AI In Biology

This is the birth of a new official category within DNA.today, with this exact name – “AI In Biology”. Since this topic is the elephant in the room, and the related posts were squeezing into other categories, following the pressure of the overall excitement related to this new era and its transformational effect on studies… Read More »

Ligand Docking with Rosetta – Mixing Docker and Mac

Summary: The complete, merged tutorial is on my tutorial page: Rosetta – Ligand Docking The Rosetta software suite includes algorithms for computational modeling and analysis of protein structures. I recently wrote a Blog elsewhere titled Rosetta Ligand Docking – Help with Docker as a first approach to helping a student run the published tutorial. The… Read More »

Classic Operating Systems That Run in Web Browser

Finding some old floppy disks I wondered how I could read them. Assuming that I have a floppy reader, how could I then open some of the old file formats? A quick search led me first to the “Mini vMac” site but this option only emulates very old Macs and has the complication that one… Read More »

Single-cell multi-omics using generative AI

Generative pre-trained models are becoming more common by the day, and such methods have now been applied to single cell sequencing, and multi-omits in general. Two main players are “scBERT” and “scGPT”: scGPT: Towards Building a Foundation Model for Single-Cell Multi-omics Using Generative AIHaotian Cui, Chloe Wang, Hassaan Maan, Bo Wang – Nature Methods doi: 10.1038/s41592-024-02201-0 CODE: https://github.com/bowang-lab/scGPT scBERT as a large-scale pretrained deep language… Read More »

Understanding Language Models: GPT-2 squeezed into an Excel spreadsheet

Source: https://arstechnica.com/information-technology/2024/03/once-too-scary-to-release-gpt-2-gets-squeezed-into-an-excel-spreadsheet/ This Blog: Once “too scary” to release, GPT-2 gets squeezed into an Excel spreadsheet OpenAI’s GPT-2 running locally in Microsoft Excel teaches the basics of how LLMs work. by Benj Edwards – 3/15/2024, 3:56 PM Summary by Copilot: (Edited) Ishan Anand, a software developer, has created a Microsoft Excel spreadsheet that runs “GPT-2”… Read More »

How useful is a home-made quantum computer?

These 2 videos are quite cool (in spite of the vocal fry speech) and teach a lot about quantum computing and q-bits in ways that make sense to a non-physicist… Video 1: 25:38 min – I made a (useless) quantum computer at home Video 2: 33:15 min – What can my homemade quantum computer do?… Read More »

Eightify: AI to crate YouTube video summaries

This is available as a plug-in for Chrome or Safari. It is free for videos that are less than 30 min. The plug-in is available at eightify.app Eightify is a cutting-edge program made to assist users in condensing the main points of lengthy YouTube films. It’s now simpler to swiftly create summaries of YouTube videos… Read More »

Generate BibTeX from URL

This is a short version of Do yourself a favor: learn Markdown – Episode 7: BibTeX for online articles Summary: Generate BibTeX from URL for web pages, blogs, articles online, etc. In a previous article (Sgro (2022)) I presented how to add bibliographical information within an Rmarkdown document (Allaire et al. (2023)) with the BibTex format in… Read More »

AI: Introduction to Large Language Models and their shortcomings

This video from November 22, 2023 provides a general introduction to Large Language Models (LLMs) suitable for general understanding. The video continues to examples, possible upcoming paradigms such as the view that LLMs have similarities with operating systems. The final part details potentials threats, including jailbreak examples. What’s wrong with LLMs and what we should… Read More »