ISMB 2008 features ten (10) half-day introductory to advanced tutorial sessions. The tutorials will be given on Saturday, July 19, 2008 one day prior to the conference scientific program – new this year, Tutorials will be 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 6, 2008.

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 Delegates registering for two tutorials. Delegates attending one tutorial only have the option to purchase a lunch ticket during on-line registration.

Tutorial participants must register for the ISMB 2008 conference.

Tutorial AM1: PLoS Professional Development
Tutorial AM2: Computational Analyses and Biological Interpretation of ChIP-chip and ChIP-seq
Tutorial AM3: Computational Biology on Multi-Core Computer Systems
Tutorial AM4: Identification of Biomedical Events and Relations in the literature with ontological support
Tutorial AM5: Introduction to Molecular Visualization

Tutorial PM6: Distances, Margins, Kernels: Machine Learning Concepts for Computational Biology
Tutorial PM7: A structured approach for the engineering of biochemical network models, illustrated for signaling pathways
Tutorial PM8: How to Make Useful Ontologies for Biomedicine
Tutorial PM9: Making informed choices about microarray data analysis
Tutorial PM10: Introduction to non-coding RNA gene finding

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Presenter(s):
Philip E. Bourne, University of California San Diego, La Jolla CA, USA, pbourne@ucsd.edu

Abstract:
Much of what professional scientists do on a daily basis is not taught, but learnt on the job. The purpose of this tutorial is to reduce the learning curve with some practical advice on topics ranging from writing a good scientific paper, writing a good fellowship or grant application, preparing a good poster, how best to collaborate and how to get the best job. The basis for this tutorial is the Ten Rules series published as a collection by PLoS Computational Biology and available at: http://collections.plos.org/ploscompbiol/tensimplerules.php

Presenter(s):
X. Shirley Liu, Harvard School of Public Health, Boston MA, USA, xsliu@jimmy.harvard.edu
Clifford A Meyer, Dana-Farber Cancer Institute, Boston MA, USA, cliff@research.dfci.harvard.edu

Abstract:
Whole genome tiling arrays and new generation sequencing technologies have enabled genome wide studies of transcription factor binding sites and epigenetic states. In this tutorial we discuss analyses of ChIP-microarray and ChIPsequencing data and workflows for the investigation of biological phenomena through the integration of sequence and gene expression data.

Presenter(s):
Kirk E. Jordan, Emerging Solution Executive
Deep Computing
IBM Systems and Technology Group
http://www-3.ibm.com/software/info/university/people/kjordan.html

Tyler Luchko
Department of Physics
University of Alberta
National Institute for Nanotechnology
National Research Council
http://www.phys.ualberta.ca/~tluchko

Jack Tuszynski, Allard Research Chair
Department of Oncology
Department of Physics
University of Alberta
http://www.phys.ualberta.ca/~jtus

Abstract: Computation is playing an ever increasing and vital role in biology creating demand for new machines. However, we can no longer rely solely on computational speed up through increases in clock speed. In order to continue the speed ups users have come to expect from computer companies, the chip manufactures are turning to multi-core and many-core chips. Much of what we have learned on large distributed systems in principle will need to be applied to these multi-core and eventually many-core efforts. In this tutorial, we provide an overview of the many systems in which multi-core chips are being implemented. New approaches to computational problems that will take full advantage of multi-core and many-core computer systems need to be investigated. Bioinformatics and computational biology simulations are definitely among these. We will show some results for biology that will illustrate the power of some of these systems. A specific example that will be discussed at length is the application of molecular dynamics modeling to tubulin both as a dimer and in its polymeric form, i.e. microtubules. This protein plays a crucial role in many cellular functions, especially cell division, as it forms mitotic spindles. Our computational effort has been directed at a better understanding of the mechanism affecting tubulin as a result of GTP hydrolysis, which causes a phenomenon called dynamic instability. The second issue of importance is the nature and strength of tubulin-ligand interactions. Important clues have been found regarding improved design of new generations of chemotherapeutic agents. We hope to provide a foundation for attendees to begin to think about problems and how to design and implement them so they will take full advantage of various multi-core systems e.g. ultra-scale systems or clusters based on multi-core chips.

Presenter(s):
Dietrich Rebholz-Schuhmann, European Bioinformatics Institute, UK, rebholz@ebi.ac.uk
Sophia Ananiadou, University of Manchester, School of Computer Science, UK Sophia.ananiadou@manchester.ac.uk
Jun’ichi Tsujii, University of Tokyo, Department of Computer Science, JP, tsujii@is.s.u-tokyo.ac.jp
Jung-Jae Kim, European Bioinformatics Institute, UK, kim@ebi.ac.uk

Abstract:
The main concepts of text mining are defined and explained, for example information retrieval (IR), information extraction (IE) and named entity recognition (NER). Methods and measures for the evaluation such as recall and precision are presented. Dependencies between precision and recall and between information extraction and information retrieval are discussed. Different standard techniques in natural language processing techniques will be explained, i.e. morphological analysis, tokenization, part-of-speech tagging, chunking, dependency parsing and full parsing. A selection of facts and types of data that text mining can provide from the literature will be discussed. Main obstacles in biomedical text mining will be presented (Zipf’s law, polysemy and ambiguity, anaphora).

Presenter(s):
Conrad Huang, University of California, San Francisco, San Francisco, CA, USA, conrad@cgl.ucsf.edu
John “Scooter” Morris, University of California, San Francisco, San Francisco, CA, USA, scooter@cgl.ucsf.edu

Abstract:
Projects such as Structural Genomics are providing increasing numbers of experimental protein and protein-complex structures. Furthermore, increasing numbers of theoretical models are being predicted from primary sequence. Biologists have an increasing need to understand and communicate the structures, functions and relationships between these protein and protein-complex structures. As a result, molecular visualization is becoming an important tool for the presentation and communication of the results of biological experiments and research. This tutorial will provide a basic foundation for the understanding of molecular structures through use of visualization tools.

Attendees will learn the basics of molecular visualization and will be provided an overview of available tools and techniques for visualization, analysis and modeling of protein structure. To make these concepts more concrete, attendees will be shown the academic program UCSF Chimera in more detail, and receive instruction in its features and use. The field of structural biology is still changing, and new techniques are continually being developed. Attendees will be shown how they can add new analysis techniques and their own.

Presenter(s):
Stefan Kramer, Technische Universität München, Munich, Germany, kramer@in.tum.de
Ulrich Ruckert, Technische Universität München, Munich, Germany, rueckert@in.tum.de

Abstract:
Distances, margins, and kernels have become essential concepts for machine learning applications in computational biology. This tutorial focuses on their theoretical foundations, clarifies the relationship among the concepts, presents advantages and disadvantages, and gives hints for the derivation of new distance measures and kernels as well as for their application.

Presenter(s):
David Gilbert, University of Glasgow, Scotland, UK, drg@dcs.gla.ac.uk
Monika Heiner, Brandenburg University Of Technology Cottbus, Germany, monika.heiner@informatik.tu-cottbus.de
Rainer Bretling, University of Groningen, Netherlands, Haren, The Netherlands, r.breitling@rug.nl
Robin Donaldson, University of Glasgow, Scotland, UK, radonald@dcs.gla.ac.ukradonald@dcs.gla.ac.uk

Abstract:
Quantitative models of biochemical networks are a central component of modern systems biology. Building and managing these complex models is a major challenge that can benefit from the application of formal methods adopted from theoretical computing science. In this workshop we provide a general introduction to the field of formal modeling, which emphasizes the intuitive biochemical basis of the modeling process, but is also accessible for an audience with a background in computing science and/or model engineering.

Tutorial PM7 Online Materials

Presenter(s):
Barry Smith, University at Buffalo, Buffalo, NY, USA, phismith@buffalo.edu
Nigam Shah, Stanford University (National Center for Biomedical Ontology)
Stanford, CA, USA, nigam@stanford.edu

Abstract:
The tutorial provides an overview of current uses of ontologies in bioinformatics, instruction on ontology development using OWL, and an outline of principles of good ontology design. It comprises an interactive session devoted to developing an ontology, and a session illustrating how good design practices effect the usefulness of ontologies in practice.

Presenter(s):
Mark Reimers, Virginia Commonwealth University, Richmond, Virginia, USA, mreimers@vcu.edu

Abstract:
This tutorial is intended to introduce non-specialist researchers in systems biology and in medicine to the best current practices for the analysis of microarray technologies currently available for expression, DNA copy number, methylation, chromatin, and SNP’s. Examples from both publication-quality and troublesome data sets will be presented.

Presenter(s):
Jan Gorodkin, University of Copenhagen, Copenhagen, Denmark, gorodkin@genome.ku.dk
Ivo Hofacker, University of Vienna, Vienna, Austria, ivo@tbi.univie.ac.at

Abstract:
The genome contains potentially numerous non-coding RNAs involved in regulation in the cell. The tutorial introduces the basic principles in RNA structure, RNA folding and gene search and provides an overview of current methods in the field with pointers to practical tools. A CD with software will be available.