Tootfinder

kegg_metabolic: Metabolic networks from KEGG (2006)
109 metabolic networks of various species, as extracted from the Kyoto Encyclopedia of Genes and Genomes (KEGG) database in March 2006. Nodes are substances involved in enzymatic reactions present in the organism, and edges represent reactant-product pairs as extracted from the KEGG ligand database and matched against the present enzymes.
This network has 754 nodes and 1748 edges.
Tags: Biological, Metabolic, Unweighted

Add richer tooltips to ggiraph with kableExtra and friends: #dataviz …

TumorHoPe2: An updated database for Tumor Homing Peptides
Diksha Kashyap, Devanshi Gupta, Naman Kumar Mehta, Gajendra P. S. Raghava
https://arxiv.org/abs/2505.20913

TumorHoPe2: An updated database for Tumor Homing Peptides
Addressing the growing need for organized data on tumor homing peptides (THPs), we present TumorHoPe2, a manually curated database offering extensive details on experimentally validated THPs. This represents a significant update to TumorHoPe, originally developed by our group in 2012. TumorHoPe2 now contains 1847 entries, representing 1297 unique tumor homing peptides, a substantial expansion from the 744 entries in its predecessor. For each peptide, the database provides critical information, …

"Vibe coding" is one of the dumbest ideas that I've heard in a long time.
Yes, there are often reasons to use tools (such as Knuth's books) to lookup methods. And well established and tested libraries are great. (Thank you "numpy".)
But "vibe coding" just turns programmers into little more than proofreaders - proofreading complex and often boring material. That is putting the cart before the horse. (Is there a modern phrase for that adage?…

An AI-powered coding tool wiped out a software company’s database, then apologized for a ‘catastrophic failure on my part’
An experiment with an AI coding tool took a disastrous turn when an AI agent reportedly deleted a live company database during an active code freeze.

Text2Cypher Across Languages: Evaluating Foundational Models Beyond English
Makbule Gulcin Ozsoy, William Tai
https://arxiv.org/abs/2506.21445 https://

Text2Cypher Across Languages: Evaluating Foundational Models Beyond English
Recent advances in large language models have enabled natural language interfaces that translate user questions into database queries, such as Text2SQL, Text2SPARQL, and Text2Cypher. While these interfaces enhance database accessibility, most research today focuses solely on English, with limited evaluation in other languages. This paper investigates the performance of foundational LLMs on the Text2Cypher task across multiple languages. We create and release a multilingual test set by translati…

«Komoot’s core tech of Leaflet map, Graphhopper routing engine, and #OpenStreetMap data are all free, open-source projects. This is in addition to all the open-source web servers, databases, and operating systems that tech companies build upon. They leech off the open-source commons»
I'm convinced that this is one of the big reasons why we need some form of @… sooner rather than later, to ensure our commons can be saved from corp capture.

"Vibe Coding Fiasco: AI Agent Goes Rogue, Deletes Company's Entire Databas"
#karma

The State of Papers, Retractions, and Preprints: Evidence from the CrossRef Database (2004-2024)
Khalid M. Saqr
https://arxiv.org/abs/2506.21232 https://…

The State of Papers, Retractions, and Preprints: Evidence from the CrossRef Database (2004-2024)
A 20-year analysis of CrossRef metadata demonstrates that global scholarly output -- encompassing publications, retractions, and preprints -- exhibits strikingly inertial growth, well-described by exponential, quadratic, and logistic models with nearly indistinguishable goodness-of-fit. Retraction dynamics, in particular, remain stable and minimally affected by the COVID-19 shock, which contributed less than 1% to total notices. Since 2004, publications doubled every 9.8 years, retractions ever…

The recording of my @… presentation "All the DataOps, all the paradigms" is now online. I have observed that most teams are not aware of differences between data processing paradigms and their practical consequences, so I tried to contribute some order and structure. As usual, I tried to squeeze in too much and rambled, but I hope that it i…

ChatGPT on what is known about chronic phosphene stimulation and use of short current return paths #BCI

ChatGPT - Pferd auf Astronauten Missverständnis
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