simonduerr.eu
Assistant Professor UAS at HES-SO Valais-Wallis 🇨🇠🤗 HF Fellow. Working on AI, Protein Design and Open Science. Creator of bioicons.com
46 posts
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Getting Started
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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...
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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 😅
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No. The other libraries have different names (e.g RCSB Mol*, PDBe Mol*). Mol* = mol* = molstar
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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...
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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...
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If you want to customize this viewer it is much more complicated.
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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.
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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 😔
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Might be related to this: bsky.app/profile/raph...
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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.
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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.
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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...)
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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...
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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.
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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/
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Gifs are the least accessible form of interactive content. The best would be interactive HTML figures.
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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.
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This is a nice primer imho.
livecomsjournal.org/index.php/li...
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Nice tool. I use visidata which reads Json, CSV and other formats and even allows to do basic calculations.
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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?
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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?
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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.
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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?
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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.
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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).
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For CC BY it doesn't matter if I want to reuse the complete figure or just part of it. The license allows me to do both at no cost without a BioRender account for any purpose (republishing same figure in a journal, extracting individual icons etc.) as long as I state the license and modifications.
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Just seeing this on my feed. Did Plos Biology ever look into BioRender being incompatible with CC BY? They say they are now but at the same do not allow reuse in other publications without a paid plan. blog.bioicons.com/post/biorend...
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This was unfortunately out of our hands and the decision of the Neurips Workshop committee. We would have loved to have the workshops on separate days
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Nice! For Input you can simplify things with the gradio_molecule3d conponent: pypi.org/project/grad...
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Yes and actually the copyright is usually retained by the authors for OA. The Journal/publisher legally cannot do anything. CC BY 4.0 also gives you 30 days to fix a violation without incurring a penalty.
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And the tender offer clearly says there is no competition when there is in fact at least one commercial service with pretty much similar offering with mindthegraph.com. Seems illogical that they weren't allowed to compete for an offer.
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Adobe is a tool somewhat in the same domain where one pays for the features (e.g CMYK/color profile support) which make no obligations how work created in the program can be used. No open alternative is available which justifies paying for it using EDU discounts.
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Partly agree. Most of the software features are also available in open software so one is essentially paying for the icon catalog. With this money 5000 illustrations at an average cost of 134$ could be procured from illustrators and made available indefinitely instead of having to pay 600k every 2y.
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Anyone working at MPG willing to share the license conditions ? I'd be curious if they have special terms. For the last contract they didn't. The info should be on this page: soli.mpdl.mpg.de/en/software/...
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I computed the mechanism of HIV-1 RNase H using QM/MM and made this interactive animation dev.simonduerr.eu/hiv/
You could also check time resolved x-ray crystallography. For example this series of crystals on the RNase H mechanism which I guess one could easily morph: www.rcsb.org/structure/6DMV
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Think about it and let me know if you want to change the license to CC BY for BioIcons :) I'm happy to host them there under CC BY SA as well but as stated the preference is for CC BY. People still need to credit you and your illustration will always need to be marked as free ressource under CC BY.
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Here are some more refs explaining why it can be difficult to adapt or to remix works licensed under CC BY SA iastate.pressbooks.pub/oerstarterki...
www.youtube.com/watch?v=Hkz4...
academia.stackexchange.com/questions/11...
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Anyone under a CC BY license requirement (e.g if funded by the above funders) creating teaching material or creating illustrations for a research paper technically cannot use your illustrations. CC BY requirements are becoming more common and nearly every OA paper is published under this license.
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These are great @dorotdesigns.bsky.social ! I'd love to host them on BioIcons. My only concern is that the license is CC BY SA. Many funders mandate CC BY(e.g Wellcome Trust, Gates Foundation, Swiss NSF, Dutch NSF). Is there a reason why you chose SA?
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The funny thing is that many of the papers technically aren't even Open Access because they aren't under CC BY but some more restrictive variant such as CC BY NC
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Use Inkscape for drawing and bioicons.com to find vector illustrations for common items. Free forever 🤩