For links to research-related resources please see the research data page.

Gemma: http://chibi.ubc.ca/Gemma

Gemma is a system for analyzing genomics data using meta-analysis techniques. Gemma replaced our old Tmm system.

ErmineJ: http://chibi.ubc.ca/ermineJ

ErmineJ performs analyses of gene sets in expression microarray data. A typical goal is to determine whether particular biological pathways are "doing something interesting" in the data. The software is designed to be used by biologists with little or no informatics background. A command-line interface is available for users who wish to script the use of ermineJ.

Tmm: http://chibi.ubc.ca/tmm

Tmm is an experimental system for exploring the coexpression of genes based on microarray data. It allows users to query across dozens of published expression data sets for recurring profiles,and can be used to infer functional relationships among genes. Tmm is now deprecated having been replaced with Gemma.

Gist: http://chibi.ubc.ca/gist

Gist contains software tools for support vector machine classification and for kernel principal components analysis. The SVM portion of Gist is available via an interactive web server at http://svm.sdsc.edu.Gist was developed withBill Noble.

ErmineDB: http://chibi.ubc.ca/ermineDB

ErmineDB is a database that assembles sequence annotations from public sources, augmented by our own sequence analysis. The system has a narrow focus on genes represented by probes on microarrays. ErmineDB has now been largely supplanted by functionality provided by Gemma.

Annotations: http://chibi.ubc.ca/microannots

We offer a comprehensive set of microarray platform annotation files, generated using Gemma. The files available for download can be used with ermineJ.

Matrix2png: http://chibi.ubc.ca/matrix2png

Matrix2png is a simple but powerful program for making visualizations of microarray data and many other data types. It generates PNG formatted images from text files of data. It is fast,easy to use, and reasonably flexible. It can be used to generate publication-quality images, or to act as a image generator for web applications. Our group has found it useful for imaging all kinds of matrix-based data, not just microarray data. A web interface is included.