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Research Tools

NeuroGem: https://neurogem.msl.ubc.ca

Database of genetic modifiers

We are interested in understanding the logic by which interactions that are mediated by intrinsically disordered proteins can regulate complex cellular processes and how defects in interactions lead to disease. In our research, we are also addressing questions related to protein misfolding and aggregation. Protein aggregation and amyloid formation have been linked to a variety of neurodegenerative disorders such as Alzheimer’s disease, Parkinson’s disease or Creutzfeldt-Jakob disease. We are developing new computational approaches to study protein aggregation and predict the structure proteins adopt in amyloid fibrils. Using high-throughput screening methods, we further aim at understanding which protein-protein interactions are affected in neurodegenerative disorders such as Huntington’s or Creutzfeldt-Jakob disease, and more specifically, which signaling pathways most perturbed.


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


Gemma: https://gemma.msl.ubc.ca

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

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


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: https://gemma.msl.ubc.ca/phenotypes.html

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.msl.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: https://matrix2png.msl.ubc.ca

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: https://gemma.msl.ubc.ca/annots/

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


Gist: https://svm.msl.ubc.ca

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