My Microarray Software Comparison - Database/ Laboratory Information Management System (LIMS) Software

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Definition of database/ Laboratory Information Management System (LIMS) software
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Database/ Laboratory Information Management System (LIMS) software (in alphabetical order)

Definition of database/ Laboratory Information Management System (LIMS) software

LIMS tends to concentrate on the earlier stage of array manufacturing information management while database focuses more on the later stage - archival of analyzed data -, they share the common function to record and organize a large collection of data for rapid search and retrieval. Sometimes the distinction between them is not clear cut.

A closely related species of database software is public microarray database, a public repository of microarray data. Please refer to My Microarray Software Comparison - Public Microarray Database for further information.

Database/ Laboratory Information Management System (LIMS) software (in alphabetical order)

Product	Company/ Institute	Interface/ Server Operating System	Features	Price	Remarks
Acuity 2.0	Axon Instruments	Windows 2000/XP client; Windows 2000 server (recommended)	various visualation tools; normalization, hierarchical, k-means, k-medians clustering with many different similarity metrics, SOM, PCA, gene shaving. Scripting engine for customizable analysis through VBScript, JavaScript or ActiveX objects store data in relational database, Supports Microsoft SQL Server 2000, ODBC-compliant	US $4,000 (U.S.A. and Canada only)	Full integration with GenePix Pro 4
AMAD	UCSF	Html/ windows, mac, linux or Unix with perl support	AMAD is a flat file, web driven database system written entirely in PERL and javascript, and intended for use with microarray generated data. Provides a means for storage, retrieval, and extraction of microarray data by means of a centralized web based server. work seamlessly with Cluster and Treeview	Free	-
ARGUS	Dr. Michael A. Gimbrone Jr lab; Harvard University	Web/ Windows 95/98/NT server/2000	database software system designed to process, analyze, manage, and publish microarray data	Free for academic user	download; reference [PubMed]
ArrayDB	NHGRI	Html/ linux or Unix	a software suite that provides an interactive user interface for the mining and analysis of microarray gene expression data. All of the analyzed expression data from a microarray experiment, as well as information about the clones used in the experiment, are stored in a relational database	Free	download (registration required); online demo; database schema; readme;
ArrayInformatics	Perkin Elmer Life Sciences	WindowsNT, Microsoft SQL server	Direct data links to SpotArray, ScanArray, and QuantArray microarray instrumentation for increased automation capabilities; Barcode automation provides increased throughput; various data analysis and visualization tools	no pricing information is available	-
BASE (BioArray Software Environment)	Department of Oncology, Lund University	Linux server, MySQL, web client	BASE is a comprehensive database server to manage the massive amounts of data generated by microarray analysis. It manages biomaterial information, raw data and images, and provides integrated and "plug-in"-able normalization, data viewing and analysis tools. The system also has array production LIMS features; support MIAME and MAGE-ML	Free, GNU GPL	download;schema; textual description; specification; reference [PubMed][pdf]
CloneTracker 2	Biodiscovery	Windows 95/98/NT4/2000/XP	managing and processing all information associated with fabrication of spotted microarrays using many of the popular commercial robotic systems	no pricing information is available	demo available upon registration; brochure;
Genedirector 2	BioDiscovery	Windows	comprehensive microarray data management system that organize, archive, retrieve, analyze and query all microarray data throughout the entire workflow; built-in LIMS for project managment; Relation Database Design deployed on Oracle; Security control; integrate with Clonetracker, Imagene and Genesight for various stage of data analysis.	no pricing information is available	-
GeNet 4.1	Silicon Genetics	Windows 2000, Unix/ Linux Oracle (optinal); web client	dynamically archive and visualize expression data from a wide range of technologies and organisms.	no pricing information is available	online demo; trial upon registration; pdf data sheet; reference (link to journal)
Genetraffic 1.2	Iobion Informatics	web client (require IE 6.0 or later)/ Linux server,	A turnkey system stores, analyzes and visualizes microarray expression data. Store raw data and images in a PostgreSQL relational database. Supports the MIAME standards. Provides data management and data validation tools. Features include normalization, hierarchical & K means clustering, PCA, multidimensional scaling and annotation storage.	no pricing information is available	demo available (registration is required); screenshots;faq;
GeneX	GeneX is an Open Source project based in SourceForge.net	web clinet/ Linux or Solaris server	GeneX is an Open Source DATABASE system. It is NOT a commercial-grade, plug and play system for analyzing single sets of gene expression.	LGPL	Install doc; download; online documentation
Genowiz	Ocimum Biosolutions	Windows, Macintosh, Unix, Linux, Solaris	Database module compliant with MIAME, manages planning, execution, and storage of microarray experiments. The module is provided with administrative access levels. Analysis Tracking, Data import and filtering, normalization, hierarchical, K-means/Forgy's clustering, SOMs, PCA, Data classification, pathway analysis.	no pricing information is available	-
Longhorn Array Database	Section of Molecular Genetics and Microbiology, Institute for Cellular and Molecular Biology, University of Texas at Austin	Linux and PostgreSQL	The Longhorn Array Database (LAD) is a MIAME compliant microarray database that operates on PostgreSQL and Linux. It is a fully open source version of the Stanford Microarray Database (SMD)	?	Download; Reference [PubMed][pdf]
LIMaS (Laboratory Information Management for Array Systems)	Mammalian Genetics Unit, Harwell UK.	Java with a relational database (MySQL, Sybase and Oracle) backend	a platform independent multi-tier Java package with a relational database backend designed to track the laboratory process and allows users to write and save protocols and parameters for each experiment as well as the expression data produced from image analysis; MIAME compliant	free for academic	download;documentation
MADAM (MicroArray DAta Manager)	The Institute of Genomic Research (TIGR)	Windows	MADAM (MicroArray DAta Manager) is a java-based application designed to load and retrieve microarray data to and from a database (also supplied with the software). MADAM provides data entry forms, data report forms and additional applications necessary to maintain microarray data for further analysis. Madam requires JRE 1.3.1.	Free (Open source)	User guide; Download Program; Download Program and Source; Reference [PubMed]
µArrayDB	Array Genetics	web client/ Linux server	a web-based database system for archiving and exchanging DNA microarray data (e.g., in .DAT, .CEL and .EXP formats). All information in the µArrayDB database can be interrogated through a web interface and down loaded through the HTTP file transfer protocol.	$9900	-
maxd (Manchester ArrayExpress Database)	Microarray group,Machester Bioinformatics	?	a data warehouse and visualisation environment for genomic expression data.	Free for academic	download;
NOMAD	UCSF	Unix/ Linux/ Mac OS X	an open source system for storing and querying the results of microarray experiments.	Free for academic	alpha release; mailing list; development site
Partisan ArrayLIMS	Clondiag	server: Linux (preferred) or Windows, ORACLE clients: web	LIMS for microarrays: array design, manufacturing, experiments, sample management, analysis, open interfaces, imaging tools, data analyis, MIAME compliant	Please quote; special academic offers	online demo;online documentation; brochure;application;screen shots; faq;
Phoretix Array Professional	Nonlinear Dynamics	Windows	A combination of Phoretix Array v3.0 and Phoretix Array Database v2.0; user friend GUI	no pricing information is available	demo upon registration;
Rosetta Resolver 3.0	Rosetta Biosoftware	JAVA/ UNIX with Oracle 8i relational database	The Rosetta Resolver system combines advanced analysis software, a high-capacity database, and high-performance server framework in one enterprise-wide tool.	no pricing information is available	-
Scierra Microarray Laboratory Workflow System	Amersham Biosciences	?	A complete management system for microarray experiments and gene expression data.	?	reference materials; faq
Stanford Microarray Database (SMD) package	Stanford University	Oracle server 8.0.6 or above; web server; UNIX with perl support	SMD stores raw and normalized data from microarray experiments, as well as their corresponding image files. In addition, SMD provides interfaces for data retrieval, analysis and visualization.	Free for academic	download upon registration; specification; about SMD; linux implementation by papa kilo

last updated: 20 Jul 2004
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