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jni, to random
@jni@fosstodon.org avatar

Hey advocates! Ever had the feeling that you wanted to download all of your open science / research software thoughts into a collaborator/grad student's brain, but your regular coffee catchups aren't cutting it??? Just point them to this new from the awesome @madicken!

https://urssi.us/blog/2024/05/20/applications-now-open-for-a-summer-school-in-open-science--research-software-engineering/

I have seen Madicken teach and chair sessions and it's going to be awesome I want to goooooo! 😭😭😭😭

jni, to random
@jni@fosstodon.org avatar

Is there a comprehensive archive, with references, of Elsevier's many sins against scientific progress? @albertcardona @brembs The lead authors of a paper I played a small role in want to submit to Cell 🤢 and I would like to dissuade them.

Follow-up Q: I have a vague vibe that, although the entire traditional publishing system needs to die in a fire, NPG are not quite as scummy as Elsie. Is that vibe justified or not really?

jonny,
@jonny@neuromatch.social avatar

@jni
You know the situation better than anyone else does, ofc, but if that was the choice ya id do what you can to not pay RELX. I dont even know what to say to folks still skeptical of preprints aside from "literally why" so u are on ur own there lol

albertcardona,
@albertcardona@mathstodon.xyz avatar

@jni @brembs

If given the amount of data out there on (and Springer Nature) the authors remain intent on submitting to their journals, there’s not much you can do. At this point throwing data at such authors doesn’t work anymore. Instead, you could try telling them about Robert Maxwell https://www.theguardian.com/science/2017/jun/27/profitable-business-scientific-publishing-bad-for-science , about how journals don’t have to be expensive to be respectable https://archive.blogs.harvard.edu/pamphlet/2012/03/06/an-efficient-journal/ and drop some shade, with comments like “do you think your grant funder will be happy to see the work published there?”. It’s not like they don’t know – they can’t not know –, it’s that they are still calculating impact towards career advancement as a function of journal impact factor. And sadly, for many institutions, they aren’t wrong.

At least try to get them to send to Science or PNAS, which are meant to be societies for scientists rather than an unapologetically exploitative business.

jni, to random
@jni@fosstodon.org avatar

I love the “reveal” at 2:25. 😍
https://fosstodon.org/@napari/112256746427753857

jonny,
@jonny@neuromatch.social avatar

@jni hahaah that rocks. is brian on fedi? cheers to this

jni, to random
@jni@fosstodon.org avatar

“I haven’t been bitten by Google killing an app or service since Google Reader, because I never again trusted them.”

👆 this.

(Also note: I am aware of Gruber’s terrible takes on the EU, and Threads, and a bunch of other stuff. But on this he is spot on. The Google Graveyard is so damaging to Google’s brand, it’s astonishing to me that (a) anyone still uses Google products, and (b) the execs still kill stuff rather than keeping it on life support just for reputation.)
https://mastodon.social/@daringfireball/112204358739653554

OpenAlex,
@OpenAlex@mastodon.social avatar

@albertcardona @ashinonyx Those are things that will be coming soon (claiming author profiles, tighter ORCID integration). In the meantime, we are taking requests for corrections to author data via this form: https://openalex.org/author-change-request

albertcardona,
@albertcardona@mathstodon.xyz avatar

@OpenAlex @ashinonyx

Thank you, that is helpful – except, now I have to collect over 80 IDs manually to redress the overmerged authors problem:

"Which works belong in your profile? Please separate multiple works with a comma"

This is a bit much. All I'd want is be presented with a list and tick the boxes of those that are mine.

jni, to random
@jni@fosstodon.org avatar

The fun thing is that this Sydney Brenner quote is from 2014, and things have gotten even worse in the past decade. 🙃
https://qoto.org/@enroweb/112150171468524351

albertcardona,
@albertcardona@mathstodon.xyz avatar

@jni

“With limited funding, incentivizing ‘promise inflation’ can be harmful to the ‘honest scientists who . . . propos[e] to [make] an important contribution to the solution of an important problem. They risk being dismissed as small-timers with no vision’ ”

https://goodscience.substack.com/p/three-thoughts-on-high-risk-research

jni, to mastodon
@jni@fosstodon.org avatar

One I think underrated aspect of is that links go to where they say they go. Not to t.co/bullshit, not to analytics.twitter.com/ayfkm, not anywhere other than the exact link that was posted. You can right-click -> copy link and get the exact link the author shared. ❤️

jni, to SciPy2024
@jni@fosstodon.org avatar

Ok so @SciPyConf @SciPy2024 call for proposals is open (🥳) at https://cfp.scipy.org/2024/cfp! (See also https://www.scipy2024.scipy.org/#CFP for more info.) This year we have a data viz and image analysis track I'm co-chairing and WE NEED YOU 🫵!

This also means I must finally share the 3D scan of The Claw from last year's @scipy2023 lightning talks! You can download it in DICOM or ome-@zarr format from FigShare at https://dx.doi.org/10.26180/25264588! 😂🦀

image/png

jni,
@jni@fosstodon.org avatar

@SciPyConf @SciPy2024 @scipy2023 @zarr these are the conference Slack posts that threw down the gauntlet claw mitt…

image/png
image/png

matthewfeickert,
@matthewfeickert@fosstodon.org avatar

@jni @SciPyConf @SciPy2024 @scipy2023 @zarr Oh heck yes!

jni, to random
@jni@fosstodon.org avatar

@simon ok I'm finally trying out your llm library and it's neat. I am intentionally limiting myself to open source and local models. Could you write a post about these? Specifically:

  • strengths/weaknesses of each model?
  • strategies for getting around context length limits? I'm currently interested in text summarisation and immediately hit this with mistral-7b-instruct-v0*
  • yes I did ask mistral itself to suggest strategies but they were distressingly manual and brittle/non-generalisable. 😂
simon,
@simon@simonwillison.net avatar

@jni I haven't found a long context model that runs locally yet, but it there are a few I've been meaning to try out using the llm-llama-cpp plugin - https://huggingface.co/TheBloke/Yarn-Mistral-7B-128k-GGUF looks promising

jni, to random
@jni@fosstodon.org avatar

vvCool: new and improved NGFF @zarr support in Fiji, courtesy of @herrsaalfeld and @BogovicJohn:

https://forum.image.sc/t/updated-ngff-support-in-fiji-hdf5-n5-zarr-ome-ngff/91705

Wanna try it out? We just published a small* 3D/3D+t/3D+c+t sample dataset in ome-@zarr** format on FigShare at https://figshare.com/articles/dataset/Data_for_McGovern_et_al_2024_Finding_and_Following_A_deep_learning-based_pipeline_for_tracking_platelets_during_thrombus_formation_in_vivo_and_ex_vivo/25137497 (Jesus sorry for the massive stub didn't know FigShare would use the whole title for the stub 😂)

Want to segment and track it? Check out my 1st PhD student's 1st paper! 👩‍💻🥳 https://www.biorxiv.org/content/10.1101/2023.10.02.560609v2.

*32+GB 😅
**well, we tried, test it out 😅

jni, to random
@jni@fosstodon.org avatar
jni, to random
@jni@fosstodon.org avatar

As we are gearing up for the @napari 0.4.19 release (it's coming!!!), @melissawm has pointed me to Astropy’s “Feature freeze frenzy" playlist to play when preparing a release. Pure gold. 😂

https://open.spotify.com/playlist/21VeY0TTrBIvfGNrRoM1YM?si=4fgJf2fISY6kbt8pTRAXig&pi=u-X1RhjFkERnqA

jni, to random
@jni@fosstodon.org avatar

The @pypi Trusted Publishers mechanism feels like magic. 🧙 Thank you to everyone who worked on it! 🤩 This page is slightly scary re the nitty gritty details but click on the quickstarts: so. Friggin. Simple. ❤️

https://docs.pypi.org/trusted-publishers/

jni, to random
@jni@fosstodon.org avatar

@protonmail wow I have just logged in to my account after briefly playing with it back in 2015, and you guys have come a long way. 😍

I have a couple of Qs:

  1. Is snooze coming to the mobile apps in the near future? I tend to snooze more when on mobile, not less.
  2. Is there an API one could hook into to snooze emails? I basically want to snooze all emails in my inbox to random times in the next three months, so I don't get them all at once again.

Anyway, congrats on all the progress! ❤️🚀

jni,
@jni@fosstodon.org avatar

@protonmail don't have or don't yet have a public-facing API? 😭🙏 I just noticed that you have a Python client so having a snooze API accessible from the Python client would immediately move me to Proton. 😊

protonmail,
@protonmail@mastodon.social avatar

@jni We'll forward your interest in an open API to the team internally, so it can be taken into future consideration.

jni, to random
@jni@fosstodon.org avatar

This is great. I'm not that harsh on people that still post on X — loss is hard to accept. But please just prioritise posting here, even if it feels like you're not getting replies. It's a low-cost way to ensure that we don't give X (or any other corp that doesn't give a shit about us) a monopoly on our thoughts and discussion. Over time, we will build a community here.

https://www.xlast.org/

jni, to Pixelfed
@jni@fosstodon.org avatar

Hi users! My Flickr Pro subscription came up for renewal, and now I know I can do better! 😃 Any tips for choosing a server? I see most servers have a per-photo storage size limit (15MB), but are there limits on bandwidth/total number of photos? Can pixelfed be used for private/semi-private photos ("Anyone with the link can view" kind of situations)?

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