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
• Orthologs: use cases for searches
• Genome sequence changes

WebSite Development

Design Stages

• Requirements analysis / Design Specifications
• Architecture Outline
• Prototyping
• Formal Development via established conventions -- Formal development strategy, coding standards, best practices
• Testing

Development Strategy

• Formal development strategy - An overview of the development process at WormBase
• Developer notes - Best practices, conventions, etc
• Coding standards

Developer Tools

• Twitter: General announcements
• FriendFeed: WormBase FF room
• WormBase Forum: Developer Forum

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)

Software platform

• Application overview - A quick tour through the software platform
• Migration matrix (GoogleDoc)

• 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
• Common Model elements - reference list of common model elements handled generically
• HOWTO migrate a CGI - quick overview of how to migrate an existing CGI into a Model, Controller, and View. Sparse
• Deployment - How to deploy the web app for production use

Hardware platform

• Logical structure
• Physical structure
• MySQL database replication - Mirroring mysql databases across production nodes
• Performance optimization - Memory, Disk, and Network I/O troubleshooting
• Hardware catalog - A complete accounting of WormBase compute resources
• Base node configuration - CentOS5 - Configuring a WormBase node from scratch (CentOS 5)
• Building a production node - Configuring a new production node

Administration

• WormBase-admin (mercurial; Bitbucket) - The WormBase administration code repository (private)
• WormBase Development Environment - Building, Configuring, and Administering the WormBase development server

Routine Administration Tasks

• NFS at WormBase
• 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 Meetings

14-18 January, 2008 - Toronto

Presentations

CSHL conference call slides

Part 1: Introduction (key, pdf)-- Catalyst, the reimplementation strategy, and roadmap

Part 2: On Configuration (key,pdf) -- Configuration basics (and freebies)

Deprecated Documentation

The good word gone bad. Cruft. Lint. Maybe useful but probably not.

• Trac installation notes
• Trac Feature Tracker / Subversion repository
• Establishing the SVN repository - Setting up the subversion repository