This page contains information pertinent to employees of WormBase.

Project Management

Web Site Documentation

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
Requirements analysis / Design Specifications

Division of Labor

Duties, current as of July 2010.

Configuration Czar -- View and application configuration
View
- CSS Czar
- Javascript Czar
- Template Czar -- define and document shared elements, keep template directory organized, enforce standards
- Searches Czar
- External URLs
WormBase::API Czar
Testing Czar (View)
Testing Czar (API)
Profiling Czar

Measuring Progress

Coding standards and Best Practices

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

Testing

Unit testing
System Testing
Validation (HTML/CSS/XML)
Security
Accessibility
Usability
Browser compatability
Performance and stress testing

Software platform

Application overview - A quick tour through the software platform

Configuration

WormBase::API

Common Model elements - reference list of common model elements like Species
Data structure documentation - codified data structure that should be returned by API classes

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
Things to document: evidence handling, linking entities, external URLs, searches

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

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