16th Annual
International Conference
Intelligent Systems
for Molecular Biology

Metro Toronto Convention Centre (South Building)
Toronto, Canada









Workshop 1: GenePattern

Wednesday, July 23 - 10:45 a.m. - 12:40 p.m.

Room 714

Presenter: Ted Liefeld, Broad Institute of MIT and Harvard, Cambridge, US



GenePattern is a freely available platform for integrative genomics. It provides access to a broad array of computational methods including over 100 computational and visualization tools for the analysis of gene expression, SNP and proteomic data. Its extendable architecture enables computational biologists to easily add analysis and visualization modules, ensuring GenePattern users access to new computational methods as they are made publicly available. GenePattern supports the sharing of reproducible in-silico methodologies through pipelines, which run on its integrated workflow engine.


This tutorial provides an introduction to microarray data analysis using GenePattern. Topics covered include formatting and loading data, identification of differentially expressed genes, clustering, prediction, and the creation of computational workflows with GenePattern.

Workshop 2: Cytoscape

Wednesday, July 23 10:00AM - 12:00PM (See below for a break down)
Location: Room 715

Workshop title: Cytoscape: An Open-Source Platform for Network Analysis and Visualization
Chair: Gary Bader

Presenters indicated in bold.

Wednesday, July 23 10:00am-11:15am
Cytoscape: An Open-Source Platform for Network Analysis and Visualization
Yeyejide Adeleye, Allan Kuchinsky, Piet Molenaar, Scooter Morris, Alex Pico, David States, Gary Bader
The Cytoscape Consortium

Cytoscape ( is an open-source software package for the visualization and analysis of biological networks and the integration of molecular state data. Cytoscape provides functionality to layout and search networks; to visually integrate networks with expression profiles, phenotypes, and other molecular states; and to link to databases of functional annotations. In this demo we will provide an introduction to the core functionality of Cytoscape and network-based analysis that will be of relevance to researchers with an interest in the analysis of biological data in the context of biological networks and pathways. The Cytoscape software will be demonstrated along with various available plugins, including the Agilent Literature Search plugin and the Pathway Commons plugin (Poster R66).

Wednesday, July 23 11:15am-11:30am
A Cytoscape Plugin to Access the MiMI Molecular Interactions
Jing Gao, V. Glenn Tarcea, Alex Ade, Barbara Mirel, James Cavalcoli, Terry Weymouth, Brian Athey H.V. Jagadish and David States
University of Michigan, National Center for Integrative Biomedical Informatics

The Cytoscape plugin for MiMI retrieves molecular interactions from the National Center for Integrative Biomedical Informatics MiMI database and displays the interaction networks using Cytoscape. The plugin integrates nature language processing tools and a graph matching tool, and an interactive annotation editor. More information available at Poster K15.

Wednesday, July 23 11:30am-11:45am
GenePro: a Cytoscape Plug-in for Advanced Visualization and Analysis of Interaction Networks
Jim Vlasblom, Shuye Pu, and Shoshana J. Wodak. Hospital for Sick Children, and Departments of Biochemistry and Molecular Genetics, University of Toronto, Toronto Canada.

GenePro features a set of versatile tools that greatly facilitates the visualization and analysis of protein networks derived from high throughput interactions data and the validation of various methods for parsing these networks into meaningful functional modules. Availability: The GenePro plugin is available for download at:

Wednesday, July 23 11:45am-12:00pm
Interactive analysis of metabolic pathways, their enzymes and metabolites
Brian Turner, Steve Constable, Zahrah Kahlid, Koji Ogata and Shoshana J. Wodak
Departments of Biochemistry and Molecular Genetics, University of Toronto, Toronto Canada.

We will demonstrate new Plug-in enabling interactive analyses of metabolic pathways. Pathways imported using the BioPAX format are displayed and interactively queried for information on metabolites (chemical structure and 3D conformation), and enzymes (Go annotations, domain structure and architecture, sequences information, homologs, 3D structure (PDB), SCOP classification etc.). Information on enzymes is obtained from the iProClass database using XML-based query tools.


Workshop 3: Ensembl/UCSC Genome Browser

Wednesday, July 23 - 10:45 a.m. - 12:40 p.m.

Room: 802


Hiram Clawson, University of California, Santa Cruz, US

Michael Schuster, EMBL - European Bioinformatics Institute, Hinxton, UK


UCSC Genome Browser Introduction (10:45 a.m. - 11:40 a.m.)


Attend this interactive wireless workshop (you must bring your own laptop) for an introduction to the UCSC Genome Browser features and functions. Example research queries will be explored with the genome browser.


Introducing the Ensembl Genome Browser System (11:45 a.m. - 12:40 p.m.)


Ensembl is a joint project of the European Bioinformatics Institute and the Wellcome Trust Sanger Institute to provide automated genome analysis and annotation. Ensembl focuses on the annotation of vertebrate genomes, with special emphasis on human, mouse, zebrafish and rat. This hands-on workshop aims at future users of Ensembl and Ensembl Genomes, who are not that familiar with the system yet, but would like pointers to further explore the information to ultimately take advantage of it for their own research. Experienced users are welcome to meet us at the EBI exhibit booth.