guillawme - Network

International Women’s Day was yesterday, but I think we shouldn’t limit ourselves to one day per year to celebrate women.In these...

International Women’s Day was yesterday, but I think we shouldn’t limit ourselves to one day per year to celebrate women.

In these troubled times with fascism on the rise almost everywhere, I’d like to celebrate Danuta Danielsson, also known as “The Woman with the Handbag”.
https://en.m.wikipedia.org/wiki/The_Woman_with_the_Handbag

I do not support violence. But I find this picture powerful in showing that ordinary people can decide to not let fascists have their way.

This is the end of this experiment with #Guix and #GuixSystem I really like the ideas behind Guix, and learned a lot by reading its...

This is the end of this experiment with #Guix and #GuixSystem

I really like the ideas behind Guix, and learned a lot by reading its documentation and playing with it. But I will put it back on a shelf for now, because what I need is a system for daily use which gets out of the way. At my current skill level with it, and in its current state, we're not quite there yet.

I'm keeping my configuration files and a fresh installation iso, so I can get going more quickly next time I feel like trying it again.

After a few days of testing, it turns out #FedoraSilverblue is going to fit the bill nicely. It shares some ideas with Guix (immutability, rollbacks, in general better isolation between OS and apps), and everything I need seems to be available and working out of the box.
It's running smoothly on this 10-year old Intel Nuc, so will also be fine on a 10-year old MacBook Pro (with slightly higher specs) whenever I'm ready to make the switch.

This other thread is what prompted me to try and find a more future-proof OS: https://fediscience.org/@Guillawme/113152436757689301

For many years I have enjoyed the feeling of going around all day with a naked wrist, because phones have a clock and I almost always have a...

For many years I have enjoyed the feeling of going around all day with a naked wrist, because phones have a clock and I almost always have a phone with me.

After recently acquiring a watch (a simple analog watch, not a mini computer always online and recording as much data as it can), I still feel a bit awkward with this thing strapped to my wrist. It's not even that big or heavy. But it's there, I feel it, it's weird.

However, a very nice side effect is that I pick up the phone much less often! All these instances when I only needed to check the time and mechanically ended up distracted by some notification waiting for me in ambush? Almost entirely eliminated! Simply by wearing an analog watch. It's making a noticeable difference in my ability to retain focus.

New preprint I contributed to: https://doi.org/10.1101/2025.02.17.638584I helped this group do atomic model building and refinement in their...

New preprint I contributed to: https://doi.org/10.1101/2025.02.17.638584

I helped this group do atomic model building and refinement in their #cryoEM maps.

This was more model building than I had done with all my previous projects combined! And it made me streamline the process I described in this thread: https://fediscience.org/@Guillawme/113281867808537736

@richardsever With the current US administration going after everything scientific and especially biomedical, wouldn't it be a good time...

@richardsever With the current US administration going after everything scientific and especially biomedical, wouldn't it be a good time to establish a European mirror of @biorxivpreprint ? Maybe hosted by the EMBL?

It would be such a huge loss if they managed to shut down #biorxiv...

Just came across this quote by poet Mary Oliver:"Pay attention.Be astonished.Tell about it."I really like it.

Just came across this quote by poet Mary Oliver:

"Pay attention.
Be astonished.
Tell about it."

I really like it.

There are still a few Google services I use occasionally, mostly forced by circumstances.Youtube because sometimes this is the only place...

There are still a few Google services I use occasionally, mostly forced by circumstances.

Youtube because sometimes this is the only place hosting some content of interest (recordings of conference talks, some live music, etc.). But only in a browser with tab isolation and adblocker, otherwise it's completely insufferable (it mostly tries to feed you ads as much as it can).

Google Scholar for the citation alerts. It is useful to know which papers cite mine, it helps keeping up with scientific literature relevant to my work. But I hate that it's impossible to have these alerts without having a public profile. The citation counts are sometimes necessary: academia being what it is, its bureaucracy sometimes asks for these numbers. But we really shouldn't put them on display like Google Scholar does (per Goodhart's law).

#degoogle #ungoogle

Since the first posts in this thread, the US has been quickly descending into fascism. Every day brings crazier news than the previous one,...

Since the first posts in this thread, the US has been quickly descending into fascism. Every day brings crazier news than the previous one, with no sign of it calming down any time soon. American big tech companies are all either totally cool with it or actively supporting...

This is a much bigger reason to adopt alternatives than end of software updates. This makes two strong reasons to seek alternatives.

Luckily, my emails have been hosted in the EU since 2017 when I got a domain name. Almost everyone I write to uses Gmail, so Google still sees everything (email is like postcards anyway). But at least I don't depend on it for something this important (can't live without an email address in this world).

Google Search has been bad for a long time, haven't used it in years. Several decent alternatives exist.

Google's recent nonsense with the Gulf of Mexico on Maps finally nudged me to abandon the services I was still using. No more Google apps on the phone. For real, since it's an iPhone (for now I plan to use it until it fails, since Apple has been less terrible than other US tech companies, and since changing smartphones more often than absolutely necessary is an environmental disaster).

Maps is easily replaced by:
- Organic Maps: https://organicmaps.app
- Magic Earth: https://www.magicearth.com
They are good at different things and complementary.

Translate (very useful for an expat) can be abandoned if DeepL has the languages you need.

#degoogle #ungoogle

First time I have time to play with #Guix and #GuixSystem since the previous post... The spring semester is getting very busy very fast,...

First time I have time to play with #Guix and #GuixSystem since the previous post... The spring semester is getting very busy very fast, leaving little time for this experiment.

Today `guix pull` really made the computer break a sweat, big time. This is telling me that, as cool as Guix is, and as much as I like the ideas it embodies, maybe I am not quite yet ready to make it my main OS. On the other hand, with today's update several CLI apps I was missing are now available. Really cool to see more things entering the package collection!

I still want to contribute some package definitions, but at the current rates at which I learn and guix improves, these might well be contributed by others by the time I figure out how to make them build* or how to send my contributions**.

*: with some I got stuck, see for example https://codeberg.org/guix-science/guix-science/issues/64

**: I wish the main guix channel was on a forge like Codeberg, it would be so much easier to contribute.

Dealing with symmetry in single-particle #cryoEM data analysis can be super interesting, but can also turn into a massive headache......

Dealing with symmetry in single-particle #cryoEM data analysis can be super interesting, but can also turn into a massive headache... 😵‍💫

The micrograph denoiser in CryoSPARC is really good! Fast training and denoising, excellent output (more helpful than topaz denoise; both...

The micrograph denoiser in CryoSPARC is really good! Fast training and denoising, excellent output (more helpful than topaz denoise; both run with their default settings).

Why didn't I start using it earlier??

#CryoEM

Hmm, seems like I can't set up a filter that hides "ICE" (the infamous US government agency doing horrible things on behalf of...

Hmm, seems like I can't set up a filter that hides "ICE" (the infamous US government agency doing horrible things on behalf of its infamous president) without also catching posts about polar and climate science that happen to contain the word "ice" (the solid state of water).

How unfortunate. And it's of course unrealistic to expect everyone to spell out the acronym systematically...

A bit frustrated with #Guix and #GuixSystem lately... Can't get 'emacs --daemon' to work reliably. I have a shepherd user...

A bit frustrated with #Guix and #GuixSystem lately... Can't get 'emacs --daemon' to work reliably. I have a shepherd user service that starts and stops cleanly. But 'emacsclient' can never bring up a graphical window despite being run from a graphical session.

But somewhat surprisingly, setting up a wifi printer was easier than I expected. Seeing the CUPS printer test page made my evening yesterday! (small things, eh?). I still need to move this to the system configuration file, since this initial test was done through the CUPS web interface.
The scanner on this same device worked with zero configuration, over the wifi too. Getting this to work was one of the main potential roadblocks to ditching macOS. I don't scan or print often, but when I need to it's for important things. And it's too inconvenient to scramble to find a scanner/printer at work or at a library, so it's got to work at home.

During the fall semester, I taught a few hours in a course called "Introduction to #biochemistry", taken by master students in a...

During the fall semester, I taught a few hours in a course called "Introduction to #biochemistry", taken by master students in a #Biophysics program. This course is for students with a bachelor in physics, to get them up to speed with biochemistry. It's really tough, they have to absorb in one semester the equivalent of a bachelor in biochemistry.

I gave a lecture on methods to determine the 3D structure of macromolecules. The exam question on this part of the course is pretty gentle (because it's impossible to go in details in one lecture): list the methods seen in class, give a very broad overview of each, give one strength and one weakness for each.

For #cryoEM, both students answered "it's expensive" as a weakness. 😂
Honestly it's a passing answer, it's so true. But funny that this is the one that came to mind first.

They also seem quite confused about #NMR.

So I think these exam results are telling a lot more about the teacher than the students. 🙃

Still convinced the CCPEM Spring Symposium will be fun, but planning the trip is quite a job... trying to make it a loop through Normandy to...

Still convinced the CCPEM Spring Symposium will be fun, but planning the trip is quite a job... trying to make it a loop through Normandy to see family around Easter weekend complicates it a bit.

Also, last time I went to the UK for real (not only in transit through an airport) in 2014 for a CCP4 Study Weekend, it was simply a matter of getting there. Today, one needs an ETA (electronic travel authorization) and the vibes from the UK government website are way too much like the US boarder control... Sigh, what a world we live in... 😔

@khinsen In case you needed one more example of computational non-reproducibility (a discussion started recently, so check back for more...

@khinsen In case you needed one more example of computational non-reproducibility (a discussion started recently, so check back for more answers): https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=CCPEM;d75b9f7b.2501

It's great to *finally* have both a direct work-related reason and enough free time these past two days to immerse myself in the two...

It's great to *finally* have both a direct work-related reason and enough free time these past two days to immerse myself in the two atomic resolution #cryoEM papers from 2020 and give them a good, thorough, cover-to-cover read. 📖 🤓 ❄️ 🔬

Feeling like it's an important step through the never-ending backlog of important papers in this field. 😌

Nakane et al. 2020: https://doi.org/10.1038/s41586-020-2829-0

Yip et al. 2020: https://doi.org/10.1038/s41586-020-2833-4

Lately I've had less free time to play with #Guix and #GuixSystem (no longer on vacation), so I haven't written to this thread....

Lately I've had less free time to play with #Guix and #GuixSystem (no longer on vacation), so I haven't written to this thread. Recent progress is like two steps forward, one back. Still progress.

I made my configuration files public here: https://codeberg.org/Guillawme/guix-config
It's a work in progress. If something is obviously wrong I'd like to know, so don't hesitate to tell me, whoever is reading this.

Thanks to Guix I resurrected my old #Emacs config, and it's been very fun!
I started it in June 2015 while procrastinating on my PhD thesis... which I wrote more efficiently, of course, once I had an Emacs config I liked. 🙃 I abandoned it in 2019 to switch to doom-emacs. Doom never felt like home, it's somebody else's config after all. It also looks too much like an operating system. I quit doom when it started doing native compilation of elisp files by default: each update would make the computer break a sweat. At this point I also had "config burn-out" (not bankruptcy, it was still manageable, but I was tired of it). Some parts of Emacs never worked well on a Mac, which made it frustrating. I settled on helix, which is excellent! I love its approach of "good defaults" and "everything built-in".

Now I realize how much the Emacs experience is better in GuixSystem. Certain things are still a pain to set up (emacs --daemon, anyone?), but I am hopeful that once done it will function forever thanks to Guix.

Model building in high-resolution #cryoEM maps is more fun when it's a protein purified from its native source and nobody knows the...

Model building in high-resolution #cryoEM maps is more fun when it's a protein purified from its native source and nobody knows the correct sequence. 😅

#ModelAngelo to the rescue!

Forgot to post this yesterday, but today is a holiday in Sweden (Epiphany), so it still feels like a #SilentSunday.It finally got cold...

Forgot to post this yesterday, but today is a holiday in Sweden (Epiphany), so it still feels like a #SilentSunday.

It finally got cold enough to freeze the lakes. Beautiful frost seen while walking in the quiet cold air on a sunny day. Wonderful. ❄️ ☀️ 😌

#Frostodon #Icetodon #Snow