iiinova — where your digital self keeps evolving

Reposted by Rhea knowledgebase

Ricardo D. Righetto @lifeonthewedge.bsky.social · 19/03/2026

Meet Stoic from @daniil-litvinov.bsky.social and @ninjani.bsky.social: embeddings to predict stoichiometry of protein complexes from sequence fast and accurately 🧬🧩💻🤩 www.biorxiv.org/content/10.6...

Stoic: Fast and accurate protein stoichiometry prediction (preprint header with authors and affiliations)

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Rhea knowledgebase @rhea-db.bsky.social · 30/01/2026

The first release of 2026 of the Rhea database is out! Release 140 (2026-01-28) contains 18,343 unique reactions and 15,125 unique reaction participants, with 25M protein sequence entries annotated with Rhea reactions in UniProtKB.

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Marc Robinson-Rechavi @marcrr.bsky.social · 04/07/2025

Very nice preprint on the importance of #FAIR data resources in the life sciences, for AI and generally for science, by a great @sib.swiss team led by @dessimoz.bsky.social. With @bgee.org inside ;) zenodo.org/records/1572...

zenodo.org

The missing link in FAIR data policy: data resources

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Alexey Amunts @amunts.bsky.social · 04/07/2025

Speak up to prevent a major loss for the field. CASP, which helped shaping structural biology including AlphaFold is on the verge of shutting down. NIH funding has lapsed, UC Davis support ends and the core team is being let go. Painfully shortsighted.

science.org

Exclusive: Famed protein structure competition nears end as NIH grant money runs out

Agency silent on funding renewal for contest that inspired creation of AIs that predicted how proteins would fold

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Dr. Rabbithole @drrabbithole.bsky.social · 07/07/2025

A science fair of cancelled grants. The research that will be represented at this event (Tuesday) ranges from neuroscience, to astrophysics, to STEM education. The awarding agencies of the now-canceled grants include the EPA, DHS, NIH, NSF, USAID, and DOD. Open to the public.

nasawatch.com

Congressional Event: A Science Fair of Canceled Grants

The Things We’ll Never Know: A Science Fair of Canceled Grants.

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Chris Mungall @cmungall.bsky.social · 06/06/2025

This is a must-read piece by @math-rachel.bsky.social about AI evaluation, and how the system of reward and apportioning credit in AI research is broken rachel.fast.ai/posts/2025-0.... TL;DR -- we need deep fact checkers!

rachel.fast.ai

Rachel Thomas, PhD - Deep learning gets the glory, deep fact checking gets ignored

an AI researcher going back to school for immunology

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Christoph Steinbeck @csteinbeck.bsky.social · 26/02/2025

This year's International Workshop on Open Molecular Informatics (IWOMI) (12.-16.05.25) will focus on the curation of open molecular data using multimodal large language models (LLM). If you are interested, please register at www.iwomi.net

iwomi.net

International Workshop on Open Molecular Informatics (IWOMI) – Getting things done for open science

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SIB Swiss Institute of Bioinformatics @sib.swiss · 11/02/2025

[BC]² Basel Computational Biology Conference 2025 will take place on 8-10 September. The conference brings together over 500 international scientists from academia, industry, and healthcare to explore advancements at the intersection of #bioinformatics and artificial intelligence. See bc2.ch

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WikiPathways @wikipathways.fosstodon.org.ap.brid.gy · 11/02/2025

Februari 2025 WikiPathways update: 313 edits by 10 contributors and 4 new pathways in the last month. Accessible via #webservices, #rstats, Pathvisio, and Cytoscape. Supported by AWSOpen www.wikipathways.org/download.html #biology #bioinformatics #openscience

New pathway "Mitochondrial carrier deficiency associated with shuttle disturbances (WP5507)" https://www.wikipathways.org/pathways/WP5507

"Reflecting the pathway as shown in Figure 43.2 of Blau et al. "Physician’s guide to the diagnosis, treatment, and follow-up of inherited metabolic diseases"

New pathway "GIP and GLP-1 function by tissue (WP5509)" https://www.wikipathways.org/pathways/WP5509

"Functions of GIP and GLP-1, two agonists of which are found in the weight-loss drug tirzepatide (a.k.a. Mounjaro). "Pancreatic and exopancreatic function of glucose‐dependent insulinotropic polypepide (GIP) and glucagon‐like peptide (GLP)‐1. GIP acts directly on the endocrine pancreas, bone, fat, gastrointestinal (GI) tract and brain. GLP‐1 acts directly on the endocrine pancreas, gastrointestinal tract, heart and brain." From Figure 2 in https://pmc.ncbi.nlm.nih.gov/articles/PMC4020673/."

New pathway: "Vedolizumab therapy for irritable bowel syndrome (WP5512)" https://www.wikipathways.org/pathways/WP5512

"Vedolizumab is a humanized monoclonal antibody with a predominantly gastrointestinal effect. It specifically inhibits leucocyte integrin α4β7, thus preventing its interaction with mucosal vascular addressin cell adhesion molecule 1 (MAdCAM-1), which is involved in the migration of lymphocytes from the blood stream to the intestinal tissue. Vedolizumab is indicated in the treatment of moderate to severe active Crohn's disease and ulcerative colitis in adult patients with poor response, loss of response, or intolerance to conventional treatment or to tumour necrosis factor alpha (TNF-α) antagonists." Inspired by Figure 1 in https://pubmed.ncbi.nlm.nih.gov/31470005/. Vedolizumab is also known by its trade name, Entyvio.

New pathway: "NSAIDs mechanism of action (WP5513)" https://www.wikipathways.org/pathways/WP5513

"Nonsteroidal anti-inflammatory drugs (NSAIDs) inhibit the cyclooxygenase isoenzymes COX1 and COX2 with varying degrees of specificity for the COX2 isoform. As a result, the conversion of arachidonic acid to prostaglandins (PGs) is inhibited. The main effects of PGs throughout the body are listed." Inspired by Figure 1 in PMID:32322101.

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Rhea knowledgebase @rhea-db.bsky.social · 07/02/2025

Out now, release 137 of Rhea featuring 17,422 reactions and 14,335 unique compounds from 18,284 publications. Rhea is used to annotate over 28 million proteins in UniProt (see www.uniprot.org/uniprotkb?qu...).

uniprot.org

UniProt

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