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Keynotes

Tuesday | Wednesday | Thursday

Tuesday, February 4

PeGASys: A Parallel Genome Annotation System
Francis Ouellette, University of British Columbia Bioinformatics Centre
Track: Keynote
Date: Tuesday, February 04
Time: 8:30am - 9:15am
Location: California Ballroom

Working with many groups on large and small genomes, a number of problems come up--especially when working with unfinished genomes, and trying to capture and share knowledge about that genome.

In his keynote address, Ouellette discusses some of the challenges in going whole genome annotation on genome. He considers large players (like EBI and NCBI), how resources can be used in a better way to minimize repetitive work and maximize throughput, the presentation of the best possible "answer" about a given genome, and how to take full advantage of all the work done worldwide.


The Genes, the Whole Genes, and Nothing But the Genes
Jim Kent, UC Santa Cruz Genome Bioinformatics Group
Track: Keynote
Date: Tuesday, February 04
Time: 9:15am - 10:15am
Location: California Ballroom

Jim Kent is the recipient of this year's Ben Franklin Award, presented by Bioinformatics.Org.

The human genome sequence is essentially complete. Finding all of the genes in the genome remains an ongoing challenge. We have many effective techniques for finding coding exons, but turning "probable coding exons" into full-length mRNA sequence on all splicing varients takes time. Though comparative genomics is a useful first step, finding the regulatory regions associated with a gene is even more difficult. Kent highlights our progress on these and other problems in genome annotation.


A New Kind of Science and Foundations For Theory in Biology
Stephen Wolfram, Wolfram Research, Inc.
Track: Keynote
Date: Tuesday, February 04
Time: 4:00pm - 4:45pm
Location: California Ballroom

Starting from a few computer experiments, Stephen Wolfram has spent more than twenty years developing a new approach to science, described for the first time in his book A New Kind of Science. Basic to his approach is the idea of studying not traditional mathematical equations but instead, rules of the kind embodied in the simplest computer programs. A key discovery is that such rules can lead to behavior that shows immense complexity and mirrors many features seen in nature. Wolfram has built on this to tackle a remarkable array of fundamental problems in science, from the origins of apparent randomness in physics, to the development of form and complexity in biology, the ultimate scope and limitations of mathematics, the possibility of a truly fundamental theory of physics, the character of intelligence in the universe, and possibilities and limitations of a predictive theory in biology. When Wolfram's book was released on May 14, 2002, it became an instant bestseller, and is now showing many signs of initiating a major paradigm shift in science. Wolfram's presentation covers some of the key ideas and discoveries in his book, discussing their personal and historical context and emphasizing their implications for the biological sciences.


Wednesday, February 5

Bioinformatics: Gone in 2012
Lincoln D. Stein, Cold Spring Harbor Laboratory
Track: Keynote
Date: Wednesday, February 05
Time: 8:30am - 9:15am
Location: California Ballroom

In his keynote address, Stein discusses the challenges of bringing bioinformatics into the biological mainstream, and charts a course for those who wish to make bioinformatics their future careers.


Alternative Splicing and Gene Regulation
Steven Brenner, UC Berkeley
Track: Keynote
Date: Wednesday, February 05
Time: 9:15am - 10:15am
Location: California Ballroom


Thursday, February 6

Establishing Standards and Infrastructure for Sharing Microarray Data
Alvis Brazma, European Bioinformatics Institute
Track: Keynote
Date: Thursday, February 06
Time: 8:30am - 9:15am
Location: California Ballroom

Microarray data are already providing important insights into mechanisms of cell development, differentiation and disease, and the networks of gene regulation. Brazma discusses current efforts by the Microarray Gene Expression Data society to make maximum use of the vast amounts of existing and potential data generated by this technology by adopting standards for describing and annotating microarray experiments, and by establishing an infrastructure for sharing these data.

The Microarray Gene Expression Data (MGED) society is an international organization for facilitating sharing of functional genomics and proteomics microarray data. MGED was initially established as a grass-roots movement in 1999, at a meeting in Cambridge, UK. MGED has developed recommendations called Minimum Information About a Microarray Experiment, known as MIAME, with the goal to outline the minimum information required to interpret unambiguously and potentially reproduce and verify array-based gene expression monitoring experiments. A standard microarray data exchange format, MAGE-ML, which is able to capture information specified by MIAME, has recently became an Adopted Specification of the OMG standards group. Many organizations, including EBI, Rosetta Biosoftware, Agilent, Affymetrix, and Iobion, have contributed ideas to the developed standards. ArrayExpress is a public repository for microarray gene expression data at the EBI, which implements MGED standards.


Java for Numerical Computing: A Tour Through Issues and Directions in the Use and Evolution of Java for Numerical Computing
James Gosling, Sun Microsystems
Track: Keynote
Date: Thursday, February 06
Time: 9:15am - 10:00am
Location: California Ballroom

Although Java has become successful in handheld devices and commercial server applications, it has garnered only a small following in the numerical and high-performance computing worlds. This is unsurprising, as it lacks some key features, such as a convenient notation for user-defined arithmetic operators, which are highly valued in these areas. Furthermore, the performance characteristics of the VM, which are desirable for numerical computations, have not received much attention. Despite this, there have been some notable successes. Gosling covers the history of issues and directions of Java for numerical computing, with a look forward to future directions.


Tuesday | Wednesday | Thursday

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