Table 1 A comparison of the different products available to handle transcriptome experimental data

maxdLoad2

Any that runs Java

Yes

maxd-ML, MAGE-ML, bulk loading from CSV files using XML

maxd-ML, text and fully expressive MAGE-ML

Yes

maxdBrowse

Server requires Apache and PHP5. Clients any web browser or program/script that can be configured to retrieve data via SOAP (if remote) or from the command-line (if run on the server)

Same as maxdLoad2

No import

Exports plain-text, HTML and XML

Yes – runs off maxdLoad2 attributes

MIAMExpress

Any (web-based)

Yes

Web-based forms

N/A

No

No bulk load facility, although it is being extended to allow uploading from spreadsheets in the future

BASE

Server is installed on GNU/Linux, with a web-based front-end

Optional

Web-based forms, bulk loading for raw data only

MAGE-ML

Potentially, via user definable fields

Plug-ins available for data normalisation, analysis and viewing

MADAM

MS Windows and GNU/Linux

Yes

Web-based forms, no bulk loading

Its own format (.mev)

Potentially, by editing the database schema

Is being adapted to read and write MAGE-ML in the future

LAD

Server is installed on GNU/Linux, with a web based front end

Yes

Batch imports using tab delimited files

Tab delimited file

No

Very limited experimental annotation. Open source version of the Stanford Microarray Database