Codetown ::: a software developer's community
Are you interested in learning about graph databases? The folks at Neo4J published a book and it's free! Here's a link to the download page: http://graphdatabases.com/
Tags:
Database representation of graph-structured information is fascinating in its own right.
I have been studying genomics technology in which graphs play a big role, both as information-structure that is the basis of certain algorithms, as well as the data driving visualizations or visually-interesting real-world structures.
As an example, here is a visualization of a protein complex that catches the eye.
See http://en.wikipedia.org/wiki/FOXP2#/media/File:Protein_FOXP2_PDB_2a...
The image is a Richardson diagram which is (mostly) automatically generated from a database describing the molecular structure of the protein. This type of diagram was invented (i.e. originally hand-drawn) by Jane Richardson, PhD.
I wonder if the book "Graph Databases" touches on this.
Presently, I am doing a research study on a particular feature of the epigenome. It involves large DNA databases (actually, structured flat files), elaborate algorithms for sequence correlation, and histone complexes. Each of these involves graph-theoretic representations and inference functions from graph structures.
The "databases" I know for DNA, the transcriptome, pathways, etc. do not lend themselves to conventional SQL, or even noSQL as far as I know to date. (Chime in anyone? )
I will be presenting a paper at the IEEE SouthCon conference in April 2015 which touches on a graph-theoretic feature of certain (sequencing) problems lending itself to massively-parallel-ization of linearly-expressable algorithms.
I am pleased to see a free book on graph databases. Thanks!
Codetown is a social network. It's got blogs, forums, groups, personal pages and more! You might think of Codetown as a funky camper van with lots of compartments for your stuff and a great multimedia system, too! Best of all, Codetown has room for all of your friends.
Created by Michael Levin Dec 18, 2008 at 6:56pm. Last updated by Michael Levin May 4, 2018.
Check out the Codetown Jobs group.
Uber Eats introduced INCA (Inventory and Catalog), a scalable system to handle vast product catalogs from supermarkets, pharmacies, and retail partners. Unlike the earlier restaurant-focused setup built for low SKUs and simple pass-through data, INCA supports large-scale inventories, rich metadata, and compliance needs essential for retail operations.
By Leela KumiliAirbnb engineering has published a detailed account of how it maintains high availability during Istio upgrades across tens of thousands of pods and thousands of VMs, all without downtime.
By Craig RisiSérgio Amorim shares how Revolut’s small DevOps team leverages a centralized systems catalog and automation to enable 1,300 engineers to build and deploy applications with speed and consistency. He explains how this approach reduces manual effort and improves observability, alerting, and database management at scale.
By Sérgio AmorimAWS has launched its eighth-generation Amazon EC2 R8i and R8i-flex instances, powered by custom Intel Xeon 6 processors. Designed for memory-intensive workloads, these instances offer up to 15% better price performance and enhanced memory throughput, making them ideal for real-time data processing and AI applications.
By Steef-Jan WiggersIn this article, authors discuss Model Context Protocol (MCP), an open standard designed to connect AI agents with tools and data they need. They also talk about how MCP empowers agent development, and its adoption in leading open-source frameworks.
By Sanjay Surendranath Girija, Lakshit Arora, Shashank Kapoor
© 2025 Created by Michael Levin.
Powered by