Developer documentation

This page contains information pertinent to employees of WormBase.

Project Management

• Project Calendar
• Conference call agendas and minutes
• Project meeting agendas and minutes
• Linking To WormBase
• Suggested pre-release data checks
• Internal documentation and standard operating procedures
• modENCODE Analysis & metadata discussion
• Genome Standards -- What criteria should a genome meet before we accept it for integration?
• WormBase Models
• Orthologs: use cases for searches
• Genome sequence changes
• WormBase Genomes

Web Site Development Guidelines

• Development Milestones

• Formal development strategy - An overview of the development process at WormBase
• Coding standards
• Developer notes -- Best practices, conventions, etc
• Browser Support Statement -- official graded browser support statement

Documents pertaining to WormBase 2.0

• Requirements analysis / Design Specifications
• Rearchitecture Development Duties
• AceDB classes -> API progress matrix
• Migration matrix (GoogleDoc)

Architecture

Software platform

• Software Platform overview -- An overview of the full software platform, including the web application, reverse proxy, and http servers
• Installing WormBase - How to get a basic installation of WormBase up and running
• Production Environment - Building and Maintaining the WormBase production environment; extends the "Installing WormBase" document

The Web Application

• Application overview - An overview of the web application, including MVC structure, request flow, caching, etc
• Configuration -- Application and view configuration: formatting and standards
• WormBase::API -- The WormBase data model, maintained external to the web application
• View -- Templating system, commom template elements, javascript, and CSS
• Model -- The web application model; thin, glued to the external Model
• Controller -- Overview of controller files and actions
• NFS at WormBase

Hardware platform

• Hardware Platform overview - A complete accounting of WormBase compute resources.

Administration

Updates

• Updating The Development Server - Staging a new release of the database on the development server
• Updating The Production Servers - Testing, staging, and deploying the web app; updating to a new release of the database

Routine Administration Tasks

• Testing - Testing guidelines for the web application and hardware platform
• Profiling - Profiling the web application, performance tuning, identifying memory and I/O bottlenecks, and historical benchmarks
• Cronjobs
• Creating a Google Sitemap
• Managing Perl Libraries - Managing Perl libraries across projects and architectures
• Log file management and analysis - rotating and analyzing logs.
• Site statistics

• GBrowse Administration -- building, configuring, and maintaining production GBrowse nodes.
• Building WormMart - How to convert a WormBase AceDB database into WormMart

Monitoring and Crises Management

• Crises Recovery Plan - Everything breaks. Here's how to fix it.
• General administration and monitoring notes - Partially redundant, sorry
• Monitoring services and servers

Load balancing and Failover

• Building Squid - How to build, install and configure Squid

Frozen Releases

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

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.

Rearchitecture

• HOWTO migrate a CGI - quick overview of how to migrate an existing CGI into a Model, Controller, and View. Sparse

• MySQL database replication - Mirroring mysql databases across production nodes
• Trac installation notes
• Trac Feature Tracker / Subversion repository
• Establishing the SVN repository - Setting up the subversion repository
• Managing GBrowse - Quick HowTo for managing GBrowse in development and production environments

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