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Life123 : Quantitative Modeling of Biological Systems

(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&quo
Recent posts

A "Seismic Shift" in Longevity Science : Mainstream Acceptance + Large Funding

"You are incredibly prescient!"   I woke up to those words from a former colleague on Jan. 19, 2022: the bombshell announcement that the Chief Science Officer of pharma giant GSK, where I worked until recently, will become the CEO at the new, $3 BILLION longevity science company Altos (presumably also funded by Amazon's Jeff Bezos.) Big Pharma is at long last embracing Longevity Science. The corollary: longevity science is entering Mainstream (with capital "M") But let me backtrack... The Decade of Longevity Science When Harvard professor David Sinclair declared the 2020's to be the " decade of the paradigm shift about age reversal ", one could perhaps be dismissive of it as just an outburst of enthusiasm... But in the past couple of years, we're seeing strong evidence that his forecast is right on the mark! While I worked at GlaxoSmithKline - a giant, top-10, pharma company - I vigorously advocated forming a Longevity Science dept., and sp

D3 Visualization with Vue.js : a powerful alliance (when done right!)

[UPDATED MAY 2022]  D3.js is a very powerful visualization tool, especially for specialized/custom needs...  On the flip side, it's rather hard to use - with a steep learning curve. Even worse if one also wants interactivity ! But why is D3 so hard/clunky to use?  And what can be done about it? Spoiler alert: Vue.js (or other modern front-end framework) to the rescue - if done right... All code in the examples is available in this GitHub repository . The Root of the Problem In a nutshell, what makes D3 awkward to use is that, for historical reasons, it tries to do too much : most painfully, it uses an old way to do direct DOM manipulation (i.e. restructuring the page layout) - an operation that nowadays is superbly handled in a far more friendly way by modern front-end frameworks, such as Vue.js Document Object Model ( DOM ) is a programming interface for web documents.  In simple terms, it's the structure of the elements on a web page (text, images, etc.) Let the front-e

WW II - Best Documentaries & Fictional Films

This blog is primarily about knowledge and discovery in Science and Technology.  But the nadir of the human race during WW II is a sharp reminder that knowledge/sophistication without humanity is not even remotely good! Well, History falls among my interests, as detailed in my blog entry on courses I took (scroll to bottom.)  And WW II is a gripping chapter of history.  Personally, I had relatives who lived thru it... so that adds an extra sharp edge. In addition to the courses mentioned in the above blog entry, I have watched large numbers of both documentaries and dramatic films about WW II...  and I wrote down my impression and evaluation. All the fictional and non-fictional suggestions here are movies/documentaries I "really" liked or "loved" . I did NOT include the ones I disliked or felt lukewarm about it. All the blurbs are my own mini reviews, from the time I watched them. NON-FICTION Operation Valkyrie: The Stauffenberg Plot to Kill Hitler Informative, e

Photonic Computer - a "supercharged GPU" with very low energy consumption

Yes, we all wish for Quantum Computers... but in the meantime we need something here and now!  Could Photonic Computers fit that role? Just about everyone has heard of fiber optics – using light for data transmission – but did you know that light can also be used for computing? There's a new commercial product expected for early next year (2022) . I contacted the CEO, Nicholas Harris, of a 4-y.o. startup, Lightmatter , interviewed in April 2021 here . Photonic computers, at least in their first commercial appearance, are essentially accelerator cards for Linear Algebra - and so of special interest for Machine Learning and some types of simulations.    Their claims are remarkable: 10X faster than some of the best GPUs using 90% less energy can be used with existing software stacks, such as TensorFlow commercially available early next year (2022) a lot of future growth, as additional wavelengths of light get used in parallel My own interest is pr

Proceedings from Longevity Science Conferences 2021

Ending Age-Related Diseases 2021 This post is in-progress!  The conference just ended on Aug. 22;  as I clean up my notes, I'll post them here.  Please come back for future updates... Link to conference  (Notes and screenshots taken - and sometimes annotated - by me.  I will later contact the presenters to offer them the option to review them for accuracy...) Science at SENS Research Foundation 2021 Talk by Alexandra Stolzing , Professor for Biogerontological Engineering, VP of Research at SENS Research Foundation ("Strategies for Engineered Negligible Senescence".) This overview talk immediately emphasizes that the aging process involves multiple broad fundamental categories of physiological change.  Those are related to what are often referred as "the Hallmarks of Aging" , as I detail in my intro post on Longevity Science .  In this talk, 7 of those categories are identified, and given convenient icons (rightmost column) that make it easier to refer to them: