Protein Geometry Database
  • Installation
    • Development Branch Installation
    • Master Branch Installation
  • Importing Data
    • Running Splicer From The Command Line
    • Example
  • Updating Protein Database
  • Site Specific Information
    • Virtual environments
    • Files generated during the update process
    • Differences between staging and production
  • Technologies Used By Protein Geometry Database
    • Django
    • jQuery
    • Raphael
    • Mysql
  • Terminology (WIP)
  • Code Modules
    • PGD Core
    • PGD Search
    • PGD Splicer
  • Protein Data Models
    • Protein
    • Chain
    • Residue
  • Optimization
  • Optimization: SQL Indexes
    • Protein
    • Residue Joined to Residue
  • SQL Aggregates
    • Statistics for Dihedral Angles
    • Average
    • Standard Deviation
  • Optimization: In Memory Tables
    • Indexing Memory Tables
    • Parallelization of Queries
    • Startup and Django Configuration Issues
    • Growth Concerns
  • Attempted Optimization: De-normalizing Residue Table
    • Table Size
  • Search Workflow
    • Models
    • Forms
    • Conversions
    • Workflow
  • Ramachandran Plots
    • Data Selection
    • Statistics Calculation
    • Coloring
    • Logarithmic Scale
    • Color Ranges
    • Algorithm
  • Search Statistics
    • Queries
    • Optimization
  • Data Dump
    • Selecting Data
    • Buffered Response
  • Browse
    • Selecting Data
  • Splicer
    • Task Structure
  • Developing Splicer
    • Django Settings
    • Running Components from the command line
  • Splicer Processor Task
    • Running From the command line
    • Libraries
    • Parsing PDBs
    • Example a3
    • Example: Ome
    • Example B-factor: Bm, Bs, Bg
    • Update Checking
  • Running Splicer
    • Slow FTP Issues
    • Maintaining Connections Between Workunits
    • Only Downloading New Files
    • Storing files in a network share
    • Workunit Thrashing Problem
    • Debugging Splicer
  • Running Splicer From The Command Line
    • Selecting Proteins
    • Options
    • Downloading PDB Files
    • Processing PDB Files
    • Parameters
    • Options
    • Example
    • Full Import
    • Update Only New
    • Update Skipping Download
  • Development workflow
    • Create an issue in the issue tracker if one does not already exist.
    • Create a branch from the develop branch based on the issue number.
    • Write the code, including tests and release notes entry if necessary.
    • Commit code and update the issue.
    • Request code review.
    • Merge changes back into the develop branch.
  • Hotfix Workflow
    • One or more show-stopping bugs are detected between releases
    • Create a hotfix branch off the master branch
    • Create bug branches off the hotfix branch
    • Merge resolved bugs back to hotfix branch and test on staging
    • When all bugs are resolved and merged, merge hotfix branch into master branch
    • Pull master on production and restart Apache
    • Merge hotfix branch back into develop
  • Release Workflow
    • Announce the upcoming release to the PGD list four weeks before release.
    • Impose a feature freeze on develop three weeks before release.
    • Start the release branch two weeks before release.
    • Freeze the release branch one week before release.
    • Release the software, close tickets and unfreeze develop on the release date.
  • Management Commands and Possible Redisign
 
Protein Geometry Database
  • Docs »
  • Edit on GitHub

© Copyright 2014, Oregon State University Open Source Lab.

Built with Sphinx using a theme provided by Read the Docs.
Read the Docs v: develop
Versions
latest
develop
Downloads
On Read the Docs
Project Home
Builds
Free document hosting provided by Read the Docs.