BioArray Software Environment (BASE)

Category Genomics>Gene Expression Analysis/Profiling/Tools

Abstract BioArray Software Environment (BASE) provides an integrated framework for storing and analyzing microarray information.

BASE is a Minimum Information About a Microarray Experiment (MIAME)- supportive customizable database and analysis platform designed to be installed in any ‘microarray laboratory’ and to serve many users simultaneously via the web.

The system integrates biomaterial information, raw images and extracted data, and provides a plug-in architecture for data transformation, data viewing and analysis modules.

Additionally, for laboratories that fabricate in-house arrays or for groups that wish to track reporter information, the system has array production Laboratory Information Management System (LIMS) features that can be integrated with the data analysis.

The structure of BASE was designed to follow the natural workflow of the microarray biologist, and it is compatible with most types of array experiments and data formats (for example, one- or two-channel hybridizations, cDNA/Oligos spotted on any substrate, Affymetrix chips, comparative genomic hybridization (CGH) on arrays).

With his/her own account and administrated access levels, a user can import data into the database, group array data together into experiments, and in a uniform and streamlined fashion, apply filters and transformations and run analyses.

To facilitate online collaboration, users can share almost any object within the database with another user.

Data can be exported in a multitude of formats for local analysis and publication.

BioArray Software Environment (BASE) features/capabilities include:

1) MIAME compliant


2) Tab2MAGE (Tab2MAGE is a format for describing a microarray experiment in a spreadsheet, part of a software package written and supported by the ArrayExpress curation team) import/export plug-in ArrayExpress (see G6G Abstract Number 20012) compliant.

3) Projects, Sharing, and Access Control Management.

4) Array LIMS.

5) Biomaterial LIMS.

6) Many microarray data formats are supported - Affymetrix, Agilent, GenePix, Illumina support, and custom formats are supported through customizable import plug-ins.

7) Extensibility via Enhanced plug-in Application Programming Interface (API).

8) Annotation Customization via Annotation Type/Categories mechanism.

9) Migration module from BASE 1.2.17 to BASE 2.6, followed by BASE 2.6 to latest upgrade.

10) Analysis tools include:

11) Ability to get data using Web-Services.

Data can be visualized at several stages of analysis.

Unmodified and transformed data sets can be plotted interactively as scatter plots, displayed in histograms, or viewed as tables.

Entire experiments can be displayed in various overview plots in the context of how they are annotated, and figures and tables can be exported for publication.

From any data-analysis step the experiment can be imported into a data- visualization interface called ‘Experiment Explorer’, in which the data can be browsed and viewed, reporter by reporter, in the context of sample and reporter annotations.

Data can also be exported for custom analyses (for example, for algorithms that are very expensive in computer power and time) and local development of new analysis methods, and in various defined formats for use in external analysis programs.

Documentation - BASE extensive documentation exists in different versions and formats.

Plug-ins - Many plug-ins are installed with the core install of BASE but many of these have to be configured before use.

The manufacturer maintains a list of 'core plug-ins' and provides a collection of sample configuration files.

Contributed plug-ins and plug-ins that depends on non-Java based software packages have to be installed separately after setting up a BASE server.

The manufacturer also provides a 'BASE plug-ins web site' for maintaining these add-on plug-ins.

System Requirements

Contact manufacturer.


Manufacturer Web Site BASE

Price Contact manufacturer.

G6G Abstract Number 20403

G6G Manufacturer Number 104034