiting for Fall 2027
Please complete this form if you are a PI recruiting graduate students for a Fall 2027 start. If you are NOT recruiting, feel free to share the response sheet with prospective students looking for lab...
0115144
Reposted by Naupaka Zimmerman
Dr. Danny Haelewaters 🏳️‍🌈🍄🪰🦇🔬🧬 @dhaelewa.bsky.social · 01/06/2026
Please take the time to review and sign this petition in support of the U.S. National Fungus Collections, which are being threatened in the face of the USDA reorganization efforts. c.org/KQWY7fNhGw 🍄
c.org
Sign the Petition
Preserve and support the U​.​S. National Fungus Collections
03331
Reposted by Naupaka Zimmerman
Botany One @botany.one · 02/06/2026
Asst Professor - Plant or Fungal Genomics // University of Wyoming jobs.chronicle.com/job/37995586... The Department of Botany and the School of Computing invites applications for a tenure-track position in Plant or Fungal Genomics at the rank of Assistant Professor. #BotanyJobs
jobs.chronicle.com
Asst Professor - Plant or Fungal Genomics - Wyoming, United States job with University of Wyoming | 37995586
Asst Professor - Plant or Fungal Genomics Join Our Campus Community! Thank you for your interest in joining the University of Wyoming. Our...
01125
Reposted by Naupaka Zimmerman
Posit @posit.co · 18/05/2026
Looking to connect with Posit folks on Bluesky? 🌐 We've updated our Posit Starter Pack! If you haven't looked at it lately (or are seeing it for the first time), discover and add some incredible data scientists, developers, and team members to your feed. bsky.app/starter-pack...
1307
Reposted by Naupaka Zimmerman
Adam Steinbrenner @adsteinbrenner.bsky.social · 13/05/2026
We hope BAT will help molecular biologists to think in terms of gene trees. Evolutionary signal within gene families is often the first clue that there is amazing, novel biology to be found. Check out our repo and try out BAT analyses of YFGs (Your Favorite Genes!) github.com/steinbrenner...
github.com
GitHub - steinbrennerlab/blast-align-tree: A pipeline to identify BLAST hits and perform phylogenetic analysis across multiple queries and local genome databases
A pipeline to identify BLAST hits and perform phylogenetic analysis across multiple queries and local genome databases - steinbrennerlab/blast-align-tree
1197
Reposted by Naupaka Zimmerman
Jae Young Choi @jychoi.bsky.social · 30/04/2026
I'm looking to hire a postdoc. Please share if you can!
04561
Reposted by Naupaka Zimmerman
David Ho @davidho.bsky.social · 24/04/2026
I’m trying to convince my institution that’s it’s worthwhile to be on Bluesky, so I volunteered to setup an account and posted at @soest.hawaii.edu. Please do me a favor and follow the account, share and like some posts before my meeting to discuss the account tomorrow. @joshuajfriedman.com
33606209
Naupaka Zimmerman @phytobio.me · 22/04/2026
I was an intern at the Forest Service in Hilo when I was in college 20+ years ago. It was that experience that led me to decide to become an ecologist. Ecologists there have been lifelong mentors. Closing this would be incredibly shortsighted and a huge loss to STEM workforce development in Hawai'i.
010
Reposted by Naupaka Zimmerman
David Ho @davidho.bsky.social · 22/04/2026
The Forest Service’s proposed closure of research facilities in Hawaiʻi, including the Institute of Pacific Islands Forestry and a biocontrol lab, threatens years of research on biocontrol agents and disease-resistant ʻōhiʻa strains, impacting efforts to protect Hawaiʻi’s forests and watersheds.
civilbeat.org
Forest Service Cuts Would Devastate Years Of Hawaiʻi Research, Experts Warn
The Forest Service is looking to close its Big Island labs — the only ones of their kind, researchers say, that help protect the Pacific's unique tropical forests.
4236111
Reposted by Naupaka Zimmerman
Noam Ross @noamross.net · 02/02/2026
NSF GRFP applicants (and mentors): Was your application Returned Without Review and deemed ineligible despite fitting in the allowed topics? 1) Write NSF 2) Write your Congressperson 3) CC us at grfp@grant-witness.us so we can compile + follow up Details and template at grant-witness.us/grfp-letter
6165200
Naupaka Zimmerman @phytobio.me · 07/04/2026
I appreciate that all the figure/table cross refs etc are built in instead of having to wrangle bookdown. Means it's a more streamlined experience for complex documents like manuscripts, which is a primary use case for me. Sweave could do all that, but it's easier to read/write markdown vs TeX.
020
Reposted by Naupaka Zimmerman
Timothée Poisot @ctrlalttim.com · 03/04/2026
Every term without a fault an undergrad tells me "I spent 2 hours on this problem and you identified it in under a minute", and every term without a fault I answer "it took me over a decade to identify it in under a minute"
06116
Reposted by Naupaka Zimmerman
Noam Ross @noamross.net · 30/03/2026
For #NSF and #NIH watchers, Grant Witness now has interactive data on numbers of grants and total funding obligations, broken down by institute and directorate, new awards and non-competitive renewals. The stranglehold on new awards is still a disaster. grant-witness.us/funding_curv...
5281154
Naupaka Zimmerman @phytobio.me · 26/03/2026
Congrats Jason!!
110
Reposted by Naupaka Zimmerman
Darren Dahly @statsepi.bsky.social · 18/03/2026
Every day is a good day for sharing one of the most useful papers about research data ever written. PLEASE get your people to understand and follow this advice. www.tandfonline.com/doi/full/10....
Data Organization in Spreadsheets
Karl W. Broman
& Kara H. Woo
Pages 2-10 | Received 01 Jun 2017, Accepted author version posted online: 29 Sep 2017, Published online: 24 Apr 2018

    1. Introduction
    2. Be Consistent
    3. Choose Good Names for Things
    4. Write Dates as YYYY-MM-DD
    5. No Empty Cells
    6. Put Just One Thing in a Cell
    7. Make it a Rectangle
    8. Create a Data Dictionary
    9. No Calculations in the Raw Data Files
    10. Do Not Use Font Color or Highlighting as Data
    11. Make Backups
    12. Use Data Validation to Avoid Errors
    13. Save the Data in Plain Text Files

ABSTRACT

Spreadsheets are widely used software tools for data entry, storage, analysis, and visualization. Focusing on the data entry and storage aspects, this article offers practical recommendations for organizing spreadsheet data to reduce errors and ease later analyses. The basic principles are: be consistent, write dates like YYYY-MM-DD, do not leave any cells empty, put just one thing in a cell, organize the data as a single rectangle (with subjects as rows and variables as columns, and with a single header row), create a data dictionary, do not include calculations in the raw data files, do not use font color or highlighting as data, choose good names for things, make backups, use data validation to avoid data entry errors, and save the data in plain text files.
311050400
Naupaka Zimmerman @phytobio.me · 12/03/2026
I used one of these in 5th grade. Could connect to the state library system! And chat with other students in the class, in the days before AIM and ICQ. Fond memories of this tech.
000
Naupaka Zimmerman @phytobio.me · 04/03/2026
hip hip foray!
010
Naupaka Zimmerman @phytobio.me · 03/03/2026
Good 'ol object of type 'closure' is not subsettable
020
Reposted by Naupaka Zimmerman
Jeremy Berg @jeremymberg.bsky.social · 01/03/2026
NSF Update (Awards through 2/27/26) Directorates to follow 1/10
A line graph showing NSF grant awards made through 2/27/26 for fiscal year 2026 compared with grant awards for fiscal years 2021-2025.
30675445
Reposted by Naupaka Zimmerman
Tiffany Timbers @tiffanytimbers.bsky.social · 04/02/2026
"Ten simple rules for teaching data science": arxiv.org/abs/2602.02874 A new preprint by @minecr.bsky.social and myself. We'd love any feedback!
arxiv.org
Ten simple rules for teaching data science
Teaching data science presents unique challenges and opportunities that cannot be fully addressed by simply borrowing pedagogical strategies from its parent disciplines of statistics and computer scie...
38025
Reposted by Naupaka Zimmerman
johnzobitz.bsky.social @johnzobitz.bsky.social · 01/02/2026
Thanks for the love! This was a bright spot to my day (and unexpected!) @phytobio.me @methodsinecoevol.bsky.social
031
Naupaka Zimmerman @phytobio.me · 16/01/2026
There's some content -- looks like someone is messing with the CSS?
000
Naupaka Zimmerman @phytobio.me · 16/01/2026
It looks like maybe somebody broke the CSS?
100
Reposted by Naupaka Zimmerman
Hadley Wickham @hadley.nz · 06/11/2025
Do you teach #rstats? Do your students complain about how lame and old-fashioned dplyr is? Don't worry: I have the solution for you: github.com/hadley/genzp.... genzplyr is dplyr, but bussin fr fr no cap.
github.com
GitHub - hadley/genzplyr: dplyr but make it bussin fr fr no cap
dplyr but make it bussin fr fr no cap. Contribute to hadley/genzplyr development by creating an account on GitHub.
42460166
Reposted by Naupaka Zimmerman
Sam Mugford @samtmugford.bsky.social · 30/10/2025
When all your PCRs fail, except for the negative control 😱
A pumpkin carved to depict an agarose gel electrophoesis with all lanes blank apart from the size ladder on the left and a single band in the lane on the far right
810923
Naupaka Zimmerman @phytobio.me · 21/10/2025
Yeah this caused quite a bit of consternation yesterday
040
Naupaka Zimmerman @phytobio.me · 21/10/2025
Just announced from @anthropic.com This stuff is moving very fast. www.anthropic.com/news/claude-...
anthropic.com
Claude for Life Sciences
Discover how Claude accelerates life sciences research with new scientific connectors, skills, and improved performance for drug discovery and clinical work.
030
Reposted by Naupaka Zimmerman
Luke Ontario @coolhand.bsky.social · 04/07/2025
I’m going to start doing “wholesome graphic of the day” posts lol. The maps and infographics have been veering political Anyhoo, here’s every apple
assisted.site
Apple Cultivar Genealogy Chart
This image is a comprehensive chart titled 'Apples: A Genealogy of Culinary Cultivars' that maps out the relationships between various apple cultivars. Each apple type is represented by a circle, with...
1832687
Reposted by Naupaka Zimmerman
Patrick Vallely @pjvphotography.bsky.social · 28/08/2025
"Pat, why do you carry that ridiculous 600mm lens on long hikes?" Buddy, I can see mountains reflected in the eyes of a trailside pika.
A pika sits on a mossy rock.Tighter crop of the same pika, focusing on its head.An even tighter crop, focusing more on the pika's eye.An extremely tight crop of the pika's eye, emphasizing their reflection of an early morning mountain scene.
6404367310931
Naupaka Zimmerman @phytobio.me · 10/10/2025
The other issue is the one you've raised as have a few others -- LLMs can be very useful for experts who can catch errors and refine responses, but bootstrapping conceptual expertise when novices start with LLMs on day 1 is going to be a hard pedagogical challenge.
050
Naupaka Zimmerman @phytobio.me · 10/10/2025
We were discussing this issue at the @cu-esiil.bsky.social meeting a few weeks ago. On one hand, LLMs seem like just higher level abstractions, like going from assembly to Fortran to R. On the other, they are probabilistic not deterministic, which makes them different.
130
Reposted by Naupaka Zimmerman
Jason “Obstacle to Progress” Williams @jasonwilliamsny.bsky.social · 25/09/2025
Please share with anyone who cares about NSF support for graduate students and take 30 seconds to sign and leave a comment. The deadline for the 2025 Graduate Research Fellowship Program is about one month away and literally no one can apply. #NSFGRFP jasonjwilliamsny.github.io/grfp2025/
jasonjwilliamsny.github.io
An Open Letter to U.S. STEM Leadership on the NSF Graduate Research Fellowship Program
An Open Letter to U.S. STEM Leadership on the NSF Graduate Research Fellowship Program
12225273
Reposted by Naupaka Zimmerman
Thomas Lin Pedersen @thomasp85.com · 11/09/2025
I am beyond excited to announce that ggplot2 4.0.0 has just landed on CRAN. It's not every day we have a new major #ggplot2 release but it is a fitting 18 year birthday present for the package. Get an overview of the release in this blog post and be on the lookout for more in-depth posts #rstats
tidyverse.org
ggplot2 4.0.0
A new major version of ggplot2 has been released on CRAN. Find out what is new here.
9851281
Reposted by Naupaka Zimmerman
ᐯIᑕTOᖇ ᑎIᘔET, ᗰᗪ @nizet.bsky.social · 15/08/2025
Saddened to learn of the passing of Moselio "Elio" Schaechter—Distinguished Professor at Tufts, SDSU and UCSD—humanist and visionary leader in the fields of microbiology and scientific communication—mentor, friend, and inspiration to me and so many others Small Things Considered Big Things Achieved
112846
Reposted by Naupaka Zimmerman
John M. Drake @jdrakephd.bsky.social · 08/08/2025
I spoke with Kari Jordan and Erin Becker of The Carpentries about why they declined a $1.5M NSF grant intended to expand data science training. Their decision highlights the growing intersection of #science, #DEI, and federal policy. Read the full story on Forbes: www.forbes.com/sites/johndr...
forbes.com
Nonprofit Refuses $1.5M Science Grant Due To New Federal DEI Rules
A coding nonprofit turned down a $1.5M NSF grant after new DEI restrictions, highlighting the clash between federal policy and scientific community values.
02322
Reposted by Naupaka Zimmerman
Jacquelyn Gill @jacquelyngill.bsky.social · 10/08/2025
Do you love alpine plants, ancient DNA, and/or population genetics? My lab will be hiring a postdoc soon to be based at the University of Maine! We’re looking for someone who uses genetic tools and thinks like a community ecologist. Happy to chat at #ESA2025 if you’re interested.
1143103
Reposted by Naupaka Zimmerman
The Carpentries @carpentries.carpentries.org · 19/06/2025
ICYMI: In September 2024, The Carpentries submitted a proposal for 1.5 million USD to the U.S. National Science Foundation (NSF) Pathways to Enable Open-Source Ecosystems (POSE) Program, and were extremely pleased to learn that the proposal was recommended for funding. However...
carpentries.org
Announcing Withdrawal of NSF Pathways to Enable Open-Source Ecosystems Proposal
In September 2024, The Carpentries submitted a proposal to the U.S. National Science Foundation (NSF) Pathways to Enable Open-Source Ecosystems (POSE) Program. This project would position The Carpentr...
12819