Julian's Polymath Explorations

NOTE:  this entry was inspired by talks I gave at the "Bio-IT World 2025" conference in Boston, and at the "Aging & Gerontology 2025" conference in San Francisco.   A VIDEO VERSION also exists    (slightly shorter and outdated to Apr. 2025)    Life123 is an open-source platform for quantitative interactomics, aiming towards simulations of virtual biological cells or parts thereof – among other things. And it has a slogan:  AI and Big Data aren't enough! We also need Dynamical modeling. What does it mean to say "engine for quantitative reactomics"?  It means that we perform dynamical modeling of biological systems. And the initial focus is towards eventually creating whole-cell simulations. The platform consists of python libraries, which allow us to do in-silico experiments. Early this year, this project left the beta stage, after a few years of development. Motivation There's a practical motiva...

(UPDATED 8/2022) - Are we ready to embark on a next-generation detailed quantitative modeling of complex biological systems , including whole-cell simulations?  An anticipated up-jump in computing power may be imminent from Photonics computers (which I discuss here ), and GPU's are rapidly gaining power as well...  Are we in ready state to put existing - and upcoming - power to good use? This is a manifest, and a call to action What's Life123? It's about detailed quantitative modeling of biological systems in 1-D, 2-D and full 3-D, as well as a multi-faceted software platform for doing so. What's (pseudo-)1D?  For now, let's say it's like the inside of a long, thin tube - with no interactions with the tube.  Likewise, (pseudo-)2D can be thought of as a Petri dish, with no interactions with the lid or the bottom. Website : https://life123.science A purposeful decision to also utilize 1D and 2D But why?  Yes, it's in part about "walk before you run...

[Updated Mar. 2022] Interactomics today bears a certain resemblance to genomics in the  1990s...  Big gaps in knowledge, but an explosively-growing field of great promise. If you're unfamiliar with the terms, genomics is about deciphering the gene sequence of an organism, while interactomics is about describing all the relevant bio-molecules and their web of interactions. A Detective Story Think of a good police-detective story; typically there is a multitude of characters, and an impossible-to-remember number of relationships: A hates B, who loves C, who had a crush on D, who always steers clear of E, who was best friends with A until D arrived... Yes, just like those detective stories, things get very complex with our biological story!  Examples of webs of interactions, familiar to many who took intro biology, are the Krebs cycle for metabolism or the Calvin cycle to fix carbon into sugars in plant photosynthesis. Now, imagine vastly expanding those cyc...