A non-exhaustive list of possible MIAME compliant software

  • MIAMExpress - a MIAME compliant annotation tool at the EBI.
  • Gene Traffic - a microarray data management and analysis software developed at iobion informatics.
  • Ipsogen Cancer Profiler -  "A Bioinformatics system composed of Discovery Software tools and of ELOGE database, utilised to identify transcriptional signatures belonging to each cancer type. This system ensures the management of gene expression measurement, traceability in a GLP environment".
  • BASE (BioArray Software Environment) - "a web-based open source MIAME-supportive microarray DB and analysis platform."
  • GeneData Expressionist™ - "is a computational system that efficiently processes gene expression data generated by high-throughput microarray technologies. In support of MIAME Expressionist provides extensive reporting capabilities for data pre-processing, quality control and statistical analysis. The system is fully extendable to encompass all areas of MIAME".
  • Partisan arrayLIMS - "a commercial LIMS for microarrays. Features: array design, manufacturing, experiment, sample management, analysis, data mining connectivity, MIAME compliant, project management, high security, web based.
    Extras: open interfaces, communication with spotters, imaging tools, data analyis."
  • LIMaS - "We have developed a non-commercial Java based platform independent LIMS for arrays called LIMaS that uses controlled vocabulary and captures every aspect of a micorarray experiment, whether affymetrix or spotted arrays.
    Available free to academics from http://www.limas.har.mrc.ac.uk/"
  • GeneDirector - "BioDiscovery is the leading provider of complete integrated software solutions for microarray research. BioDiscovery's GeneDirector, Data Management Platform, is a microarray LIMS and full image and data analysis platform with Oracle database capability to enhance microarray discovery."
  • GeneSpring and GeNet - "GeneSpring and GeNet now have a MIAME (Minimum Information About a Microarray Experiment) compliant list of Standard Attributes and Attribute Values. The Standard Attributes file creates a list of attributes and units that can be associated with individual samples." - submitted by Kai Kumpf.
  • MCHIPS [Multi-Conditional Hybridization Intensity Processing System] - "M-CHiPS is a system for microarray data warehousing and microarray data analysis. It can be used as a LIMS for DNA chip experiments, also. Unlike other microarray data repositories, it entirely dispenses with free-text format, instead holding all the information in a format ready for statistical analysis"
  • maxd - "maxd is a data warehouse and visualisation environment for genomic expression data. It is being developed by the Microarray Group at the University of Manchester. The software is free for academic use, download it now and try it for yourself;source code included! If you'd like to be informed of new developments as they occur, please join the maxd_announce mailing list."
  • Genowiz™  - A comprehensive multi platform package for tracking and analyzing Gene Expressions data. GenowizTM conforms to internationally accepted MIAME standards. It is equipped with a suite of analysis tools for efficient analysis of Gene Expression data. Various graphical tools help the individual researcher to establish biological significance and relevance of gene expression results. GenowizTM can connect to various public databases including metabolic pathways database that can provide quick access to pertinent knowledge base to add value to research. It has an integrated relational database that keeps track of all the data and results."
  • RAD - "The RNA Abundance Database (RAD) provides a comprehensive MIAME-supportive infrastructure for gene expression data management and makes extensive use of ontologies. Specific details on protocols, biomaterials, study designs, etc., are collected through a user-friendly suite of web annotation forms. Software has been developed to generate MAGE-ML documents to enable easy export of studies stored in RAD to any other database accepting data in this format (e.g. ArrayExpress). RAD is part of a more general Genomics Unified Schema (GUS: www.gusdb.org), which includes DoTS (Database of Transcribed Sequences) for sequence and sequence annotation thus providing a platform that integrates genomic and transcriptomic data from multiple organisms."
  • GenePix Pro 6.0 - "Exports only analysis results in MAGE-ML format"
  • TeraGenomics™ - "TeraGenomics(tm) is a scalable, high-performance data warehousing solution for analyzing and sharing Affymetrix® GeneChip® data. TeraGenomics has a MIAME-compliant metadata structure comprised of 140 data elements within controlled vocabularies (e.g., for organism, anatomy, and disease type) accessed through pull-down menus. GeneChip data in the warehouse can be browsed and queried by any of these elements. TeraGenomics is a browser-based thin client solution that can be securely deployed over the web or on an intranet. TeraGenomics is an ideal solution for scientists in multiple locations who perform GeneChip experiments to consistently manage their data and share it for collaborative research."
  • almaZen™ - "almaZen™ is the only system currently available that assists researchers in organizing and managing the large number of biological samples involved in a typical DNA array experiment. The system provides on-screen simulation of the fabrication of a DNA array, covering all stages from obtaining the primary multiwell plates to the final layout, design and fabrication of the array. In addition, the system records all manipulations of the multiwell plates made by a liquid-handling robot, so creating an audit trail which is then used to identify, annotate and correct any incidences arising."
  • GeneSifter.Net - "To Understand the Biology underlying complex expression patterns in microarray data requires determining the statistical and biological significance of individual data points and groups. GeneSifter.Net is the integrated analysis system designed de novo for just that. Sift out gene lists, zoom in to particular items and annotations, or manipulate groups based on gene ontologies, clustering, and your own filter definitions as you examine the interplay of your data with factors of both statistical and biological relevance. For a free, no-obligation trial account Please visit www.genesifter.net"
  • SeqExpress - "SeqExpress is a standalone application for the analysis of gene expression experiments"
  • MIAME Spice - "A MIAME compliant microarray data annotation and packaging tool."
  • ArrayHub - "ArrayHub is a LIMS database application to store, organize and track a complete set of descriptive information for all tasks performed in microarray experiments (experimental factors, hybrizations, samples, labeled extracts, slides, images, files ...). It supports configurable workflows, integration with third-party data analysis tools (e.g. Spotfire) and MIAME compliance."
  • Feature Extraction 7.5 (Agilent) - "Exports only analysis results in MAGE-ML format"
  • TM4 - "The TM4 suite of tools consist of four major applications, Microarray Data Manager (MADAM), TIGR_Spotfinder, Microarray Data Analysis System (MIDAS), and Multiexperiment Viewer (MeV), as well as a Minimal Information About a Microarray Experiment (MIAME)-compliant MySQL database, all of which are freely available to the scientific research community at TIGR's Software Download Site"
  • SAS Microarray - "provides a sophisticated yet easy-to-use platform that enables scientific organization to consistently generate and utilize microarray results to identify targets and assess potentially successful leads more quickly and with confidence, as well as better assess clinical safety. It incorporates data management components (including audit trail, versioning and security which enable compliance), powerful analytics and interactive visualization technology. In addition, by leveraging SAS XML technologies, the platform can support import as well as export MAGE-ML data format capabilities."
  • GenStat - GenStat is a GENeral STATistics package developed by VSN International Ltd. GenStat is a comprehensive statistics system which offers ease-of-use for the novice user through a Windows menu interface, or power and flexibility for the more experienced user through a powerful command language interface.
    One of the main strengths of GenStat is the range of powerful statistics techniques available which have been tested time and again by practicing statisticians. The range of statistics available includes basic statistics, design and analysis of designed experiments, analysis of linear and generalized linear mixed models, microarray analysis, regression (linear, nonlinear and generalized linear), hierarchical generalized linear models, spatial analysis, multivariate analysis techniques, time series, statistical process control methods, survival analysis, sample size calculations and resampling methods.
    For comprehensive details see
    For a downloadable evaluation see:
  • GeneMaths XT - "GeneMaths XT is a complete and professional software package for microarray analysis. Its advanced concept of layers and subsets makes it is possible to work with different layers for different data outputs, for example Cy3 and Cy5, standard deviations, error values, etc., as well as different subsets of genes and/or arrays. Also unique is the full error handling through all analysis, mining, and statistics functions. Contact us for an evaluation version: info@applied-maths.com"
  • Tab2MAGE - "Tab2MAGE is a software package/web tool that generates a spreadsheet template for you to complete and upload with your data files."

If you are aware of any other MIAME compliant tools, please send a link to


[Disclosure: Please be aware that the software listed here have not undergone any kind of rigorous tests for MIAME compliance. MGED is in the process of determining how this may be accomplished in the future. MGED does not also endorse any of the software.]

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