The missing link in FAIR data policy: data resources
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...
04.07.2025 10:54 โ ๐ 6 ๐ 5 ๐ฌ 0 ๐ 0
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
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.
04.07.2025 12:06 โ ๐ 62 ๐ 45 ๐ฌ 0 ๐ 3
Congressional Event: A Science Fair of Canceled Grants
The Things Weโll Never Know: A Science Fair of Canceled Grants.
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.
06.07.2025 23:15 โ ๐ 56 ๐ 25 ๐ฌ 0 ๐ 3
Rachel Thomas, PhD - Deep learning gets the glory, deep fact checking gets ignored
an AI researcher going back to school for immunology
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!
06.06.2025 04:49 โ ๐ 11 ๐ 6 ๐ฌ 1 ๐ 1
A large collection of bioinformatics questionโquery pairs over federated knowledge graphs: methodology and applications
Got a #knowledgegraph want some use cases and example queries and how to share them: Read our paper in GigaScience https://academic.oup.com/gigascience/article/doi/10.1093/gigascience/giaf045/8133871?searchresult=1 Join us in #SPARQLing your #SPARQL to improve your #SPARQL ;)
16.05.2025 21:18 โ ๐ 2 ๐ 5 ๐ฌ 0 ๐ 0
Nice! As Metaboverse uses ChEBI, have you considered using Rhea or Rhea annotations from UniProt too?
25.03.2025 10:48 โ ๐ 0 ๐ 0 ๐ฌ 0 ๐ 0
International Workshop on Open Molecular Informatics (IWOMI) โ Getting things done for open science
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
26.02.2025 08:51 โ ๐ 4 ๐ 1 ๐ฌ 0 ๐ 0
[BC]ยฒ 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
11.02.2025 09:01 โ ๐ 20 ๐ 15 ๐ฌ 1 ๐ 1
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. "Physicianโs 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 glucoseโdependent insulinotropic polypepide (GIP) and glucagonโlike peptide (GLP)โ1. GIP acts directly on the endocrine pancreas, bone, fat, gastrointestinal (GI) tract and brain. GLPโ1 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 ฮฑ4ฮฒ7, 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-ฮฑ) 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.
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 https://www.wikipathways.org/download.html
#biology #bioinformatics #openscience
11.02.2025 06:37 โ ๐ 3 ๐ 4 ๐ฌ 0 ๐ 0
'Data representation of small molecules and their application' - Dutch Techcentre for Life Sciences
BioSB HotTopics 2025 Spring meeting 25 March, 12:30, VU auditorium O2, Amsterdam Programme of the day: Registration is free! Please register until 7 March 2025 via this google form
Next BioSB @biosb.bsky.social HotTopics meeting: BioSB HotTopics meeting on Data representation of small molecules and their application March 25 in Amsterdam www.dtls.nl/data-represe... with Daniel Probst @skepteis.bsky.social, Gerard van Westen @gjpvwesten.bsky.social, and Gabriel Vogel
11.02.2025 07:20 โ ๐ 5 ๐ 3 ๐ฌ 0 ๐ 0
UniProt
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...).
07.02.2025 15:47 โ ๐ 2 ๐ 2 ๐ฌ 0 ๐ 0
