CSHL documentation

The WormBase Cold Spring Harbor team is in charge of developing, maintaining, and hosting WormBase. This page contains links to documentation relating to those topics.

Development

• Formal development strategy - An overview of the development process at WormBase
• Developer notes - Best practices, conventions, etc
• Using private development sites - How to use the private, self-contained developer sites on brie3
• Javascript libraries - Javascript libraries in use at WormBase
  • Using collapsible sections - API for DHTML open/close sections
  • Balloon Tooltips - API and architecture for AJAX/DHTML-based tooltips
• Session management - API and architecture for CGI::Session-based state memory and user authentication
• RSS implementation - Documentation and caveats concerning the WormBase RSS implementation
• Converting GFF2 to GFF3 - Converting Wormbase GFF data from GFF2 to GFF3
  • GFF3 features (C. elegans) - GFF3 features included in the C. elegans GFF3 file
  • GFF3 features (C. briggsae) - GFF3 features included in the C. briggsae GFF3 file
• GFF3 validation - GFF3 Validator Code Base
• N-Browse installation & interaction data - Wormbase N-Browse installation and preparation of Wormbase interaction data
• Interaction display in the gene page - Interaction Display in the Gene Page
• BLAST/BLAT Page - BLAST/BLAT page and databases
• Importing protein structure data - Importing protein structure data from TargetDB and PDB
• Importing protein structure data images - Importing protein structure images for structure data
• Importing PFAM images - Importing protein structure images for PFAM domains on the gene page
• Geographic displays - Geographic map displays
• Establishing the SVN repository - Setting up the subversion repository

Administration

Hardware

• WormBase Infrastructure
• Building and configuring the front end caching server

General Admin

• Updating WormBase
• General administration
• Monitoring servers
• Emergency plan for server outtages
• Cronjobs
• Managing Perl libraries across nodes
• Site statistics
• Creating a Google Sitemap
• Optimizing site performance

Virtual Machines / Freezes

• 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

Developer Tools

• BaseCamp project management site

Reimplementation

Hardware platform

• Logical structure
• Physical structure
• 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)

Software platform

• Coding standards
• Third-party libraries - installing and managing third-party libraries, namely GBrowse and BioPerl
• Installing the Web Application - Here's how to install the WormBase web application -- including Catalyst -- on your system

Administration

• Monitoring services and servers
• Crises Recovery Plan - Everything breaks. Here's how to fix it.

Load balancing and Failover

• Building Squid - How to build and install Squid
• Configuring Squid - basic squid configuration at WormBase

Development notes by release

As part of the formal development strategy at WormBase, software freezes occur on the Wednesday before the release of each new database. This corresponds with the CSHL WormBase conference call.

For a new feature to enter production, developers must send an email to cshl@wormbase.org by the software freeze deadline briefly describing the new feature and any new module or database requirements. This section collates those notes for easy access

• WS173
• WS172
• WS171
• WS170
• WS167
• WS166
• WS165
• WS164
• WS163
• WS159
• WS158
• WS157