IC Bioinfs/Project1/toydatabase

Toy Database

An SQL database created from the DAS and FASTA output of the MIT Parts Registry.

Online Database

The toy database has been established on codon.

• Database name: msc_09_das
• Username/password: as above.
• Host name: db-bss.lesc.doc.ic.ac.uk

Access Via Codon

Login to your codon account, then enter the following command at the prompt:

mysql msc_09_das -u msc_09_das -p

Access via Other Servers

At the prompt:

mysql msc_09_das -u msc_09_das -p -h db-bss.lesc.doc.ic.ac.uk

Versions

Please make sure to use the latest version of the database schema, and associated data.

Version 2

Created week of 08/02/2010

Changes

• New internal identifiers for each table
• Shifting of columns between tables
• The feat_info table is now non-redundant

Files

• Schema & important MySql commands
• CSV files: partsinfo.csv (same file as before), and seqfeatall.csv (new file) - data extracted from first 500 parts listed in the FASTA file.
• Two new parser files for creating partsinfo.csv [1] and seqfeatall.csv [2] (must first download FASTA file before use)

Tables

Version 1

Created week of 01/02/2010

Files

• Suggested SQL Schema based on Parts Registry DAS & FASTA output. Includes SQL commands to create database and tables.
• Perl script to parse DAS/FASTA output of Parts Registry (ZP, 04/02/10)
• CSV files for Toy Database: Partsinfo.csv, Seqfeat.csv, Featinfo.csv (first 500 parts only).