Tutorials Program
ISMB/ECCB 2011 features a number of half-day introductory to advanced tutorial sessions. The tutorials will be given on Saturday, July 16, 2011 one day prior to the conference scientific program. Tutorials are held on the same day as the second day of the SIG and Satellite meetings. Tutorial programs provide participants with lectures and instruction, on either well-established or new "cutting-edge" topics, relevant to the bioinformatics field. It offers participants an opportunity to learn about new areas of bioinformatics research, to get an introduction to important established topics, or to develop higher skill levels in areas in which they are already knowledgeable.
Tutorial attendees should register using the on-line registration system when registration opens on March 14, 2011. Tutorial participants must be registered for the conference.
Attendees will receive a Tutorial Entry Pass (coupon) at the time they register on site. Tutorial handouts and CD can be picked up at on-site registration in exchange for the coupon. Lunch is included in the registration fee for attendees registering for two tutorials. Those attending one tutorial only have the option to purchase a lunch ticket during on-line registration.
AM1: Using formalized ontologies for verification and integration of biomedical data
AM2: An insight into computational and statistical mass spectrometry-based proteomics
AM3: CANCELLED - 3D microscopic image informatics and high-performance large-scale 3D image visualization assisted analyses
AM4: Genetics of gene expression in humans: Data structures, algorithms, and inference
Lunch Break 12:30 p.m. - 1:30 p.m.
PM1: Sequence searching and alignment: exploring different publically available tools and the biological interpretation of the results
PM2: Grant-writing 101: how to write a winning grant proposal
PM3: Tools for Genomic Computation, Visualization, and Integration: GenePattern and the Integrative Genomics Viewer (IGV)
PM4: On Modern Statistical and Sparse Coding Methods for Genetic Association Study: Structured Genome-Transcriptome-Phenome Association Analysis
PM5: Biological Networks: Integrating, Analysing, and Visualizing ‘omics Data in Cytoscape
Presenters:
Michel Dumontier, Carleton University, Ottawa, Canada, This email address is being protected from spambots. You need JavaScript enabled to view it.
Robert Hoehndorf, University of Cambridge, United Kingdom, This email address is being protected from spambots. You need JavaScript enabled to view it.
Time: 8:30 a.m. - 12:30 p.m.
Room: A355
This tutorial will provide detailed instruction for scientists to create and make use of formalized biomedical ontologies for more advanced bioinformatic knowledge discovery including functional enrichment analysis and answering questions over semantically integrated data and web services.
Tutorial level: Intermediate to advanced
Requirements:
The intended audience for the tutorial are researchers in bioinformatics, computational biology or systems biology who want to leverage the power of formal ontologies for data integration and in data analyses.
Presenter(s):
Olga Vitek, Purdue University, West Lafayette, United States, This email address is being protected from spambots. You need JavaScript enabled to view it.
Lukas Käll, Stockholm University, Sweden, This email address is being protected from spambots. You need JavaScript enabled to view it.
Time: 8:30 a.m. - 12:30 p.m.
Room: B631
The tutorial focuses on computational and statistical methods and tools for bottomup mass spectrometry-based proteomics. We briefly introduce proteomic workflows, and discuss computational challenges and state-of-the-art solutions for identification, quantification, and characterization of peptides and proteins. We further highlight opportunities and resources for bioinformatics research in this field.
Tutorial level: Intermediate
Requirements: A prior exposure to statistical methodology at the level of one introductory course is required. A prior exposure to proteomic workflows is desirable, but not required. Access to laptop computers during the tutorial is not required.
Presenter(s):
Vincent J. Carey, Harvard Medical School, Boston, United States, This email address is being protected from spambots. You need JavaScript enabled to view it.
Time: 8:30 a.m. - 12:30 p.m.
Room: A353
This tutorial addresses high-level preprocessing of expression data, methods of SNP calling and imputation, and joint analysis of expression and genotype in HapMap and 1000 genome resources using open source software in Bioconductor. Primary objective: accurate inference on regulation of gene expression and transcriptional consequences of structural DNA variants.
Tutorial level: Advanced
Requirements: This tutorial will focus on concepts and designs of workflows and an analyses addressing the genetics of gene expression. Attendees will be expected to have a good appreciation of
- the use of DNA microarrays for human transcript profiling and statistical
analysis of differential expression;
- the use of SNP chips for high-density genotyping;
- genetic models that can be used to relate DNA variants (chiefly SNP) to transcriptomic and phenotypic patterns.
Attendees who wish to make use of hands-on components of the tutorial should have a basic understanding of the R programming language; software for windows, mac, and linux laptops will be provided with documentation.
To obtain maximum benefit from this tutorial, attendees are requested to bring a laptop, or to arrange to share a laptop with another attendee.
Having the the statistical package R, version 2.14 installed will be an advantage.
Presenters:
Jennifer McDowall, European Bioinformatics Institute, Cambridge, United Kingdom, This email address is being protected from spambots. You need JavaScript enabled to view it.
Aidan Budd, EMBL, Heidelberg, Germany, This email address is being protected from spambots. You need JavaScript enabled to view it.
Time: 1:30 p.m. - 5:30 p.m.
Room: A355
Sequence searching and alignment are key to many bioinformatics tools and applications. Familiarity with the range of tools available offers bioinformaticians and database-curators the opportunity to bring new approaches to their work. This tutorial reviews sequence searching and alignment tools, how to set parameters, and the biological interpretation of results.
Tutorial level: Introductory
Requirements: Basic knowledge of biology and statistics is suggested - no prior knowledge of sequence searching and alignment needed. Hands-on practical included, so participants need to bring their own laptops for the session.
Organizers:
The tutorial organizers are Yana Bromberg, Rutgers University, Magali Michaut, University of Toronto, Venkata P. Satagopam, EMBL and Andrea Schafferhans, Technical University of Munich. Recruited funding agency representatives and members of review committees will teach the actual tutorial.
Time: 1:30 p.m. - 5:30 p.m.
Room: B631
This tutorial is the first part of a two-part session dedicated to securing grant funding. The tutorial will aim to explain in detail how to write a fundable proposal, while a conference track workshop held during the main ISMB/ECCB conference program (second part) will familiarize the audience with the available government and private research-funding resources (including a discussion on choosing the proper RFI). Some universities offer similar courses to post-docs and young faculty. The ISMB/ECCB workshop will deal more specifically with the issues encountered by researchers in a translational field of science, which often does not fit very well into the defined goals of the funding agencies.
Tutorial level: Intermediate. We will assume knowledge of scientific writing, but not of grant-writing per-se
Presenter(s):
Michael Reich, Broad Institute, Cambridge, United States, This email address is being protected from spambots. You need JavaScript enabled to view it.
James Robinson, Broad Institute, Cambridge, United States, This email address is being protected from spambots. You need JavaScript enabled to view it.
Helga Thorvaldsdóttir, Broad Institute, Cambridge, United States
Time: 1:30 p.m. - 5:30 p.m.
Room: B552
The Broad Institute has developed GenePattern and IGV to allow researchers to analyze, visualize, and integrate genomic data, including gene expression, sequence alignment and variation, flow cytometry, proteomics, and epigenetics, from both traditional microarrays and next-generation sequencing platforms. Learn how to use these tools in an interactive, hands-on environment.
Tutorial level: Introductory
Requirements:
No prior experience is necessary
There will be hands-on exercises, so participants should come with a laptop running Firefox (http://www.mozilla.com/en-US/firefox/personal.html) and Java 6 (http://www.java.com/en/download/index.jsp)
Additional instructions will be given before the start of the workshop.
To obtain maximum benefit from this tutorial, attendees are requested to bring a laptop, or to arrange to share a laptop with another attendee.
Presenter(s):
Eric P. Xing, Carnegie Mellon University, Pittsburgh, United States, This email address is being protected from spambots. You need JavaScript enabled to view it.
Seyoung Kim, Carnegie Mellon University, Pittsburgh, United States, This email address is being protected from spambots. You need JavaScript enabled to view it.
Time: 1:30 p.m. - 5:30 p.m.
Room: J241
Whole-genome association study has been widely used to unravel the genetic causes of diseases such as Crohn’s disease, diabetes, and asthma. In this tutorial, we provide a comprehensive overview of the challenges and statistical tools to address the challenges in association analysis, within the framework of genome-trascriptome-phenome-wide structured association.
Tutorial level: About half of the tutorial will be devoted to introductory level, and the second half will be given at the advanced level.
Requirements: The participants of the tutorial will be expected to have an introductory knowledge of statistics. Prior experience with association analysis is not necessary, although we expect that experienced practitioners will benefit from this tutorial.
Presenter(s):
John “Scooter” Morris, University of California, San Francisco, United States, This email address is being protected from spambots. You need JavaScript enabled to view it.
Allan Kuchinsky, Agilent Laboratories
Alex Pico, Gladstone Institutes, UCSF
Time: 1:30 p.m. - 5:30 p.m.
Room: A353
This tutorial will provide a basic background for researchers and bioinformaticians in the analysis and visualization of biological networks. We will use that background to explore the most common tool used for the analysis and visualization of biological networks, Cytoscape. We will learn the basics of Cytoscape, as well some of the
plugins commonly used for the analysis of protein-protein interaction networks and microarray expression data.
Tutorial level: Introductory
Requirements: No specific background will be required beyond a basic understanding
of biology, including biological pathways and typical microarray data analysis
To obtain maximum benefit from this tutorial, attendees are requested to bring a laptop, or to arrange to share a laptop with another attendee.
