Software Demo
Session
Monday,
August 16th
HDBStat!
: An integrated software suite for statistical analysis of high dimensional biology data
David Allison and Prinal Trivedi
University of Alabama at Birmingham
HDBStat!, which stands for High-Dimensional Biology-Statistics, is a
software package designed for analysis of high dimensional biology
data. HDBStat! was initially developed for analysis of microarray gene
expression data, but can also be used for some applications in
proteomics and other aspects of genomics. HDBStat! allows researchers
to analyze complex microarray data using data preprocessing methods
such as Quantile-Quantile normalization, Chip-Mean normalization,
Linear Model Normalization, various log transformations; quality
control method such as Deleted Residuals;
hypothesis testing methods such as Equal and Unequal Variance t-tests,
Bootstrap, Chebby Checker; multiplicity control methods such as
Bonferroni, Sidak, False Discovery Rate, Mix-o-matic; and estimation
methods such as Empirical Bayes Estimates. These methods take
into account non-normal data and small sample sizes. Other
features of HDBStat! include platform-independent Java implementation,
and flexible, easy-to-use interface. This software is freely
available to academic institutions and non-profit organizations at http://www.soph.uab.edu/ssg_content.asp?id=1164.
The
Statistical Reality Engine: A Collaborative Environment for Data
Analysis
Richard Boyce and A.J. Rossini
Virtual Reality has underperformed its promise for data
analysis. We present a prototype of a system based on commodity
tools,
systems, and hardware. This prototype, while incomplete, has been
used
for needs assessment for our second generation data analysis
environment. It can be easily deployed on a single machine, in a
cluster of machines, or a fully immersive VR environment, and employs
both command-line functionality and low-cost I/O devices including
joysticks, gamepads, and "gaming gloves" for interfacing. While
the
system fails to provide some critical functionality, it is usable as a
simple extension of the RGL OpenGL package for R. One of the
target
applications is collaborative data analysis in the bioinformatics
domain.
The
TM4 System for DNA Microarray Analysis
John Quackenbush
The Institute
for Genomic Research
TM4 is a comprehensive, open source, platform independent system for
collecting, managing, and analyzing microarray data. The system
consists of four primary applications as well as a set of ancillary and
other derived tools. MADAM is a java-based data entry and management
system with an intiutive graphical user interface built on top of a
MIAME-compliant MySQL database. MADAM is the first freely-available
database system capable of exporting data in MAGE-ML. Spotfinder is an
image processing tool written in platform-independent c/c++ that
provides a range of quailty control assessments for microarray images.
MIDAS is a data normalization and filtering tool designed with a
graphical scripting interface that allows the creation of a complex
analysis pipeline. MeV is a data mining and statistical analysis tool
that provides access to more than twenty sophisticated algorithms and
allowsusers to interact with and compare the results from a range of
individual analyses. All software is provided with source code under
the Artistic License with a well-defined API and many groups have
contributed analysis modules or used modules to construct still other
tools. The goal of this demo will be to highlight the capabilities of
the various tools, with a focus on MeV.