iiinova — where your digital self keeps evolving

Justin Westerfield @justmwest.bsky.social · 12/12/2025

How many editorial manager accounts is too many?

Justin Westerfield @justmwest.bsky.social · 08/09/2025

Progress report on my Relion bayesian polishing job on a local computer: ``` + Performing loop over micrographs ... 166.67/166.67 hrs .....................~~(,_,"> + Combining frames for micrographs ... 4.05/122.07 hrs .~~(,_,"> ``` I think it's going well. #CryoEM

030

Justin Westerfield @justmwest.bsky.social · 09/08/2025

Zotero finally has an Android app 🙌

000

Justin Westerfield @justmwest.bsky.social · 12/05/2025

Seems like some of this could be alleviated with a temporary visa given to those awaiting a visa renewal decision. Currently, non-EU citizens cannot leave Sweden while awaiting a decision, because there's no guarantee they would be able to return.

010

Justin Westerfield @justmwest.bsky.social · 12/05/2025

SULF's Doctoral Candidate Assocation warns internationals against starting a PhD Sweden and it seems like most of the complaint is with Migrationsverket, the Swedish Migration Agency. The negative effects of these excessive wait times are starting to pile up. universitetslararen.se/2025/05/08/i...

universitetslararen.se

International PhD students advise against doctoral studies in Sweden - Universitetsläraren

Sweden is no longer an attractive country for international early-career researchers, says the SULF Doctoral Candidate Association in a new report.

100

Justin Westerfield @justmwest.bsky.social · 12/05/2025

The number of postdocs employed in Sweden keeps going up. www.uka.se/om-oss/nyhet...

001

Justin Westerfield @justmwest.bsky.social · 30/04/2025

The program is out for the 2025 Membrane Protein Folding GRS! Applications are open until the end of May. Join us this June in Castelldefels, Spain! 🧪🧬🥼🔬 www.grc.org/membrane-pro...

grc.org

2025 Membrane Protein Folding (GRS) Seminar GRC

The 2025 Gordon Research Seminar on Membrane Protein Folding (GRS) will be held in Castelldefels, Barcelona Spain. Apply today to reserve your spot.

010

Reposted by Justin Westerfield

Katherine Stefanski @kmstefanski.bsky.social · 26/03/2025

Calling all membrane/membrane protein folks! Join us this summer in Barcelona for the Membrane Protein Folding Gordon Conference and Seminar. GRS chaired by @justmwest.bsky.social and myself! We are soliticiting abstracts from trainees for talks! Deadline - April 6. www.grc.org/membrane-pro...

grc.org

2025 Membrane Protein Folding (GRS) Seminar GRC

The 2025 Gordon Research Seminar on Membrane Protein Folding (GRS) will be held in Castelldefels, Barcelona Spain. Apply today to reserve your spot.

344

Justin Westerfield @justmwest.bsky.social · 31/01/2025

Proteins preferentially insert into membranes that have a similar hydrophobic thickness to the protein, even without cells or chaperones! Implies sufficiency of physical properties of membranes and proteins for proper sorting to organelles. Cool paper! 🧪 doi.org/10.1038/s414...

doi.org

Hydrophobic mismatch drives self-organization of designer proteins into synthetic membranes - Nature Communications

The organization of membrane proteins is critical to cellular function. Here the authors explore how computational protein design, MD simulation, and cell-free systems can be combined to elucidate how...

010

Justin Westerfield @justmwest.bsky.social · 28/01/2025

Feels a bit strange to call out preprints specifically, as if preprints constitute some sort of threat. At least there's hope that things will change by Feb 1st.

000

Justin Westerfield @justmwest.bsky.social · 28/01/2025

Oh my. This would have enormous ripple effects throughout research. Like tsunami effects.

000

Justin Westerfield @justmwest.bsky.social · 27/01/2025

It's especially pernicious that getting anything done requires ignoring all the Bad Things in the news, yet that plays directly into the hand of the Bad Things

020

Justin Westerfield @justmwest.bsky.social · 25/01/2025

Or on Mac: Alt+- for en dash (–) Alt+shift+- for em dash (—) On windows it's apparently the same with one caveat—you have to use the '-' on the numeric keypad (haven't tried though)

000

Justin Westerfield @justmwest.bsky.social · 24/01/2025

Very nice work outlining a new method to determine dimerization energies of TMDs in unbiased MD simulations 🧪

010

Justin Westerfield @justmwest.bsky.social · 24/01/2025

My colleague and I are co-chairing the GRS on Membrane Protein Folding this Summer near Barcelona, Spain ⛱️ If you are a grad student or postdoc and work on membrane protein folding, apply! www.grc.org/membrane-pro...

grc.org

2025 Membrane Protein Folding (GRS) Seminar GRC

The 2025 Gordon Research Seminar on Membrane Protein Folding (GRS) will be held in Castelldefels, Barcelona Spain. Apply today to reserve your spot.

020

Justin Westerfield @justmwest.bsky.social · 24/01/2025

(iv) The head of each agency shall include in every contract or grant award: ... (B) A term requiring such counterparty or recipient to certify that it does not operate any programs promoting DEI that violate any applicable Federal anti-discrimination laws. Insane.

141

Justin Westerfield @justmwest.bsky.social · 23/01/2025

I like my lab coats to feel like I'm wearing an armored vehicle but also a snuggie

010

Justin Westerfield @justmwest.bsky.social · 23/01/2025

Is this because of the DEI components of the grants they review? Re: the exec. order for agencies to shut down all DEI activity?

040

Justin Westerfield @justmwest.bsky.social · 22/01/2025

Just learned that one of the most productive scientists I know uses a cardboard box as a reference manager. I'll be over here existentially questioning the value of my neatly curated zotero library.

020

Justin Westerfield @justmwest.bsky.social · 25/11/2024

Does this account for the cost of clearing and smoothing the road? I wonder mountain bikes on natural terrain would fare against fish eFISHency.

000

Justin Westerfield @justmwest.bsky.social · 13/11/2024

Beautiful night in Stockholm 🌃

000

Justin Westerfield @justmwest.bsky.social · 10/11/2024

If anyone knows of starter packs for biochemistry / biophysics, I would love to check them out!

100

Justin Westerfield @justmwest.bsky.social · 08/11/2024

Goodreads has a popular list of books everyone should read. It's 33k books. Reading a book a day, this would take 90 years. Goodreads, this is not a serious list.

000

Justin Westerfield @justmwest.bsky.social · 26/07/2024

Update: found this helpful documentation here In case anyone finds this in the future, you have to turn the iterator into a list to use it more than once :)

000

Justin Westerfield @justmwest.bsky.social · 26/07/2024

Anyone familiar with BioPython? When I read a file with SeqIO, I see strange behavior. If I assign a SeqRecord object to a variable, it is only iterable once. In the code below, the output is nothing, but if I switch the print statement to the first loop it prints fine. What am I missing?

python code showing two for loops, where only the second one should print.

100

Justin Westerfield @justmwest.bsky.social · 25/07/2024

Something tells me they did not, in fact, read my preprint.

Screenshot of email where they refer to a preprint titled ""

000

Justin Westerfield @justmwest.bsky.social · 02/06/2024

Has anyone figured out how to name the individual chains for a job in the #Alphafold3 server? The output of a job with mutliple chains just has them labeled as A, B, C, etc.

010

Justin Westerfield @justmwest.bsky.social · 30/05/2024

I see similar clashes occasionally. Not sure why it happens only sometimes. Out of curiosity, were you using multiple copies of a subunit? This is when it happened for me.

000