iiinova — where your digital self keeps evolving

Fiona Brinkman @fionabrinkman.bsky.social · 11/07/2025

I can’t recommend this IMPACTT microbiome research meeting enough, so note the July 15th abstract deadline. Fantastic meeting. Amazing location. @SydneyMorgan is also one of the best meeting organizers I know. Plus 19 prizes for students/postdocs for this meeting size is also pretty good odds. :)

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Fiona Brinkman @fionabrinkman.bsky.social · 11/07/2025

So humbly honoured to have this recognition. But as we all of know, it really does take a village. This is a tribute to many. It’s important we look wholistically at what enables research innovation. I also invite you to think of all those who support you and be so grateful for them all - as I am.

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Fiona Brinkman @fionabrinkman.bsky.social · 06/06/2025

In part by request, we are moving www.pseudomonas.com and other web-based resources back to being hosted in Canada. This distracts from moving forward with development/updates/research, but we're honouring user needs. Thank you @glwinsor.bsky.social and SFU Research Computing for tireless efforts!

pseudomonas.com

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Fiona Brinkman @fionabrinkman.bsky.social · 31/05/2025

@reactome.org - a leading, carefully curated, human-focused biological pathway database - has made impressive changes. This includes to their new chat bot, with still a focus on quality (have to mention quality is still a focus if anything involving LLMs is noted 😊). Worth checking out.

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Fiona Brinkman @fionabrinkman.bsky.social · 31/05/2025

What’s really cool is that thanks to @xkcd.com I’m now further thinking about how Exceptionally Weird phage-mediated bacterial virulence is, and how it evolved. Art stimulating science. (With thanks to @makemydna.bsky.social for earlier chats and @iddux.bsky.social for encouraging this)

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Fiona Brinkman @fionabrinkman.bsky.social · 13/03/2025

Great to see the inspiring Margaret Dayhoff getting profiled: www.nature.com/articles/s43... I also smiled at her (appropriately) being google's response to the question asked by people "who is the father of bioinformatics" 😊

People ask "who is the father of bioinformatics?" and google's response is Margaret Dayhoff.

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Fiona Brinkman @fionabrinkman.bsky.social · 11/03/2025

Music streaming services like Spotify wonderfully have albums, but older album *sides* are lost. The sides were part of the experience. R.E.M. side names are so fun. Bauhaus "Press the eject and give me the tape out of it" line is the end of an album. Wiki documents sides (TY!). Could Spotify?...

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Fiona Brinkman @fionabrinkman.bsky.social · 02/03/2025

Re the #NIH downtimes (including #NCBI #genbank #pubmed etc) See tldr.nettime.org/@ww/11408997... "Someone is doing networking... Badly..." Really feel for all those dealing with this (from NIH IT, to global users). In general, the decimation of so much critical infrastructure is hard to fathom.

tldr.nettime.org

ww (@ww@tldr.nettime.org)

Attached: 2 images So, three nameservers out of seven for the pubmed.ncbi.nlm.nih.gov are broken. If you try to look at the web site, you stand a 3/7 chance of encountering something that is broken. ...

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Fiona Brinkman @fionabrinkman.bsky.social · 22/02/2025

Re DNA sequence DBs: While sequence is shared across #INSDC databases #ENA #Genbank #DDBJ, the presentation and granularity of annotations/metadata can differ notably, with diff. benefits, impacting searches and downstream analyses. All INSDC databases must be maintained - annotations are important

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Fiona Brinkman @fionabrinkman.bsky.social · 22/02/2025

A brief thread of a personal illustration of the benefits of science, antibiotics, and vaccines over this past century: - I discovered in my twenties that I had an aunt I didn’t know had existed. They had died young, in the 1930’s, of meningitis at age 2 (no antibiotics/vaccines at the time)

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Fiona Brinkman @fionabrinkman.bsky.social · 09/02/2025

Anyone know more re this “ #Starling removal ” to address a flu #H5N1 concern? Are they removing a whole flock? Culling migratory wild birds will have other impacts. I encourage tackling more the root of the problem, knowing it’s challenging (but I need more info) www.cidrap.umn.edu/avian-influe...

cidrap.umn.edu

Avian flu strikes more Nevada dairy herds, leading to starling removal

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Fiona Brinkman @fionabrinkman.bsky.social · 09/02/2025

Funniest email I've received re @pseudomonas.com in over 20 yrs of hosting this DB: "Hello There, Would you be open to get pseudomona com for 500 usd? I noticed that you're the owner of pseudomonas, the plural version, so I believe this could be of interest to you too."

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Fiona Brinkman @fionabrinkman.bsky.social · 02/02/2025

Grateful for @glwinsor.bsky.social and his tireless efforts to maintain this Pseudomonas.com resource for this WHO priority pathogen for over two decades! We encourage any feedback - still accepting responses... bsky.app/profile/pseu...

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Fiona Brinkman @fionabrinkman.bsky.social · 08/12/2024

Check out this soap made by my fantastic #SFU colleague @minisciencegirl.bsky.social. She said she was not happy with her streak plating, 😂 but I think it’s awesome. #microsky #IDsky #microbiology #sciart

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Fiona Brinkman @fionabrinkman.bsky.social · 08/12/2024

I discovered this outhouse I walk by in the day on a trail near SFU has a motion-activated floodlight at night - even though the outhouse is always LOCKED at DUSK. Why??!

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Fiona Brinkman @fionabrinkman.bsky.social · 28/11/2024

This is really niche, but @makemydna.bsky.social from our group made this wee app “SMDP: SARS-CoV-2 Mutation Distribution Profiler” tinyurl.com/smdpapp so #SARSCoV2 #variant #trackers can quickly check unusual #Lineages (mutation distributions likely due to mulnupiravir use, chronic infection etc?)

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Reposted by Fiona Brinkman

Laura Hug @lhug.bsky.social · 02/08/2024

Eight years later, I revisit the tree of life. “Future trees may need to distinguish not only between cultured and uncultured lineages, but between extant and extinct” rdcu.be/dPNpB

rdcu.be

The ever-changing tree of life

Nature Microbiology - The tree of life is a galvanizing image, anchoring biological diversity within a common framework. From a new view in 2016, the tree has continued to grow, and with it, our...

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Fiona Brinkman @fionabrinkman.bsky.social · 24/11/2024

Science is amazing - we are always learning. Learned this week that some bacteria (Corynebacterium matruchotii) can divide into as many as 14 cells at once, and some wolves may aid pollination? There's so much we still don't know. tinyurl.com/3wtvp6xd tinyurl.com/5n74b353

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Fiona Brinkman @fionabrinkman.bsky.social · 23/11/2024

Love that this study of microbiome transmission and social interactions involves communities with low antimicrobial (antibiotic) use. Would be great to compare with communities more impacted by such drugs, to appreciate antibiotic impact. bsky.app/profile/fbeg...

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Reposted by Fiona Brinkman

Dr. Dawn Bowdish @msmacrophage.bsky.social · 22/11/2024

I spoke to the CBC Radio about a large measles outbreak in New Brunswick - article link below. I cannot stress enough how serious an infection measles is - recycling an op-ed I wrote on the topic(see link on my webpage for explainer video). www.cbc.ca/news/canada/... www.bowdish.ca/lab/2024/03/...

Image of a Globe & Mail op-ed on measles. For an accessible read see http://www.bowdish.ca/lab/2024/03/07/measles-is-not-a-harmless-childhood-infection-dr-bowdish-explains/

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Fiona Brinkman @fionabrinkman.bsky.social · 23/11/2024

So when I messaged a lab member about the Dev version of one of our database resources, my device kept autocorrecting Dev to Dave. So we've decided just to call it Dave.

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Fiona Brinkman @fionabrinkman.bsky.social · 20/11/2024

California reporting a possible bird flu case in a child. Mild upper respiratory symptoms and "also positive for respiratory viruses." "No known contact with an infected animal", but "investigating a possible exposure to wild birds." Family tested negative. www.cdph.ca.gov/Programs/OPA...

cdph.ca.gov

California Department of Public Health

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Fiona Brinkman @fionabrinkman.bsky.social · 19/11/2024

At this key time, I encourage you to add your name to this letter campaign, affirming the critical importance of sustaining the world’s biodata resources. globalbiodata.org/open-letter-...

globalbiodata.org

OPEN LETTER CAMPAIGN - Global Biodata Coalition

Careers at the Global Biodata Coalition.

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Fiona Brinkman @fionabrinkman.bsky.social · 18/11/2024

After the 1st ever report of #H5N1 in Hawaii last week (notable thanks to wastewater surveillance for initial detection), it turns out there’s an infected flock on Oahu. Hope this can get controlled, as Hawaiian wildlife were so beautifully protected before. health.hawaii.gov/docd/disease...

health.hawaii.gov

Avian Influenza | Disease Outbreak Control Division

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Fiona Brinkman @fionabrinkman.bsky.social · 17/11/2024

Flu note: These mutations showing up in this first-in-Canada Influenza H5N1 case in a teen are indeed not good news, and this is a great analysis, but note that to date there has been no evidence of onward transmission from this case to others. Still, monitoring is key. bsky.app/profile/scot...

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Fiona Brinkman @fionabrinkman.bsky.social · 12/11/2024

I'll add this here: HOPE is "an account of complexities and uncertainties, with openings.” - Rebecca Solnit (heard during a stellar Climate Change talk by Sarah Burch)

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Fiona Brinkman @fionabrinkman.bsky.social · 12/11/2024

Note @theo.io's nice tool to "find people followed by lots of the people you follow (but not you)". There are caveats (finding "big accounts" etc), and this type of tool will likely evolve, but it is helpful - I will look over the list it generated more... bsky.app/profile/theo...

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Fiona Brinkman @fionabrinkman.bsky.social · 12/11/2024

OK, I'm jumping back in to the blue! As millions have already said, its great to see more people on here. :) Now if I could just figure out how to search by keyword, but limited only to those I follow... Seems that isn't implemented (yet?)

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Fiona Brinkman @fionabrinkman.bsky.social · 06/10/2023

HUGE THANKS to @glwinsor.bsky.social for leading Pseudomonas.com development for - I can't believe it - 20 years! 🎉 Thank you Geoff for all you've done, and continue to do, for multiple projects. Keen to see your current amazing research get out too!

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Reposted by Fiona Brinkman

David Coil @davidacoil.bsky.social · 30/09/2023

A reminder for all the new science folks here on Bluesky... the default setting is to only show replies that have at least two likes. You can change this in your settings and the conversations will seem less fragmented.

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Fiona Brinkman @fionabrinkman.bsky.social · 28/09/2023

Keen to check out Foldtree - trees based on protein structures! Lots of further development likely in this area - both tree methods and insights into protein evolution… www.biorxiv.org/content/10.1...

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Reposted by Fiona Brinkman

Michelle Wille @duckswabber.bsky.social · 25/09/2023

In only a few months H5N1 killed >100,000 birds of 24 different species in protected areas of Peru, with hug eimpacts on boobies, cormorants and pelicans. Virus has severely affected bird populations and the ecosystem services they provide. sciencedirect.com/science/arti...

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Reposted by Fiona Brinkman

Ryan Morin 🇨🇦 @morinryan.bsky.social · 23/09/2023

I made another simple Shiny app that uses Google Scholar instead of PubMed. This one can generate clouds based on words in publication titles and can summarize where you publish. Thanks for the helpful suggestions! shiny.rcg.sfu.ca/u/rdmorin/sc...

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Fiona Brinkman @fionabrinkman.bsky.social · 23/09/2023

Best functional characterization this week: An Adorable mutation! 😊 www.nature.com/articles/s41...

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Reposted by Fiona Brinkman

Ryan Morin 🇨🇦 @morinryan.bsky.social · 21/09/2023

I whipped up a basic Shiny app (using the PubMedWordCloud R package) to generate word cloud summaries of any researcher based on their abstracts in PubMed. Here's mine! The app is available here: shiny.rcg.sfu.ca/u/rdmorin/pu...

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Fiona Brinkman @fionabrinkman.bsky.social · 22/09/2023

This is fun. Thanks @morinryan.bsky.social for making this wee Shiny app to make a word cloud from a researchers PubMed abstracts. Not surprised by the words that show up for my cloud, with the one microbe sneaking in there being Pseudomonas 😁

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Fiona Brinkman @fionabrinkman.bsky.social · 21/09/2023

At a meeting with hospitals/public health, hearing too often that their databases are “clunky” (data entry issues). Best quote: “The only reasons fax machines still exist is because of our healthcare system.”

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Fiona Brinkman @fionabrinkman.bsky.social · 21/09/2023

Did you know “duotang” is a genericized term in Canada? 😊https://en.m.wikipedia.org/wiki/Duo-Tang We therefore thought it’d be a good name for our collection/notebook of open analyses of Canadian viral data (currently expanding to other pathogens). covarr-net.github.io/duotang/duot...

covarr-net.github.io

CAMEO - Duotang

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Fiona Brinkman @fionabrinkman.bsky.social · 21/09/2023

I strongly support open microbial data & tools, but thanks to OCAP Training I keep finding situations where community partnership is key to avoid unwitting harm and translate to positive policy community change. Great course to think about holistic issues around data sharing. fnigc.ca/ocap-training/

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Reposted by Fiona Brinkman

Finlay Maguire @finlaym.bsky.social · 14/09/2023

Day 2 #GMI13 starts with Indigenous Data Governance Principles and Data Sharing Experiences. Taylor Morriseau (FNHS MB) explains centrality of OCAP principles (fnigc.ca/ocap-training/), specific FN benefits+principles (not pan-indigenous), free+prior informed consent. Emphasises Inclusion != Equity

fnigc.ca

The First Nations Principles of OCAP® - The First Nations Information Governance Centre

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Fiona Brinkman @fionabrinkman.bsky.social · 14/09/2023

At the awesome #GMI13 (Global Microbial Identifier) meeting today gmi13.org/program/. Big Kudos to Ruth Timme who noted planning an October Hackathon-style "Metadata Cleanup Challenge" of old GenomeTrakr records. Not trivial! Emma Griffith made the good point to document the process/what's learned

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Fiona Brinkman @fionabrinkman.bsky.social · 14/09/2023

Hello World! Is this going to be like early twitter was? Or (to really date myself) early dialup BBS's? Here's to hoping, and great to see a bunch of you here!

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