Blog Contents

Discussing Neuroscience with ChatGPT

UPDATED Apr. 2023 - I'm excited by ChatGPT 's possibilities in terms of facilitating advanced learning . For example, I got enlightening answers to questions that I had confronted when I first studied neuroscience. The examples below are taken from a very recent session I had with ChatGPT (mid Jan. 2023.) Source: https://neurosciencestuff.tumblr.com In case you're not familiar with ChatGPT, it's a very sophisticated "chatbot" - though, if you call it that way, it'll correct you! 'I am not a "chatbot", I am a language model, a sophisticated type of AI algorithm trained on vast amounts of text data to generate human-like text'. For a high-level explanation of how ChatGPT actually works - which also gives immense insight into its weaknesses, there's an excellent late Jan. 2023 talk by Stephen Wolfram, the brilliant author of the Mathematica software and of Wolfram Alpha , a product that could be combined with ChatGPT to imp...

Graph Databases (Neo4j) - a revolution in modeling the real world!

UPDATED Oct. 2023 - I was "married" to Relational Databases for many years... and it was a good "relationship" full of love and productivity - but SOMETHING WAS MISSING! Let me backtrack. In college, I got a hint of the "pre-relational database" days... Mercifully, that was largely before my time, but - primarily through a class - I got a taste of what the world was like before relational databases. It's an understatement to say: YUCK! Gratitude for the power and convenience of Relational Databases and SQL - and relief at having narrowly averted life before it! - made me an instant mega-fan of that technology. And for many years I held various jobs that, directly or indirectly, made use of MySQL and other relational databases - whether as a Database Administrator, Full-Stack Developer, Data Scientist, CTO or various other roles. UPDATE: This article is now part 1 of a growing, ongoing series on Graph Databases and Neo4j But ther...

Using Schema in Graph Databases such as Neo4j

UPDATED Feb. 2024 - Graph databases have an easygoing laissez-faire attitude: "express yourself (almost) however you want"... By contrast, relational databases come across with an attitude like a micro-manager: "my way or the highway"... Is there a way to take the best of both worlds and distance oneself from their respective excesses, as best suited for one's needs? A way to marry the flexibility of Graph Databases and the discipline of Relational Databases? This article is part 5 of a growing, ongoing series on Graph Databases and Neo4j Let's Get Concrete Consider a simple scenario with scientific data such as the Sample, Experiment, Study, Run Result , where Samples are used in Experiments, and where Experiments are part of Studies and produce Run Results. That’s all very easy and intuitive to represent and store in a Labeled Graph Database such as Neo4j . For example, a rough draft might go like this: The “labels” (b...

What are Graph Databases - and Why Should I Care?? : "Graph Databases for Poets"

This is a very gentle introduction to the subject. The subtitle is inspired by university courses such as "Physics for Poets"! (if you're technically inclined, there's an alternate article for you.) It has been said that "The language of physics (or of God) is math". On a similar note, it could be said that: The language of the biological world - or of any subject or endeavor involving complexity - is networks ('meshes') What is a network? Think of it as the familiar 'friends of friends' diagram from social media. Everywhere one turns in biology, there's a network – at the cellular level, tissue level, organ level, ecosystem level. The weather and other earth systems are networks. Human societal organization is a network. Electrical circuits, the Internet, our own brains... Networks are everywhere! What can we do with networks, to better understand the world around us, or to create something that we need? Broadly ...

Anti-Aging Research: Science, not Hype

Last updated May 2023 Q: "How is aging a disease?" A: It's a dynamic system that veers away from its homeostasis (normal equilibrium point): hence a form of slow-progressing illness. Labeling it as 'natural' is a surrender to our traditional state of ignorance and powerlessness, which fortunately is beginning to be changed! Aging is "normal" only from the point of view of the "selfish gene", for whom the body is a disposable carrier. Individuals organisms - for whom self-preservation has a different meaning than for genes - have received scant help from evolution... with rare exceptions such as the T. dohrnii jellyfish (which I discuss here )... but now the time has finally arrived for our rational design to remedy some of the cellular flaws that evolution never bothered to correct! The above is my standard answer to an oft-asked question. The science of aging is by all evidence very misunderstood by the general public. Hype,...

Using Neo4j with Python : the Open-Source Library "NeoAccess"

So, you want to build a python app or Jupyter notebook to utilize Neo4j, but aren't too keen on coding a lot of string manipulation to programmatic create ad-hoc Cypher queries? You're in the right place: the NeoAccess library can do take care of all that, sparing you from lengthy, error-prone development that requires substantial graph-database and software-development expertise! This article is part 4 of a growing, ongoing series on Graph Databases and Neo4j "NeoAccess" is the bottom layer of the technology stack provided by the BrainAnnex open-source project . All layers are very modular, and the NeoAccess library may also be used by itself , entirely separately from the rest of the technology stack. (A diagram of the full stack is shown later in this article.) NeoAccess interacts with the Neo4j Python driver , which is provided by the Neo4j company, to access the database from Python; the API to access that driver is very p...

Visualization of Graph Databases Using Cytoscape.js

(UPDATED APR. 2024) I have ample evidence from multiple sources that there are strong unmet needs in the area of visualization of graph databases. And whenever there's a vacuum, vendors circle like vultures - with incomplete, non-customizable, and at times ridiculously expensive, closed-box proprietary solutions. Fortunately, coming to the rescue is the awesome open-source cytoscape.js library , an offshoot of the "Cytoscape" project of the Institute for Systems Biology , a project with a long history that goes back to 2002. One can do amazing custom solutions, relatively easily, when one combines this Cytoscape library with: 1) a front-end framework such as Vue.js 2) backend libraries (for example in python) to prepare and serve the data For example, a while back I created a visualizer for networks of chemical reactions, for another open-source project I lead ( life123.science ) This visualizer will look and feel generally ...

Neo4j Sandbox Tutorial : try Neo4j and learn Cypher - free and easy!

So, you have an itch to test-drive Neo4j and its Cypher query language. Maybe you want to learn it, or evaluate it, or introduce colleagues/clients to it. And you wish for: fast, simple and free! Well, good news: the Neo4j company kindly provides a free, short-term hosted solution called "the Neo4j sandbox" . Extremely easy to set up and use! This article is part 2 of a growing, ongoing series on Graph Databases and Neo4j Register (free) for the Neo4j "Sandbox" Go to sandbox.neo4j.com , and register with a working email and a password. That's it! Note that this same email/password will also let you into the Neo4j Community Forums and Support ; the same login for all: very convenient! Launch your instance - blank or pre-populated After registering, go to sandbox.neo4j.com , and follow the steps in the diagram below (the choices might differ, but the "Blank Sandbox" should always be there): Too good to be true? Is there...

Life123 : Quantitative Dynamical 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...

Graph Database Series - Beginners to Advanced, Full-Stack (Neo4j focus)

A growing, ongoing series on Graph Databases and Neo4j. The series has grown so large that I'm "factoring out" their Table of Contents as a separate entry, here! A series on Graph Databases and Neo4j part 0 (alternate version of part 1 for a general, non-technical audience) : What are Graph Databases - and Why Should I Care?? : "Graph Databases for Poets" part 1 : Intro to Graph Databases (Neo4j) - a revolution in modeling the real world! part 2 : Neo4j Sandbox Tutorial : try Neo4j and learn Cypher the free and easy way part 3 : Neo4j & Cypher Tutorial : Getting Started with a Graph Database and its Query Language part 4 : Using Neo4j with Python : the Open-Source Library NeoAccess part 5 : Using Schema in Graph Databases such as Neo4j part 6 : Putting it All Together - a Technology Stack on Top of a Graph Database SPECIAL TOPICS *...

Julian's Polymath Explorations

Search This Blog