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October 2011 GMOD Meeting

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October 2011 GMOD Meeting

12-13 October 2011
Ontario Institute for Cancer Research
Toronto, Canada
Ontario Institute for Cancer Research

The next GMOD meeting is being held in October 12-13, 2011 at the Ontario Institute for Cancer Research (OICR) in Toronto, Canada. OICR is the home of GBrowse and BioMart.

If you're curious to see what happens at a GMOD meeting, see the writeup of the September 2010 GMOD Meeting, or the March 2011 GMOD Meeting page.


Registration is now closed.


Keynote speakers

Gary D. Bader

Gary D. Bader
Gary works on biological network analysis and pathway information resources as an Associate Professor at The Donnelly Centre at the University of Toronto. He completed post-doctoral work in the group of Chris Sander in the Computational Biology Center (cBio) at Memorial Sloan-Kettering Cancer Center in New York. Gary developed the Biomolecular Interaction Network Database (BIND) during his Ph.D. in the lab of Christopher Hogue in the Department of Biochemistry at the University of Toronto and the Samuel Lunenfeld Research Institute at Mount Sinai Hospital in Toronto. He completed a B.Sc. in Biochemistry at McGill University in Montreal. See for more information on Gary.

Michael Brudno

Michael Brudno
Mike's main research interest is the development of computational methods for the analysis of High throughput, a.k.a. Next-Generation sequencing data. His group is working on algorithms for assembly, mapping, visualization, and variation discovery with short reads. In addition, they also work on cloud computing, whole-genome alignment, as well as on detection and analysis of genome variation in the sea squirt C. savignyi.

After receiving a BA in Computer Science and History from UC Berkeley, Mike worked on his PhD at the Computer Science Department of Stanford University, developing several approaches for comparison of genomic sequences, including the LAGAN Alignment Toolkit. He then completed a postdoc at the Computer Science Division, UC Berkeley and was a Visiting Scientist at CSAIL (MIT) before starting as an Assistant Professor at the University of Toronto in January 2006. He is the recipient of the Alfred P. Sloan Research Fellowship, Ontario Early Researcher Award, and a Canada Research Chair in Computational Biology. See for more information on Mike.


The Main meeting (Days 1 and 2) will take place at HL31 in the MaRS Centre. Here are the directions once you are outside the building:

Directions to the HL31 are as follows:

  • Enter the MaRS Centre (101 College Street, Toronto ON M5G 1L7) through the main doors (with the stairs & ramp)
  • In the main lobby area, turn right and walk towards the west end of the building
  • Pass the RBC bank machine and proceed through a glass door on your right
  • Go down the stairs marked “Stair 16, Ground Floor” (or take the elevator)
  • At the bottom of the stairs, enter the hallway through the door marked “Stair 16, Upper Concourse”
  • The corridor to HL31 boardroom is immediately on your left

Day 1: Wednesday

Time Topic Presenter(s) Links
9:15 Introductions Scott Cain
9:35 Welcome to OICR and the State of GMOD Scott Cain slides
10:10 Keynote: Network and pathway information for systems biology Gary Bader PPT
11:00 Coffee break
11:30 GBrowse2: What's New Lincoln Stein PPT
12:00 Lunch
1:30 JBrowse and WebApollo Mitch Skinner PDF
2:00 The Mycoplasma Genome Database: marrying microscopy and genomics Andrew Oberlin PDF
2:30 Coffee break
3:00 MAKER Carson Holt PDF
3:30 InterMine Alex Kalderimis
and/or Richard Smith
4:00 Improving MOD interoperation (A Discussion) Josh Goodman PDF,PPT
4:45 Wrap up and dinner Mata Hari Grill 39 Baldwin St. Toronto PDF

Day 2: Thursday

Time Topic Presenter(s) Links
9:15 Keynote: The Savant Browser and MedSavant Michael Brudno PDF,PPT
10:00 Galaxy Dan Blankenberg PDF
10:30 Coffee
11:00 SADI for GMOD: An RDF/OWL Interface to GMOD Data Ben Vandervalk Prezi, PDF
11:30 The Comprehensive Antibiotic Resistance Database Andrew McArthur PDF,PPT
12:00 Lunch
1:30 Lightning talks (Please feel free to give a 5-10 minute talk on whatever; if you are interested enough to put together a talk, others will likely be interested in the content! :-)

Day 3: Friday

Time Workshop Location
9:00 BioMart OICR, 8th floor Boardroom
9:00 Galaxy OICR room HL-31
2:30 MAKER OICR, 8th floor Boardroom

Suggested agenda items

Please feel free to add suggested talks or topics for the meeting.

Scheduled Satellite Meetings

BioMart Galaxy InterMine MAKER

You can register for the BioMart, Galaxy, and MAKER Workshops on the meeting registration site. If you are interested in the InterMine development meeting, please let Richard Smith know.

Galaxy Workshop

This workshop will cover an introduction to Galaxy, including analyzing data with tools and visualizations, using Galaxy in the cloud, and running your own instance and adding new tools. Dan Blankenberg of the Galaxy Project will lead the workshop.

Galaxy is an open-source analysis and data integration framework that is available as a free public service and as open source software that can be deployed both locally or on cloud resources. The Galaxy platform empowers transparent and reproducible research by providing interactive access to popular tools, including those that allow manipulation of raw sequencing reads, mapping, peak calling, genomic interval operations, visualization at genome browsers and more, as well as a point-and-click workflow system.

The Galaxy workshop will be held on Friday, 14 October, from 9am-2pm in the Ontario Institute for Cancer Research, room OICR HL-31. Table seating is limited to 18 participants, with space for an additional 10 participants, so please register and arrive early.

Workshop Slides
An Introduction to Galaxy
Using Galaxy for High-throughput Sequencing (HTS) Analysis and Visualization
Running and Enhancing your own Galaxy
Second Half: Running Your Own Instance

InterMine Development Meeting

This meeting is intended for organisations that have an InterMine, or are thinking of setting one up, to discuss development priorities, as well as production and implementation issues. This meeting is part of the InterMod project, which involves supporting InterMine data-warehouses for D. melanogaster, R. norvegus, M. musculus, S. cerevisiae, D. rerio and C. elegans. Groups representing other efforts to use InterMine for biological data-warehousing are welcome to attend (as indeed some aleady are) - please contact Richard Smith for more details.

BioMart Workshop

This workshop will include an introduction to the BioMart system, followed by a brief demonstration of BioMart applications in the BioMart Central Portal ( and the International Cancer Genome Consortium (ICGC) Data Portal (, and a hands-on tutorial to show how to create and configure a local data mart, how to import external mart and link it with the local mart, how to deploy the BioMart server to provide data access, and how to query BioMart server via web GUI and REST API. Junjun Zhang of the BioMart Project will lead the workshop.

Requirements: Parts of the tutorial will be taught using a VirtualBox Open Virtualization Appliance (OVA) image file. You will need a laptop with the latest version of VirtualBox, VMware Player, or VMware Workstation installed and running. VirtualBox is freely available from VMware player for Linux and Windows operating systems is freely available from VMware ( Mac users may use VMware Fusion ( on a 30 day free trail).

The BioMart workshop will be held on Friday, October 14, from 9-12 in the Ontario Institute for Cancer Research, 8th floor NorthEast Boardroom.

MAKER Workshop

The MAKER workshop will include a brief introduction to MAKER as well as demonstrations in using the pipeline to generate gene annotations, perform downstream analysis of the gene models, and ingrate the output into other GMOD tools. To make demonstrations as hands on as possible, the web version of MAKER will be used to give everyone access to the pipeline ( Examples will include demonstrations of the command line version of MAKER as well (but the online examples will be hands on). You can follow along online, or you can just watch and take notes.

Requirements for online examples: WiFi capable laptop, a javascript enabled web browser, and Java 6 or greater.

The MAKER workshop will be held on Friday, October 14, from 2:30-5:00 in the Ontario Institute for Cancer Research, 8th floor NorthEast Boardroom.



We don't have a block of rooms reserved due to unfavorable contracts offered. We're suggesting staying at Delta Chelsea hotel, as it is convenient to OICR.

Next Meeting

April 2012 GMOD Meeting