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
• What criteria should a genome meet before we accept it for integration?
• WormBase Models
• Orthologs: use cases for searches
• Genome sequence changes

Web Site Documentation

Rearchitecture Design Stages

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

Measuring Progress

• AceDB classes -> API progress matrix
• Migration matrix (GoogleDoc)

Coding standards

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

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

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

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

All Hands Meeting Agendas and Notes

• 2010.05 OICR WebDev Meeting
• WebDev_2010.03.17-Agenda_and_Minutes

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