building an interactive tree with d3.js php and sqlite: an annotated webliography

I want to make a tree with rectangular nodes containing text, such that I can add nodes or remove nodes on the fly. I want the tree to be "multiplayer": everybody who visits the site sees the same tree, and when one of them modifies it, it the updates are applied to everyone's view.
I know nothing about d3, and very little about PHP, but a bit about sqlite and Apache.
For this project I'm using a minimal number of libraries, and a very simple server setup, which leads to some inefficiencies. The server is Ubuntu 14.04 with Apache 2.4 with PHP 5.6. Client side the only library I'm using is d3.js 3.5.

A consequence of the simplicity is that I don't have a good way to push data to clients, so I can't use long polling or web sockets. Instead, I rely on repeated client requests for updates, which adds some latency, but hopefully not too much.


Requirements for graph:
Nodes are boxes that can contain about 50 words
terminal nodes can be added or removed (capability to add or remove internal nodes is not necessary)
root is on the left
subtrees can be expanded or collapsed
zoom-in zoom-out capability
pan capability
sort nodes with the older siblings above newer siblings


Let's get this figured out!

MGR CMS: a simple Django-based content management system for genomic data

MGR-CMS (Mint Genomics Resource) is a content management system for genomic and transcriptomic data. The code for MGR-CMS can be found Here. As implied by the name, it was originally built to house data for mint plants, but it can be easily adapted for data from other organisms. I made MGR because I couldn't figure out how to get Tripal to behave how I wanted it to. I later found out that was my fault, not Tripal's fault, so if you want a more or less feature complete genomics content management system, look there. If you want a simple system written in Python (Django), or you have the misfortune of having a Windows server (as I do), then MGR might be just the thing for you (but it still might be worth your while to shoot the Tripal people an e-mail, just to make sure it really can't handle your situation).