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This page contains information pertinent to employees of WormBase.
- 1 Project Management
- 2 Web Site Documentation
- 2.1 Rearchitecture Design Stages
- 2.2 Coding standards
- 2.3 Software platform
- 2.4 Hardware platform
- 2.5 Administration
- 2.6 Updates
- 2.7 Developer Tools
- 2.8 All Hands Meeting Agendas and Notes
- 2.9 Source Code Repositories
- 2.10 Deprecated Documentation
- Project Calendar
- Conference call agendas and minutes
- Project meeting agendas and minutes
- Doodle Polls for conference call scheduling
- 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?
- Orthologs: use cases for searches
- Genome sequence changes
Web Site Documentation
Rearchitecture Design Stages
- Requirements analysis / Design Specifications
- Architecture Outline
- Formal Development via established conventions
- Data structure documentation
- Common template elements -- how to include common elements like references and species in a page
- 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
- 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
- GBrowse Administration -- building, configuring, and maintaining production GBrowse nodes.
- Webserver Administration -- building, configuring, and maintaining non-GBrowse production nodes.
Routine Administration Tasks
- NFS at WormBase
- 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.
- 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
- 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
All Hands Meeting Agendas and Notes
Source Code Repositories
We use the distributed source code management system Mercurial. Projects are hosted on BitBucket.
The good word gone bad. Cruft. Lint. Maybe useful but probably not.