Simon Dürr

Stay tuned for details on the 6th edition of MLSB, officially happening this December in downtown San Diego, CA!

Unfortunately, the MLSB Workshop @ NeurIPS (@workshopmlsb.bsky.social) was rejected this year.

Feedback from the deciding committee indicates it was a coin flip decision, with 283 proposals & a number related to “computational biology”

More on the future of MLSB soon…

Exactly. Also for some countries like Germany where people have been complaining about the conditions for research for years (people finishing their thesis with unemployment money and other shenanigans) it's kinda a slap in the face that suddenly there is money to bring in new hires...

Not as pretty but this should give you a vector you can tune easily in a similar way with reduced color complexity (might be a bit slow for large proteins in contour mode) bioicons.com/pdb2vector/ And uses less CO2 😅

No. The other libraries have different names (e.g RCSB Mol*, PDBe Mol*). Mol* = mol* = molstar

Google Colab

It would be nice if molviewspec would support trajectories because you could easily set up your scene from python and then just use an iframe viewer. colab.research.google.com/drive/1O2Tld...

But seems only pdb/cif and map data so far: molstar.org/mol-view-spe...

The problem is that there are various libraries packaging mol* into various viewers. I don't think the PDBe one supports xtc files, Mol* supports it though. Here is an example using native mol* taken from the quarto-molstar package.

plnkr.co/edit/TjTgopo...

If you want to customize this viewer it is much more complicated.

The various flavours of Mol* should be pretty easy to integrate but can be a bit more tricky if you use SSR in a modern webstack. Example: embed.plnkr.co/plunk/eMPsfu... You need to convert the trajectory into e.g a PDB trajectory. Try with a NMR structure like 3GB1.

Yes but it requires a certain level of understanding of copyright. So many papers that don't even acknowledge 3rd party material properly... I'm looking for funding to build a fully CC0 db to make this easier... currently we spend ~10-20 Mio $ annually on BioRender globally 😔

CC BY is great but also requires that we replace some of our tools. Many currently published CC BY papers are actually not fully CC BY because of BioRender www.chemistryworld.com/news/thousan...

Might be related to this: bsky.app/profile/raph...

Installation and running it was a breeze 🤗 Diversity of the generated structures is quite good. Quality is a bit hit and miss. Most samples at default params have at least one or two weird C-N peptide bonds >1.6A/<1.1A and also had a few (<0.5%) samples with quite severe clashes.

Yes that's true but afaik ZeroGPU might get Docker support as well (although I think there is no timeline). You can also ask them for the old community GPU grant which works with generic docker images but has different set of limitations especially for high traffic applications.

Docker Spaces We’re on a journey to advance and democratize artificial intelligence through open source and open science.

One can build quite complex interfaces with gr.Blocks() in my opinion. Are you using Blocks? Blocks works basically like flexbox layouts. HF spaces also supports generic Docker containers (just expose a port and you use anything you like huggingface.co/docs/hub/spa...)

In earlier work, we already analyzed how AllMetal3D given a structural input and no information about metal stoichiometry fares against co-folding methods given metal stoichiometry but no structure: doi.org/10.1101/2024...

We compared to a few other tools that perform either metal identity prediction or location prediction and found that is very important to include negative classes during training and also cluster metal ions by biological similarity.

ChimeraX preview

We've made available a ChimeraX extension and a Webapp to easily run predictions. AllMetal3D is now also easily installable using pip.

ChimeraX: cxtoolshed.rbvi.ucsf.edu/apps/chimera...

HuggingFace: huggingface.co/spaces/simon...

Docs for Python Package:
lcbc-epfl.github.io/allmetal3d/

Performance of AllMetal3D vs. Metal3d.

Excited to share our new AllMetal3D model building on Metal3D. AllMetal3D predicts the location, identity and geometry of the major biologically relevant metal ions doi.org/10.1101/2025...

It’s been a tough few weeks. My 10yo daughter was diagnosed with a very rare, aggressive cancer called interdigitating dendritic cell sarcoma (IDCS). I’m reaching out to identify clinicians/patients who have encountered pediatric IDCS or other (non-LCH) dendritic or histiocytic sarcomas cases.

Gifs are the least accessible form of interactive content. The best would be interactive HTML figures.

I've seen cases with open code for the webserver without the actual model or method used for the research published as well ... Code review should be part of peer review.

This is a nice primer imho.
livecomsjournal.org/index.php/li...

Nice tool. I use visidata which reads Json, CSV and other formats and even allows to do basic calculations.

Good for you, the people who published these articles did as well. Nevertheless, the company says the people who paid them for a license violated their copyright and need to correct their article when I asked for reusing it under the stated license. Is that open science for you?

I asked BioRender about reusing illustrations from a CC BY article some time ago and they told me the license of the article is not correct and a correction will have to be issued. Do you want to track down all authors to correct all 153 articles in PloS Biology that make use of BioRender?

Totally, I have been building bioicons.com since a few years. However, more funding for truly open science illustrations will not happen if stakeholders like journals continue to believe BioRender's ridiculous attempts to salvage their business model.

Why does PLOS enforce CC BY for all 3rd party content if not to allow reuse in other journals without filling permission forms or hidden copyright complexities?

Also BioRender's new "CC BY" license requires that users put a specific link where above conditions are displayed because they have to explain that they differ from standard CC BY. (CC BY doesn't allow modification of the conditions). This is not the case for this PLOS article.

In the fictional universe of the BioRender lawyers they can claim they are compatible with CC BY but fact is the figures created in BioRender cannot be reused under CC BY because they say one needs a paid account which is against the CC BY terms (compare BioRender vs. @creativecommons.bsky.social).