Tutorials Program
ISMB 2010 features a number of half-day introductory to advanced tutorial sessions. The tutorials will be given on Saturday, July 10, 2010 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 9, 2010.
Attendees will receive a Tutorial Entry Pass (coupon) at the time they register on site. Tutorial handouts and CD can be picked up at the door of each tutorial session 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.
Tutorial participants must be registered for the conference.
*please note start and finish times are subject to change
Morning Tutorials: 8:30 a.m. - 12:30 p.m.
AM 1: Teaching bioinformatics in high school biology coursesAM 2: How to understand the cell by breaking it - computational analysis of single and combinational gene perturbations.
AM 3: Pathway analysis of expression data: Deciphering functional building blocks of complex diseases.
AM 4: Integrative Genomics Viewer (IGV)
AM 5: An insight into computational and statistical mass spectrometry-based proteomics.
Lunch Break 12:30 p.m. - 1:30 p.m.
Afternoon Tutorials 1:30 p.m. - 5:30 p.m.
PM 1: Using All the Data: Large Scale Biological Data Mining for Functional Genomics and Metagenomics.PM 2: The next generation biological network visualization and analysis. The size does matter.
PM 3: Functional Genomics with Deep Sequencing
PM 4: Galaxy: Analyze, Visualize, Communicate
Presenter(s): David Form, Nashoba Regional High School, Bolton, MA, USA, This email address is being protected from spambots. You need JavaScript enabled to view it.
Fran Lewitter, Whitehead Institute for Biomedical Research, Cambridge, MA, USA, This email address is being protected from spambots. You need JavaScript enabled to view it.
Room: 303
Abstract: Bioinformatics has become an important component of research in the life sciences. Researchers routinely exploit bioinformatics tools and databases in every phase of a project. The wealth of information available in these databases is increasing and much of it is easily accessible to high school teachers and their students.
This tutorial is aimed at high school biology and chemistry teachers who want to include bioinformatics in their curricula. We will offer strategies for teaching bioinformatics at the high school level, including examples of student work. We will present concrete examples of "hands-on" exercises for your students that have been designed to insert readily into current high school biology curricula and correlate with the Massachusetts State Biology Standards. Teachers attending this tutorial will leave with access to these classroom - tested exercises, suitable for a variety of student levels.
Tutorial AM1: part of ISCB's High School Outreach program promoting life sciences education for high school teachers - A registration form for this individual Tutorial (AM1) is available here
This tutorial is aimed at high school biology and chemistry teachers who want to include bioinformatics in their curricula. We will offer strategies for teaching bioinformatics at the high school level, including examples of student work. We will present concrete examples of "hands-on" exercises for your students that have been designed to insert readily into current high school biology curricula and correlate with the Massachusetts State Biology Standards. Teachers attending this tutorial will leave with access to these classroom - tested exercises, suitable for a variety of student levels.
Tutorial AM1: part of ISCB's High School Outreach program promoting life sciences education for high school teachers - A registration form for this individual Tutorial (AM1) is available here
AM 2: How to understand the cell by breaking it - computational analysis of single and combinational gene perturbations.
Presenter(s): Florian Markowetz, Cancer UK Cambridge Research Institute, Cambridge, UK, This email address is being protected from spambots. You need JavaScript enabled to view it.
Chad Meyers, University of Minnesota, Minneapolis, MN, USA, This email address is being protected from spambots. You need JavaScript enabled to view it.
Room: 301
Abstract: The analysis of genome-wide single or combinatorial gene perturbation screens is moving to the center-stage of computational systems biology as more and better experimental systems are established in humans and model organisms. This tutorial will provide a comprehensive overview of recent advances both in experimental technologies and computational analysis methods.
Tutorial level: Introductory to intermediate. The tutorial will serve as a thorough introduction to gene perturbation screens and their analysis, but some advanced issues will also be introduced.
AM 3: Pathway analysis of expression data: Deciphering functional building blocks of complex diseases.
Presenter(s): Frank Emmert-Streib, Queen’s University Belfast, Belfast, UK, This email address is being protected from spambots. You need JavaScript enabled to view it.
Galina Glazko, University of Rochester Medical Center, Rochester, NY, USA, This email address is being protected from spambots. You need JavaScript enabled to view it.
Room: 309
Abstract: The analysis of differentially expressed (DE) gene sets is an important step forward from the analysis of individually DE genes. In this tutorial we present a survey of statistical methods for the analysis of DE gene sets. These methods are applied to data from complex diseases, compared and discussed.
Tutorial level: The majority of the tutorial will be given on an introductory level but at the end we will also discuss some more advanced topics.
Requirements: The participants of the tutorial should have an introductory knowledge of statistics. To maximize the practical outcome it would be desirable to have also some basic programming skills in any language. Prior knowledge with expression data is desirable but not necessary.
Presenter(s): Jim Robinson, Broad Institute, Cambridge, MA, USA, This email address is being protected from spambots. You need JavaScript enabled to view it., Helga Thorvaldsdottir, Broad Institute, Cambridge, MA, USA This email address is being protected from spambots. You need JavaScript enabled to view it.
Room: 305
Abstract: Rapid improvements in next-generation sequencing and array-based profiling methods are enabling researchers to study the genome at unprecedented resolution. This tutorial introduces the Integrative Genomics Viewer (IGV), a tool for visual exploration of large, integrated, genomic datasets. Participants will learn to prepare and visualize data from next-generation sequencing, including ChIP-seq and RNA-seq, as well as microarray-based platforms such as aCGH, SNP arrays, tiling arrays, and expression arrays. Real world examples will be drawn from The Cancer Genome Atlas and 1000 Genomes projects.
The tutorial will include several hands on exercises. Participants should bring laptop computers.
Presenter(s): Olga Vitek, Purdue University, West Lafayette, IN, USA, This email address is being protected from spambots. You need JavaScript enabled to view it.
Lukas Kall, Stockholm University, Stockholm, Sweden, This email address is being protected from spambots. You need JavaScript enabled to view it.
Room: 310
Abstract: The tutorial focuses on computational and statistical methods and tools for bottom-up 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.
PM 1: Using All the Data: Large Scale Biological Data Mining for Functional Genomics and Metagenomics.
Presenter(s): Curtis Huttenhower, Harvard School of Public Health, Boston, MA, USA, This email address is being protected from spambots. You need JavaScript enabled to view it.
Oliver Hofmann, Harvard School of Public Health, Boston, MA, USA, This email address is being protected from spambots. You need JavaScript enabled to view it.
Room: 303
Abstract: This tutorial will provide an overview of computational methods for mining very large data collections, both for single assays generating sizeable outputs and for integrating thousands of diverse experimental results. We will focus on microbial and metagenomic community characterization as a biological application.
Tutorial level: Introductory
Requirements:An introductory knowledge of statistics, basic familiarity with experimental data types (e.g. expression arrays, interactions, short read sequencing), and basic familiarity with bioinformatic software systems. A laptop will not be required, but pointers and information will be provided for computational materials that the participants can follow up on independently.
Presenter(s): Igor Jurisica, Ontario Cancer Institute and University of Toronto, Toronto, ON, Canada, This email address is being protected from spambots. You need JavaScript enabled to view it.
Room: 301
Abstract: One size does not fill all. There are many visualization software packages, such as Cytoscape, VisANT, NAViGaTOR, Pajek, Osprey, Ondex, PathwayLab, Interviewer3, Geomi, Forg3d to name a few. Some are open source while others are public or commercial; some are established while others are emerging. Individual systems differ greatly in terms of features and standards they support, and consequently analyses they enable.
Tutorial level: Introductory/Intermediate. The intended audience will include both biology users and visualization tool developers. This tutorial relates to the ISMB-10 Special Session on Visualization of Biological Networks and will provide useful background.
Requirements: Only rudimentary biology knowledge will be required. The tutorial will include practical examples and participants are encouraged to bring their laptops, ideally with Internet connection so that online searches and datasets can be used. Prior to the tutorial, all related datasets and workflow examples will be provided on a web server.
Presenter(s): Gunnar Rätsch, Friedrich Miescher Laboratory, Tubingen, Germany, This email address is being protected from spambots. You need JavaScript enabled to view it.
Ali Mortazavi, California Institute of Technology, Pasadena, CA, USA, This email address is being protected from spambots. You need JavaScript enabled to view it.
Room: 309
Abstract: The rapid adoption of next-generation sequencing for the study of protein-DNA interactions and transcriptomes is revolutionizing functional genomics. This tutorial
introduces the main technologies and protocols, the currently available tools for analysis, and outlines some of the main challenges of analysing and integrating ChIP-seq and RNA-seq datasets.
Tutorial level:Introductory
Requirements: No specific knowledge will be required since the tutorial is self contained and most fundamental concepts are introduced during the course.
Presenter(s): The Galaxy Team | http://bitbucket.org/galaxy/galaxy-central/wiki/Home
Room: 305
Abstract: Galaxy makes it easy to perform analysis interactively through the web, on arbitrarily large datasets. With hundreds of tools there are few limits on what can be done. Now with NGS workflows, trackster browser, and collaborative pages you can do more in the Cloud.
The goal of this session is to bring together developers, data producers, tool creators and biomedical researchers to highlight the coolest features of Galaxy framework with a particular emphasis on NGS data management and analysis.
Requirements: Just decide who you are: consumer (perform analyses) or producers (write tools and maintain IT) -> the session will be split into two sections:
1). Biologist oriented (the first 2 hours)
2). Developer oriented (the last 2 hours)
But we promise both to be equally entertaining, so plan to attend the whole thing. And, you will get an unpredictable Galaxy T-shirt!
