Peter Rose

Director, Structural Bioinformatics Laboratory, San Diego Supercomputer Center, UC San Diego

[Peter Rose @peterwrose]

Ten Simple Rules for Reproducible Research in Jupyter Notebook preprint now available: https://t.co/4KZmtvPQkm and example notebooks: https://t.co/eu3Yh689Ar
#jupyter #jupyterproject #mybinderteam #jupytercon

[Peter Rose @peterwrose]

Claude Fable 5: Not So Fabulous (Yet)

Tried Fable 5 for biomedical knowledge graph tasks. Every biology-related request was blocked by safety controls.

Too restrictive for many life-science workflows.

Anyone else seeing this?

#Bioinformatics #BiomedicalAI #AI

[Peter Rose @peterwrose]

Our mcp-genelab AI agent connects AI assistants with the @NASAGeneLab knowledge graph, built from multi-omics spaceflight data, and integrates biomedical context from the SPOKE KG for deeper insights.
https://t.co/cKiM1oGkxo
https://t.co/l6lkBG8VUl #MCP

[The Nobel Prize @NobelPrize]

BREAKING NEWS
The Royal Swedish Academy of Sciences has decided to award the 2024 #NobelPrize in Chemistry with one half to David Baker “for computational protein design” and the other half jointly to Demis Hassabis and John M. Jumper “for protein structure prediction.”

[Mohammed AlQuraishi @MoAlQuraishi]

OpenFold paper is now out in @naturemethods. Timely. I’ll say more about AF3 at the end of this thread, but first I wanted to highlight what’s new since our initial release. (1/9)

[Peter Rose @peterwrose]

@UCSDJacobs @UCSanDiego @theNAEng @KnightLabNews @ucsdbe @ucsd_cse @UCSDMedSchool @UCSDHealthSci @CMIdigest @microsetta @HDSIUCSD @radychildrens Congrats, Rob, well deserved.

[rcsb pdb 💉🧬💻🔬💊🌱🧠🦠 @buildmodels]

Today's the day: PDB no longer has 3-character chemical component IDs for incoming depositions. 1st structure with a 5-character CCD has been deposited.
Details at wwPDB: PDB Entries w/Novel Ligands Now Distributed Only in PDBx/mmCIF & PDBML File Formats
https://t.co/J3n5lItu79

[Rohith Krishna @r_krishna3]

Very excited to share RoseTTAFold All-Atom and RFdiffusion All-Atom, methods for structure prediction and design of biomolecular assemblies! https://t.co/iG6rD0LHsi 1/n

[OpenAI @OpenAI]

ChatGPT can now see, hear, and speak. Rolling out over next two weeks, Plus users will be able to have voice conversations with ChatGPT (iOS & Android) and to include images in conversations (all platforms).
https://t.co/uNZjgbR5Bm

[Peter Rose @peterwrose]

@thesteinegger @ebetica This is called "Normalized Compression Distance" https://t.co/183UsWVi4z

[Peter Rose @peterwrose]

617M Protein model: ESM Metagenomic Atlas: The first view of the ‘dark matter’ of the protein universe https://t.co/e1lIHHvLtG

[Nathan Benaich @nathanbenaich]

LLMs can also learn the language of Covid-19. Here, @BioNTech_Group and @instadeepai built a model to predict high-risk Covid-19 variants far before the WHO designated them as variants. The model ingests viral spike protein sequences and predicts their immune escape and fitness.

[Nathan Benaich @nathanbenaich]

🪩The @stateofai 2022 is live!🪩

In its 5th year, the #stateofai report condenses what you *need* to know in AI research, industry, safety, and politics. This open-access report is our contribution to the AI ecosystem.

Here's my director's cut 🧵:
https://t.co/QtkXZcQpJj

[Peter Rose @peterwrose]

I reached a lifetime climb of 35,000 floors and earned the Satellite badge today with Fitbit! https://t.co/t274vQ1Y0a #Fitstats

[Google DeepMind @GoogleDeepMind]

Today in partnership with @emblebi, we’re releasing predicted structures for nearly all catalogued proteins known to science, which will expand the #AlphaFold database by over 200x - from nearly 1 million to 200+ million structures: https://t.co/GjVES2pBFY 1/

[Peter Rose @peterwrose]

@betatim Here is a benchmark for https://t.co/IwFnTcZfjH:

conda: 5:54 min, 4.2 GB
mamba: 2:24 min, 321 MB

[San Diego Supercomputer Center @SDSC_UCSD]

@MelaxTech & SDSC secure a $300,000 Phase I @NIH #SBIR contract focused on the development and enhancement of innovative user-focused informatic tools for basic and clinical research on infectious, immune and allergic diseases.

Read the full story: https://t.co/QvnGyplPkC

#AI

[Demis Hassabis @demishassabis]

The #AlphaFold database has doubled in size today & now includes more than 800,000 structures. This is just one more step towards releasing 100+ million protein structures over the next year, that will cover almost every sequenced protein known to science!!

[Demis Hassabis @demishassabis]

Proud of our latest work applying AI to Quantum Chemistry published in @ScienceMagazine! The properties of materials largely depend on their electrons. We introduce a new SOTA functional DM21 (open-sourced) that can accurately model many types of molecules https://t.co/sVLKp5TxMW