Programs and databases used in the analysis of microarray data
Bioconductor is an open source and open development software project to provide tools for the analysis and comprehension of genomic data. The broad goals of the projects are to provide access to a wide range of powerful statistical and graphical methods for the analysis of genomic data, to facilitate the integration of biological metadata in the analysis of experimental data, and to allow the rapid development of extensible, scalable, and interoperable software.
http://www.bioconductor.org/
http://www.bioconductor.org/
Version: 1.4
Labs: Scientific Development and Visualization Lab, Computational Genetics Laboratory,
Scientific Development and Visualization Lab-sdvlapp1
System(s): All Sun machines and PC(sdvlapp1)
Categories: Bioinformatics, Microarray Analysis
The Bioinformatics Toolbox extends MATLAB to provide an integrated software environment for genome and proteome analysis. People can use the basic bioinformatic functions provided with this toolbox to create more complex algorithms and applications in drug discovery, genetic engineering, and biological research.
http://www.mathworks.com/access/helpdesk/help/toolbox/bioinfo/ug/
http://www.mathworks.com/access/helpdesk/help/toolbox/bioinfo/ug/
Version: 1.1
Labs: Scientific Development and Visualization Lab, Computational Genetics Laboratory,
Scientific Development and Visualization Lab-sdvlapp1
System(s): All Sun machines and PC(sdvlapp1)
Categories: Bioinformatics, Microarray Analysis
Cluster and TreeView are programs that provide a computational graphical environment for analyzing data from DNA microarray experiments, or other genomic datasets. The program Cluster organizes and analyzes the data in a number of different ways. TreeView allows the organized data to be visualized and browsed.
http://rana.lbl.gov/EisenSoftware.htm
None
Manual available
Version: v2.11 (Cluster) and v1.60 (TreeView)
Labs: Scientific Development and Visualization Lab-sdvlapp1
System(s): PC
Categories:Microarray Analysis, Data Analysis and Data Mining, Bioinformatics
The GeneData Expressionist suite is a computational system from GeneData Inc. for analyzing gene expression data from any one- or two-channel microarrays.
It consists of three closely integrated modules:
Refiner Data quality diagnosis and correction tool, which can be set up to pre-process data either in a fully interactive or in a entirely automated way.
CoBi: Oracle®-based data management system, which includes project and user management capabilities as well as gene annotation content for all commercially available Affymetrix® chips.
Analyst: Tools used for statistical analysis. Among other functionalities it features the latest machine learning algorithms to perform experiment classification and allows for automation of repetitive analysis tasks.
http://cgls1.msi.umn.edu/
http://www.genedata.com/
Getting Start Tour is available
Documentation Library is available
Please register with Computational Genetics Laboratory to get your Expressionist username and password.
You then can logon to Expressionist at http://cgls1.msi.umn.edu/
Client requirement: Window PC with a minimum of 256 MB RAM; web browser supporting Java Web Start,
Version:5.0, 4.0, and 3.1
Labs:Computational Genetics Laboratory
System(s): Web Access
Categories: Microarray Analysis, Bioinformatics
GeneChip Operating Software (GCOS) from Affymetrix is the software system for expression and DNA analysis.GCOS, GCOS Manager, and GCOS Administrator are a trio of applications that:
capture and analyze the array image provide workflow tracking of experiment data (image, cell intensities, probe analysis data) manage experiment data automate basic expression analysis and publishing
http://www.affymetrix.com/support/technical/tutorial/gcos/index.affx
Tutorial can be found at Affymetrix web site at: http://www.affymetrix.com/support/technical/tutorial/gcos/index.affx
User guides is available at http://www.affymetrix.com/support/technical/manuals.affx
You can run GCOS as regular PC program
Version: 1.1.1.052
Labs: Computational Genetics Laboratory, Basic Sciences Computing Lab
System(s): Windows (cpc2 at CGL)
Categories:Microarray Analysis, Bioinformatics
Description
GenePix(R) Pro is a software from Axon Instruments, Inc. for analyzing DNA and protein micrarrays, tissue arrays and cell arrays. These images acquired from either Axon Scanner or third-party scanners can be used.
http://www.axon.com/GN_GenePixSoftware.html
The user manual and tutorial book from Axon Instruments Inc. is available at bscl.
The user manual and tutorial book from Axon Instruments Inc. is available at bscl.
You can use GenePix after you loggin to the sdvlapp1.msi.umn.edu.Start -> Programs -> Axon Laboratory -> GenePix Pro 6.0 -> GenePix Pro 6.0
Version: 6.0
Labs: Scientific Development and Visualization Lab-sdvlapp1
System(s): PC
Categories:Microarray Analysis, Bioinformatics
The GeneSpring from SiliconGenetics is a visualization and analysis tool designed for use with gene expression data. It is capable of displaying and analyzing large data set on a typical desktop computer. GeneSpring provides a flexible set of analysis tools. Data from a variety of sources can be imported with case.
http://www.silicongenetics.com/cgi/SiG.cgi/Products/GeneSpring/index.smf
Online presentations are provided by Silicon Genetics
.
You can Download Demo software directly from Silicon Genetics.
GeneSpring User Manual can be viewed from GeneSpring "Help" menu.
GeneSpring is stand-alone software. Currently, it needs to be installed on the user local machine (PC, MAC, or Unix). However, the license key was installed on cgls1 server. The license key monitors and controls the registered users. In order to access and use this software:
1. Register as CGL user. See instruction
2. Contact MSI user support by phone 612 624 0802, email: help@msi.umn.edu, or directly contact Dr. Wayne Xu, or Dr. Zhengjin Tu. We come to your lab to install and set up geneSpring on your local computer.
Currently, geneSpring is not available on our sdvlapp1 Windows server. We are still working that. This web page will be updated as soon as geneSpring works on sdvlapp1 windows server.
Version:6.2
Labs:Computational Genetics Laboratory
System(s): ALL
Categories: Microarray Analysis, Bioinformatics
GeneTraffic Multi is web-based software for either one- or two-color microarray data management and data analysis. It can also be used for web publication of your microarray data.
http://cgl1.msi.umn.edu/
http://www.iobion.com/products/products.html
The online tutorials (IOBION VIDEOS) can be accessed through Iobion's web site
The User Manuals can be downloaded through Iobion's web site
Software are web accessible. However you need register with Computational Genetics Laboratory to get your username/passwd.
URL for accessing GeneTraffic: http://cgl1.msi.umn.edu/
Client requirement: Internet Explorer 6 running on Windows platform plus Flush 6
Version:3.1-4 Multi
Labs:Computational Genetics Laboratory
System(s): PC with Internet Explorer 5 and Internet Access
Categories: Microarray Analysis, Bioinformatics
Description
PathwayAssist, Stratagene commercial software, can build and examine biological association networks, including traditional pathways. One can see protein, small molecule and cellular processes all together for a more complete systems biology network view. In addition, it allows you to parse scientific text or build fact databases from your own research, such as information from PubMed. It also allows for the importation and overlay of microarray gene expression data within a built biological association network.
http://www.stratagene.com/products/displayProduct.aspx?pid=559
Training
download Manual
1. loggin to sdvlapp1.msi.umn.edu
2. Start PathwayAssist from Start | all programs | Stratagene
3. If the first time:
. Ignore the "not found data directory" error message.
. go to manu Database | Manage database | Download database | check From Internet.
. Save to your local V drive, or save to your citrix My Document (the Resnet data file is 660 mb,
larger than the user's default 500 mb space. So you need to send us request for increase space
if you want.
. Then go to Database | Manage database | Open databse | browse to db location.
If you have the databse already, directly Database | Manage database | Open databse | browse to the db location.
Version: 2.5
Labs: Scientific Development and Visualization Lab-sdvlapp1
System(s): Windows
Categories:Microarray Analysis, Bioinformatics
Picky is an oligo microarray design program that identifies probes that are very unique and specific to input sequences. These calculations are based on parameters inputted by the user including optimal probe length, ideal percentage of guanine and cytosine content, target-melting temperature, salt concentration and the maximum length to which a target sequence matches any non-target sequence.
http://www.complex.iastate.edu/download/Picky/index.html
Tutorial can be found at http://www.complex.iastate.edu/download/Picky/tutorials.html
Version: 1.10
Labs: Computational Genetics Laboratory, Netfinity,
Scientific Development and Visualization Lab-sdvlapp1
System(s): All Sun machines and PC(sdvlapp1)
Categories: Bioinformatics, Microarray Analysis
S+ArrayAnalyzer is an S-PLUS module from Insightful Corp. It is powerful tool for analyzing Affymetrix MAS and CEL data, and cDNA microarray data. S+ArrayAnalyzer has both the graphical user interface (GUI) dialogs and the commands window. It can be used for statistical analysis to determine differential gene expression in microarray.
http://www.insightful.com
None
User guide can be found at http://www.insightful.com/products/s-plus_arrayanalyzer/usersguide.pdf
You can use S+ArrayAnalyzer when you login sdvlapp1 server.
Follow these steps to start S-PLUS:
Start -> Programs -> S-PLUS 6.1 Professional for Networks server -> S-PLUS 6.1
Then EITHER go S-PLUS Menu -> File -> Load Module ... -> Choose ArrayAnalyzer module
OR use S-PLUS - Commands window, type module(ArrayAnalyzer)
A new "ArrayAnalyzer" menu item will show up. You then can access ArrayAnalyzer.
One user concurrent license was purchased.
Version: 1.1 for Windows
Labs: Scientific Development and Visualization Lab-sdvlapp1
System(s): Windows
Categories: Microarray Analysis, Statistics
SAM: Significance Analysis of Microarrays is a supervised learning software for genomic expression data mining.It correlates gene expression data to a wide variety of clinical parameters including treatment, diagnosis categories, survival time and time trends. SAM provides estimate of False Discovery Rate for multiple testing. With its convenient Excel Add-in, program works with data from both cDNA and oligo microarrays. Can also be applied to protein expression data and SNP chip data.
http://www-stat.stanford.edu/~tibs/SAM/
None
Documentation can be found at SAM home page http://www-stat.stanford.edu/~tibs/SAM/
Program is Microsoft Excel add-in, you can call SAM function within Excel.
Version: 1.21
Labs: Basic Sciences Computing Lab
System(s): PC
Categories:Microarray Analysis, Bioinformatics, Data Analysis and Data Mining
Spotfire is general data analysis and visualization software with the stress on commonly used microarray data analysis methods. Spotfire has a Web interface and works with large amounts of data. It can import data from databases (Oracle, SQL-Server, Informix and Sybase), arbitrary tables and Excel spreadsheets. It allows user to select data for analysis during import and during the analysis itself. The software exports results in a variety of formats, including HTML, PowerPoint, Word.Data Format
Any usual separator will work with the flat files. Parameters can be both textual and digital in arbitrary order. The table can have empty values also.
The software treats rows as objects and columns as parameters, describing the objects.
Visualization
Scatter plots, histograms, line plots can be easily created. If there is a categorical parameter dividing objects on groups, the program can create plots for each group for comparison.
Statistics Method Example of Genomics Use Hierarchical and k-means clustering with various metrics and flavors You can group together both similar genes and tissues Box plot Visually compare distributions of gene expressions across groups Comparison of means in the groups (column anova) Compare gene expression between groups Normalization by mean and std To make values of expression of different genes comparable Decision tree (logical rule, how one categorical variable depends on some set of variables) How to make diagnosis by values of gene expression Principal Component Analysis Visually compare the groups of arrays Normal probability plot To check normality of distributions
http://www.spotfire.com
None
User guides and reference manuals are available at http://home.spotfire.net/spotfire/support/manuals/manuals.jsp