Developer documentation
From WormBaseWiki
This page contains information pertinent to employees of WormBase.
Contents
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 Specifications
- Scalability -- Todd
- Database Connectivity -- Xiaoqi
- API -- Norie
- Templates -- Abby
- CSS -- Abby
- Authorization and Authentication -- Xiaoqi
- Application request flow / REST interface -- Todd
- Application Configuration -- Abby
- Interactivity -- Norie
- Testing Guidelines -- Todd
- Production management -- Todd
Development Strategy
- Formal development strategy - An overview of the development process at WormBase
- Developer notes - Best practices, conventions, etc
- Coding standards
Developer Tools
- Twitter: WormBase source commits; 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
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
