EcoliHouse: A Publicly Queryable Warehouse of E. coli K12 Databases

Overview

EcoliHouse is a publicly queryable set of Escherichia coli K12 databases constructed using the BioWarehouse biological database warehousing system. It provides an environment for large-scale data mining using SQL statements issued across the Internet. User registration is required to access EcoliHouse.

Datasets currently loaded within EcoliHouse:

Dataset Name	Release Version/Date
EcoCyc	17.5
EcoGene	10/16/2013
Eco2Dbase	July 2000
Palsson Fis binding in E.coli ChIP-chip	1.0
Palsson RNAP binding in E.coli ChIP-chip	1.0
Reppas RNAP binding in E.coli ChIP-chip	1.0
GenBank E. coli K-12 substr. MG1655 genome	10/16/2013
UniProt Complete Proteome for E. coli K12	10/16/2013

The EcoliHouse server runs the MySQL relational database management system (v. 5.1.41), and is based on version 4.6 of BioWarehouse. The server has 33 GB of RAM and eight Intel Xeon 2.66 GHz processor cores.

In order to use EcoliHouse, you must register to obtain an EcoliHouse login.
A graphical user interface for EcoliHouse is provided by using phpMyAdmin.

www.isb-sib.ch/
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Usage Guidelines

User registration is required to access EcoliHouse. After registering, you will have access to the PublicHouse database, but not EcoliHouse. Please contact BioWarehouse Support at support@biowarehouse.org to obtain additional access to EcoliHouse.

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Connection parameters: IP = ecolihouse.ai.sri.com (192.12.5.33), port number = 3306 (default), database name = ecolihouse. When prompted, please give your user name and the password you were provided after EcoliHouse registration.

Please note that the server will terminate queries which take longer than 60 min to run. Should you require greater processing power, we suggest you install BioWarehouse locally at your institution.

Example Queries

Please see the EcoliHouse Example Query page for a comprehensive list of sample SQL queries.

https://biospice.org/ for more information.
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Documentation

Please see the BioWarehouse documentation.

Note: a good understanding of the BioWarehouse schema is necessary for most queries. The schema documentation is available here.

Current Limitations of EcoliHouse:

Loaders: Limitations of individual loaders are described in each loader’s documentation
Database performance: If you encounter what you believe to be unacceptable query performance, please send us your query (email address below) so we can investigate available performance tuning options.

Support

For support and inquiries please contact

Periodic announcements about the availability of EcoliHouse and BioWarehouse releases are sent via the BioWarehouse Announce mailing list. EcoliHouse registrations are automatically subscribed to the announcement list.
Please send email to
to join the list.

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