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Research Tools

CAZypedia - a community-driven encyclopedia of carbohydrate-active enzymes

Please see the research data page for our journal article supplements.


Gemma: http://gemma.chibi.ubc.ca/

Gemma is a system for analyzing genomics data using meta-analysis techniques.


ASPIREdb: http://aspiredb.chibi.ubc.ca/

ASPIREdb is a web-based software system for the analysis of genomic variants (CNVs, SNVs, and Indels) and phenotypes.


Phenocarta: http://phenocarta.chibi.ubc.ca/

Phenocarta is a knowledgebase that consolidates information on genes and phenotypes across multiple resources and allows tracking and exploring of the associations.
Formerly known as Neurocarta.


ErmineJ: http://erminej.chibi.ubc.ca/

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.


NeuroElectro: http://neuroelectro.org/

NeuroElectro is a web-based database that stores measurements of basic biophysical properties from diverse neuron types throughout the nervous system.


NeuroExpresso: http://neuroexpresso.org/

NeuroExpresso is a web-based application designed to facilitate the visualization of gene expression in mouse brain cell types.


gotrack_logo

GOtrack: http://gotrack.msl.ubc.ca

GOtrack is a user-friendly tool to browse the development of gene product annotations. GOtrack currently supports annotation data for 14 different organisms.


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.


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.


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://chibi.ubc.ca/cgi-bin/nph-SVMsubmit.cgi. Gist was developed with Bill Noble.