CDSbank Files

CDSbank was primarily developed to provide online access by end users via a web browser. However, power users who desire direct access or customized data subsets may wish to build and query their own database. CDSbank was developed and tested on Ubuntu linux with python 2.7 and mongodb version 2.0.3. Newer versions are expected to work but older versions may not. To my knowledge all python programs and dependencies are available on all common hardware platforms but may need some modifications, for instance in shell scripts and makefile.

The most complete installation descriptions are found on the SourceForge wiki. I am happy to help trouble shoot installation issues and would like to receive feedback about success/failure, especially for non-linux installations.

Release 0.9.1(alpha): August 19, 2013
- Completely reworked makefile and updateDB.sh script to perform all steps of database building, updating, checking, and clean-up
- Example for crontab usages to automated daily updates
- Taxonomy database is now a collection of the main database, no longer a standalone entity
- Collection "versions" in separata "CDSbank" database keeps track of all available versions and indicates their status. Only one database is defined as "active" and will be used by the CDSbank.py program
- Added a mongoSettings.py program to query/set properties of the databases

Status/stability
The current release was used to completely build the most recent Genbank release (genbank197) and refseq version 60. All BUILD, CHECK, UPDATE, INDEX, and ACTIVE stages completed flawlessly and took approximately 45 hours for data download and processing. A daily crontab update has been set up and is working.

I have designated the current version as an alpha release to allow for one full cycle of testing. If a full rebuild is completed successfully next month (after refseq version 61 comes out) the release status will be upgraded to beta.