Developer Information
From BioPerl
This is currently just a list of general BioPerl developer resources.
Contents |
Starting out
- Are you interested in Bioinformatics?
- Do you want to become a developer?
- A brief History of BioPerl
- Getting BioPerl
- Installing BioPerl
Where to go for answers
- Frequently Asked Questions
- Mailing lists
- BioPerl chat
- How to ask questions
- PDoc documentation for BioPerl
Bugs
- How to submit bugs
- BioPerl Bugzilla - bug tracking system
- Submit Patch HOWTO
- How to effectively report bugs.
Git help
- The Git repository for getting access to the latest code is available here.
- Specifics on Using Git
- Tracking Git commits using RSS
BioPerl Code
- BioPerl Locations sandbox.
- Bioperl Best Practices
- An Emacs template for those Emacs fanatics
- A page for Vi users (no templates yet)
- Advanced BioPerl
- BioPerl class diagrams - Note - these are quite out-of-date but give you an idea of the class hierarchy in BioPerl
- How to choose a module name
- Why is BioPerl slow?
- Project priority list
- List of BioPerl classes which could use some code optimization
- List of BioPerl classes with unimplemented methods - Note- this does not include abstract interface class methods, which by definition are not implemented
- List of BioPerl classes marked for deprecation
- List of BioPerl classes which lack tests
BioPerl releases
- BioPerl Release Schedule
- Change log
- How to make a BioPerl release
- What is a Release Pumpkin?
- Who are the Core developers?
- Who are the contributing authors?
- Making a BioPerl PPM distribution
Helping out on the BioPerl Wiki
- Torsten/Brian/Jason's BioPerl wiki style guide
- The official MediaWiki User's Guide to editing Wiki pages
- Customizing the Wiki interface
- When editing something is considered a minor edit
Parsing data
- SearchIO HOWTO - describes the Bio::SearchIO system
- Preferred list of XML parsers
Writing data
- Preferred list of XML writers
