Installing a Local Copy of the Reactome Web Site and Database
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- Abstract
- Table of Contents
- Figures
- Literature Cited
Abstract
The Reactome project builds, maintains, and publishes a database of biological pathways. The information in the database is gathered from the experts in the field, peer reviewed, and edited by Reactome editorial staff and then published to the Reactome Web site, http://www.reactome.org (see UNIT ). Reactome software is open source and builds on top of other open?source or freely available software. Reactome data and code can be freely downloaded in its entirety and the Web site installed locally. This allows for more flexible interrogation of the data and also makes it possible to add one's own information to the database. Curr. Protoc. Bioinform. 21:9.10.1?9.10.9. © 2008 by John Wiley & Sons, Inc.
Keywords: pathways database; open source software
Table of Contents
- Introduction
- Basic Protocol 1: Installation of the Reactome Web Site and Data
- Installation of Other Applications and Libraries
- Support Protocol 1: Installing Apache, Perl, and Java
- Support Protocol 2: Installing MySQL
- Support Protocol 3: Installing Perl Modules and Supporting Software
- Commentary
- Figures
- Tables
Materials
Figures
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Figure 9.10.1 Screenshot of the Web site front page after successful installation of a local copy of the Reactome database and Web site. View Image -
Figure 9.10.2 Architectural diagram of the Reactome software. The information is entered into the database with the help of Reactome Curator Tool. To enable off‐line work, the latter can also store information in an XML file in the local file system. End users usually access Reactome database content with a Web browser via the Web server, where the request is handled by the CGI scripts that interrogate the MySQL database via Perl API. View Image
