This page contains information pertinent to employees of WormBase.

Project Management

Web Site Documentation

Rearchitecture Design Stages

Requirements analysis / Design Specifications
Architecture Outline
Formal Development via established conventions
1. Formal development strategy - An overview of the development process at WormBase

Measuring Progress

Coding standards

Data structure documentation
Developer notes - Best practices, conventions, etc
Coding standards

Testing

Testing

Software platform

Application overview - A quick tour through the software platform
Installing the Web Application (legacy code) - Here's how to install the classic WormBase web site for development purposes
Installing the Web Application - Here's how to install the WormBase web application -- including Catalyst -- on your system
HOWTO migrate a CGI - quick overview of how to migrate an existing CGI into a Model, Controller, and View. Sparse

Configuration

WormBase::API

Common Model elements - reference list of common model elements like Species

View

Template Overview -- a quick tutorial on the templating system
Common template elements -- how to include common elements like references and species in a page

Model

Controller

Deployment

Deployment - How to deploy the web app for production use

Hardware platform

Physical structure
MySQL database replication - Mirroring mysql databases across production nodes
Performance optimization - Memory, Disk, and Network I/O troubleshooting
WormBase Infrastructure - A complete accounting of WormBase compute resources and topology.
WormBase Development Environment - Building, Configuring, and Administering the WormBase development server

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GBrowse Administration -- building, configuring, and maintaining production GBrowse nodes.
Webserver Administration -- building, configuring, and maintaining non-GBrowse production nodes.

Administration

Routine Administration Tasks

Cronjobs
Creating a Google Sitemap
Managing Perl Libraries - Managing Perl libraries across projects and architectures
Managing GBrowse - Quick HowTo for managing GBrowse in development and production environments
Log file management and analysis - rotating and analyzing logs.
Site statistics

Load balancing and Failover

Building Squid - How to build and install Squid
Configuring Squid - basic squid configuration at WormBase

Monitoring and Crises Management

Development Server Administration - Monitoring and fixing the development server
General administration and monitoring notes - Partially redundant, sorry
Monitoring services and servers
Crises Recovery Plan - Everything breaks. Here's how to fix it.

Frozen Releases

Building Frozen Releases - The most current documentation on how to build a frozen release

Frozen Releases as Virtual Machines

How to build a WormBase Virtual Machine -- also describes how to create a VMX for a frozen release
Configuring a server to host virtual machines -- quick guide to setting up a frozen release server
Managing servers hosting virtual machines
How to build a frozen release -- how to configure a WormBase VM as a frozen release server
Creating Virtual Disks - How to create VMDKs for unlimited portable storage

Updates

Updating The Development Server - Updating the development server with a new release of the database
Building WormMart - How to convert a WormBase AceDB database into WormMart

Developer Tools

All Hands Meeting Agendas and Notes

Source Code Repositories

We use the distributed source code management system Mercurial. Projects are hosted on BitBucket.

How-To create, check out, and manage our repositories

WormBase - The WormBase web application (public)
WormBase-admin - Administrative code (private)

Deprecated Documentation

The good word gone bad. Cruft. Lint. Maybe useful. Probably not.

NFS at WormBase
Trac installation notes
Trac Feature Tracker / Subversion repository
Establishing the SVN repository - Setting up the subversion repository

Developer documentation

Contents