BASE - a free microarray database system

Carl Troein¹, Johan Vallon-Christersson², Lao Saal, Jari Häkkinen
¹carl@thep.lu.se, Dept. of Theor. Phys., Lund University; ²johan.vallon-christersson@onk.lu.se, Dept. of Oncology, Lund University

BASE is a free microarray database system with a clean and intuitive web interface. Designed by microarray biologists, it offers a natural work-flow for microarray experiments, all the way from microarray production to the analysis of results. The system is meant to be set up as a local repository for a microarray laboratory's data, including raw images if so desired.

The administrator defines users and their privileges (e.g. the right to enter samples), and has full access to all data in the database. Users can easily share their data with other users through a system similar to the group/world rights on Unix systems. In addition, groups may have appointed reviewers with escalated access rights to their groups' data.

BASE has been designed to work with a variety of microarray platforms, and the array LIMS part can be entered at different levels or not at all, depending on what level of information is available or relevant. This, together with almost complete flexibility in what raw data is stored in the database and support for an arbitrary number of channels in the analysis part, makes it possible to use BASE not only with 2-channel cDNA arrays, but also with Affymetrix and other platforms.

The analysis part of BASE revolves in great part around a simplistic plugin interface, where data is passed in tab-separated files. This makes it a simple task to get existing analysis tools work with BASE. A recent user-contributed plugin demonstrates how the statistics language R can be used from BASE.

The main part of BASE is written in PHP. It works against a MySQL database, and in recent versions PostgreSQL support has also appeared. The combination of PHP and MySQL is very common for web projects, which means that it is easy to find someone with the competence to set up and maintain a BASE installation, and to extend the functionality if needed.

We have chosen to release BASE under the GNU General Public License, and since the release of version 1.0 last year, a small community has grown around the project. In the latest version, 1.2, contributions from outside the original team have started to appear, and this bodes well for the future. In parallell with the development of versions 1.x, a small team has started planning and design of BASE 2.0, intended to be a re-implementation in Java, drawing from the know-how gained in the creation of BASE 1.

The BASE web site is http://base.thep.lu.se/.