CAGED 1.1 – Cluster Analysis of Gene Expression Dynamics

CAGED 1.1

:: DESCRIPTION

CAGED (Cluster Analysis of Gene Expression Dynamics) is a model based,Bayesian clustering procedure developed by Ramoni et al. to cluster gene expression profiles measured with microarrays in temporal experiments. Contrary to popular clustering methods, CAGED takes into account explicitly the fact that expression profiles in temporal experiments may be serially correlated and uses a model-based, Bayesian procedure to identify the best grouping of the gene expression data in an automated way.

CAGED implements a Bayesian clustering method designed to handle temporal experiments and subsuming standard independent experiments as a special case.

::DEVELOPER

Marco Ramoni & Paola Sebastiani

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

CAGED

:: MORE INFORMATION

You will need a password to use this program. Please email sebas@bu.edu for a password.

Spotfinder v3.2.1 – Microarray Images Analysis & Gene Expression Quantification

Spotfinder v3.2.1

:: DESCRIPTION

Spotfinder is an image processing program created at The Institute for Genomic Research (J. Craig Venter Institute now) for analysis of the image files generated in microarray expression studies. Spotfinder uses a fast and reproducible algorithm to identify the spots on array and provide quantitation of expression levels.

Image analysis is a crucial step in the microarray process. TIGR Spotfinder was designed for the rapid, reproducible and computer-aided analysis of microarray images and the quantification of gene expression. TIGR Spotfinder reads paired 16-bit or 8-bit TIFF image files generated by most microarray scanners. Semi-automatic grid construction defines the areas of the slide where spots are expected. Automatic and manual grid adjustments help to ensure that each rectangular grid cell is centered on a spot. Two available segmentation methods (histogram and Otsu) define the boundaries between each spot and the surrounding local background. Spot intensities are calculated as an integral of non-saturated pixels, although other options including spot median and mean values are available. Local background subtraction for each reported value is applied by default but can be disabled. The calculated intensities, medians, and means along with each spot position on the array, spot area, background values, and quality control flags are written to a MEV file or the database. Reusable grid geometry files and automatic grid adjustment allow user to analyze large quantities of images in a consistent and efficient manner. To complement the automated methods, particularly in noisy areas of the slide, the user may manually identify or discard spots. Quality control views allow the user to assess systematic biases in the data.

::DEVELOPER

J. Craig Venter Institute

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows/Mac OS X on Intel chips/Mac OS X on PowerPC chips/Linux

:: DOWNLOAD

Spotfinder v3.2.1 for Win ; for Mac OS X on Intel chips ; for Mac OS X on PowerPC chips ; for Linux ; Manual ; Source Code ; Training Documents

:: MORE INFORMATION

Referencing Spotfinder

Saeed AI, Sharov V, White J, Li J, Liang W, Bhagabati N, Braisted J, Klapa M, Currier T, Thiagarajan M, Sturn A, Snuffin M, Rezantsev A, Popov D, Ryltsov A, Kostukovich E, Borisovsky I, Liu Z, Vinsavich A, Trush V, Quackenbush J. TM4: a free, open-source system for microarray data management and analysis. Biotechniques. 2003 Feb;34(2):374-8.

MADAM 4.1 – MicroArray DAta Manager

MADAM 4.1

:: DESCRIPTION

Madam (Microarray Data Manager) is a suite of tools used to upload,download, and display a plethora of microarray data to and from a database management system (MySql). Working as an interface for the MySql, Madam allows scientists and researchers to manage their microarray data efficiently to meet the requirement of experiment annotation and data mining.

Madam implemented in Java, facilitates the entry of data into a relational database. MADAM guides users through the microarray process from RNA procurement to data analysis, offering intelligent forms to simplify the tracking of experimental parameters and results that are essential for the interpretation of expression results in downstream analyses. Canned reports provide information on RNA samples, studies, slide maps and other pertinent data and a general SQL query window allows freeform access to the underlying database.

MADAM also serves as a platform for launching other data entry and management tools. Through the use of these integrated modules, users can view and score PCR plates, design experiments and studies, and track laboratory materials. Although not yet supported, MADAM is being adapted to read and write MAGE-ML, the XML data exchange format being developed by an international consortium of leading public databases and microarray research centers. A MAGE-ML version of MADAM should be available by the end of this year and will facilitate submission of microarray data to public repositories such as Array Express and GEO.

::DEVELOPER

J. Craig Venter Institute

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

MADAM v4.0 for Win ; MADAM 4.1 for Linux ; Source Code ;  Manual ; Training Documents

:: MORE INFORMATION

Referencing MADAM

Saeed AI, Sharov V, White J, Li J, Liang W, Bhagabati N, Braisted J, Klapa M, Currier T, Thiagarajan M, Sturn A, Snuffin M, Rezantsev A, Popov D, Ryltsov A, Kostukovich E, Borisovsky I, Liu Z, Vinsavich A, Trush V, Quackenbush J. TM4: a free, open-source system for microarray data management and analysis. Biotechniques. 2003 Feb;34(2):374-8.

GAL File Generator 1.2 – Well Plates Files Conversion

GAL File Generator 1.2

:: DESCRIPTION

GAL File Generator . Conversion of a file of 96 well plates into a file of 384 well plates, and conversion of a file of 384 well plates into an Axon GenePix Gene Array List file (.gal file). Several options are available for this latter function, including spot size, spacing, and orientation of plate in the arrayer with respect to the slides

::DEVELOPER

Derisi Lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

GAL File Generator 1.2

:: MORE INFORMATION

GAL File Generator also named for Gal File Maker.

AMIADA 2.0.7 – Analysis of Microarray Data

AMIADA 2.0.7

:: DESCRIPTION

AMIADA is an integrated computer program for organizing, exploring, visualizing, and analyzing microarray data. It features an EXCEL-like user interface and performs data transformation, principal component analysis, a variety of cluster analysis and extensive graphic functions for visualizing expression profiles.

::DEVELOPER

Dr. Xuhua Xia

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

AMIADA

:: MORE INFORMATION

Citation : Xia, X., and Xie. Z., 2001 AMADA: Analysis of microarray data. Bioinformatics 17:569-570.

MAExplorer 0.96.34.01 – MicroArray Explorer Tool

MAExplorer 0.96.34.01

:: DESCRIPTION

The MAExplorer is a Java-based bioinformatics exploratory data-analysis and data-mining program for analyzing sets of quantitative spotted cDNA or oligonucleotide microarray data . It includes data management, graphics, statistics, clustering, reports, gene data-filtering, user written MAEPlugins, documentation, tutorials, demo data. The exploratory data analysis environment provides tools for the data-mining of quantitative expression profiles across multiple microarrays.

With MAExplorer, it is possible to: 1) analyze the expression of individual genes; 2) analyze the expression of gene families and clusters; 3) compare expression patterns and outliers; 4) directly access other genomic databases for genes of interest. Previously quantified array data is copied to your local computer where it is read by MAExplorer and intermediate results as well as the data mining session state may be saved between data mining sessions.

::DEVELOPER

Dr. Peter Lemkin (LECB/NCI-Frederick) with help from Gregory Thornwall (SAIC) and Jai Evans (DECA/CIT, NIH)

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows
  • Linux
  • MacOsX
  • Java

:: DOWNLOAD

MAExplorer 0.96.34.01 , Manual

:: MORE INFORMATION

MAExplorer is available as Open Source at the SourceForge at http://maexplorer.sourceforge.net/ under the Mozilla Public License 1.1 (MPL 1.1) with an acompanying LEGAL document required by the U.S. Government.

ArrayMaker 2.6 – Provides Robotic Control of Microarrayer Robots

ArrayMaker 2.6

:: DESCRIPTION

ArrayMaker provides high performance robotic control of microarrayer robots with an incredibly intuitive, easy to use interface. ArrayMaker is optimized for use with the new generation of ultra fast linear servo driven arrayers, yet it is backwards compatible with the original MGuide style of ball-screw driven arrayers.

Features highly flexible configuration options, orange packing, replicate spots, replicate arrays, multiple slide and plate orientations.

::DEVELOPER

Derisi Lab

:: SCREENSHOTS

:: REQUIREMENTS

Windows 98/2000/NT/XP, Galil DMC-1832 Series PCI Bus Controller Card

:: DOWNLOAD

ArrayMaker 2.6, File Size:2,494K

:: MORE INFORMATION

This version has a new parameter in the “motor.cfg” file for a separate acceleration value for the x-stage during test prints. This value should be entered on the 19th line of your “motor.cfg” file, inserted between the “HPrintZ” line and the “SpeedX” line.

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