Birds of a Feather (BoF) Schedule

 

BOF01: Curriculum Guidelines for Bioinformatics and Computational Biology  (An Open Forum of the Curriculum Task Force of the ISCB Education Committee)
Leader: Lonnie Welch
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Affiliation: Ohio University

Day: Monday July 22, 1:00 p.m. - 2:00 p.m. (NEW CHANGE)
Room: Hall 4/5
 
Description:
The Curriculum Task Force of the ISCB Education Committee will hold an open forum to discuss a draft set of bioinformatics core competencies (derived from the findings of surveys of career opportunities, bioinformatics core facility directors, and existing curricula).  Three different categories of bioinformatics training will be considered.

 


 

BOF02: GPU Acceleration of Bioinformatics Pipeline
Leader: Mark Berger
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Affiliation: NVIDIA Corporation


Day: Monday July 22, 5:40 p.m. - 6:40 p.m.
Room: TBA

Description:

Summary: NVIDIA Engineering has been working to accelerate  several bioinformatics algorithms on graphics processing units (GPUs).  Our Engineering team would like feedback on their work, potential future collaborations and priorities planned.

NVIDIA has been developing an internal-only library called NVBIO as a starting point for understanding how to map modern short-read mappers to GPU architectures.  We agree that alignment is the obvious place to start and we have had good success for seed-and-extend algorithms like Bowtie2 as well as the basic FM-Index backtracking schemes like BWA-Short.  NVBIO includes a from-scratch rewrite of the Bowtie2 algorithm that achieves 4-5x for a GPU versus a multicore CPU on single-ended reads, and slightly less for paired-end reads.  We can get similar numbers for BWA-short, and we believe BWA-MEM should fit into our paradigm as well.  We are at the point where we’d like to start sharing our library and aligners for testing with real genome centers.

Because read mapping is fast on GPU, we have recently started looking into reference-based compression schemes like CRAM – we are working on simple proof-of-concept for a GPU-accelerated CRAM compressor.

We have also been collaborating with the developers of the SeqAn library to implement GPU-accelerated versions of some of their computational primitives.

We would be interested in discussing possible collaborations, trying to understand where in bioinformatics pipelines GPUs could be beneficial, and generally updating you on our plans.

 


 

BOF03: Bioinformatics Support for *Molecular Ageing Research* based on Omics data
Leader: Georg Fuellen
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Affiliation: Rostock University Medical School, Institute for Biostatistics and Informatics in Medicine and Ageing Research -- IBIMA

Day: Monday July 22, 5:40 p.m. - 6:40 p.m.
Room: TBA

Description:
Slowing down the ageing process itself (as a kind of super-prevention scheme by e.g. diet or phyto- chemicals) could extend *healthspan* much more than any disease-specific intervention, and omics data become available *now* to start solid research.

 


 

BOF04: BioFabric BoF: (nodes == lines) -> !hairballs
Leader: Bill Longabaugh
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Affiliation: Institute for Systems Biology


Day: Monday July 22, 5:40 p.m. - 6:40 p.m.
Room: TBA

Description:

BioFabric (www.BioFabric.org) is a new network visualization tool that represents nodes as lines instead of as points, which creates highly organized, unambiguous, and scalable node-link diagrams. This BoF will provide users, potential users, and just the nodes-as-lines-curious to explore and discuss how BioFabric can help you to visualize your network data.

 


 

BOF05:Jalview and JABAWS users, developers, and educators
Leader: Geoff Barton
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Affiliation: University of Dundee, Scotland, United Kingdom

Day: Monday July 22, 5:40 p.m. - 6:40 p.m.
Room: TBA

Description:
This BoF is for delegates who employ JABAWS and Jalview in their teaching or research work, or are interested in detailed discussions about the development of these Java based tools for bioinformatics sequence analysis and visualisation.

 


 

BOF06: Unconferences/Unseminars in Bioinformatics - Sharing our Experiences
Leader: Aidan Budd
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Affiliation: European Molecular Biology Laboratory (EMBL), Heidelberg, Germany

Day: Monday July 22, 5:40 p.m. - 6:40 p.m.
Room: TBA

Description:
Join us for the first ever ISMB unseminar! A chance to learn more about, experience for the first time, and share your experiences of organising, participating, enjoying unconferences/unseminars, with their participant-focused, open, flexible structure, and focus on promoting interaction between participants. Tweet ideas for the BoF with #ismb2013unconf more info here http://ismb2013unconf.wordpress.com

 


 

 

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ISCB 2013 Overton Prize Award

Goncalo AbecasisGoncalo Abecasis

Center for Statistical Genetics, Department of Biostatistics,
University of Michigan School of Public Health, United States

website: http://www.sph.umich.edu/csg/abecasis/

Presentation Title: Insights from Sequencing Thousands of Human Genomes

Presentation Time: Sunday, July 21 4:35 PM - 5:35 PM

 Room: Hall 1

 

 

 

Abstract:

Identifying and characterizing the genetic variants that affect human traits is one of the central objectives of human genetics. Ultimately, this aim will be achieved by examining the relationship between interesting traits and the complete genome sequences of many individuals. Whole genome re-sequencing of thousands of individuals remains challenging, but advances in laboratory methods and in statistical methodology have resulted in substantial progress in our understanding of complex disease biology.
 
Here, we discuss results of the first generation of large scale sequencing studies. I illustrate findings from analysis of sequence data in 1,000s of individuals and, in particular, on the insights from two studies where my group is actively involved, a case-control study of age-related macular degeneration and an ongoing population sequencing study in the island of Sardinia. Along the way, I will highlight analytical challenges and opportunities posed by next-generation sequence data - ranging from methods for the analysis of low-coverage data, to strategies for estimating individual ancestry using sequence data, to methods for combining the results of sequencing studies across samples.

 

Biography:

Gonçalo Abecasis is the Felix Moore Collegiate Professor of Biostatistics at the University of Michigan School of Public Health, where he has been a faculty member since 2001. He has a Ph.D. in Human Genetics from the University of Oxford, where he worked with William Cookson and Lon Cardon.
 
Dr. Abecasis' research focuses on the development of statistical tools and computational methods that enable studies of genetic variation and its connections to human disease. Software and algorithms developed by Dr. Abecasis are used in human genetic studies around the world. He has made important contributions to our understanding of patterns of genetic variation across the genome, its relationship to a variety of complex traits and diseases, and developed algorithms that enable analysis of large challenging datasets. He is currently deploying next-generation sequencing technologies to study the genomes of thousands of individuals.

2013 ISCB Accomplishment by a Senior Scientist Award

David EisenbergDavid Eisenberg

UCLA-DOE Institute and Howard Hughes Medical Institute
UCLA, Los Angeles, CA

website: http://www.doe-mbi.ucla.edu/people/eisenberg

Presentation Title: Protein Interactions in Health and Disease

Presentation Time: Tuesday, July 23, 4:35 PM - 5:35 PM

 Room: Hall 1




Abstract:

To aid research on proteins and metabolism, we have set up several databases and servers, all available at www.doe-mbi.ucla.edu.  One is the Database of Interacting Proteins (DIP), a curated collection of experiments on protein interactions.  Another is ProLinks, a collection of functional linkages between proteins in many organisms, inferred from whole genome sequences.  A third is ZipperDB, a database containing predictions of fibril-forming proteins identified by the 3D Profile Method.

ZipperDB has enabled our efforts to determine more than 100 atomic structures of the ‘steric zipper’ spines of amyloid fibers.  These fibers are associated with dozens of fatal diseases, as well as numerous evolved protein functions.  Knowledge of these atomic structures has permitted the design of inhibitors of formation of fibers involved in Alzheimer’s Disease, HIV, and cancer.

 

Biography

As a Harvard undergraduate, David Eisenberg had the good fortune to be assigned to study with John T. Edsall, one of the pioneers of protein chemistry, who oriented him to his life’s work.  As a Rhodes Scholar at Oxford, Eisenberg earned a D.Phil. in theoretical chemistry for study with Charles Coulson on hydrogen bonding in ice. Returning to the States, Eisenberg worked as a postdoctoral fellow with Walter Kauzmann, the discoverer of the hydrophobic interaction.  Together they wrote a monograph, The Structure and Properties of Water, still in print after 44 years.  In further postdoctoral study at Caltech, Eisenberg learned X-ray crystallography.  Since 1969, Eisenberg has been on the faculty of UCLA, now as the Paul D. Boyer Professor of Biochemistry and Molecular Biology, Investigator of the Howard Hughes Medical Institute, and Co-Director of the Center for Global Mentoring.  Eisenberg now concentrates on proteins in the amyloid state.   He has coauthored a text Physical Chemistry for Students of the Life Sciences, as well as some 350 research papers and reviews, with over 50,000 Google Scholar citations.

 

 

2013 ISCB Fellows Keynote

Gary StormoGary Stormo
Department of Genetics, Center for Genome Sciences and Systems Biology
Washington University in St. Louis School of Medicine, United States

website: http://stormo.wustl.edu/

Presentation Title: Searching for Signals in Sequences

Presentation Time: Monday, July 22, 4:35 - 5:35

Room: Hall 1
 

 

Abstract

DNA is an information carrying molecule, encoding not only for the RNAs and proteins that perform the functions necessary for cellular and organismal viability, but also encoding the instructions for when, where and under what conditions those functional molecules are expressed. Most of my career has been devoted to studying the signals, cis-regulatory elements, in DNA and RNA that controls various aspects of gene expression. This talk will provide some background on the nature of the signals we seek, some history of approaches to find them, how current technology facilitates the search and where I think the field is headed.


Biography

Gary Stormo is the Joseph Erlanger Professor in the Department of Genetics and the Center for Genome Sciences and Systems Biology at Washington University School of Medicine in St Louis. He received his B.S. degree in biology from the California Institute of Technology and his and Ph.D. in molecular biology from the University of Colorado at Boulder. He remained at the University of Colorado as a faculty member in the Department of Molecular, Cellular and Developmental Biology until joining the faculty at WUSM in 1999. Beginning with his graduate thesis work he has combined experimental and computational approaches to understanding gene regulation. Most of that work has focused on identifying, modeling and predicting regulatory sites in DNA and RNA and their contributions to regulatory networks that control gene expression in vivo.

Lior PachterLior Pachter
Department of Mathematics, Molecular & Cell Biology and Electrical Engineering & Computer Science
University of California, Berkeley, United States

website: http://math.berkeley.edu/~lpachter/

 

Presentation Title: Sequencing based functional genomics (analysis)

Presentation Time: Monday, July 22, 9:00 AM - 10:00 AM

Room: Hall 1

 

 

Abstract:
Sequence census methods couple high-throughput DNA sequencing to biochemical assays and are transforming standard functional genomics assays into powerful genome-wide probes of biochemical activity. We will survey the plethora of *-Seq assays that have been developed and describe examples of how computational advances are going hand-in-hand with the biotechnology to enable biological discovery.

 

Biography
I am a computational biologist working in genomics. My career began in comparative genomics, and initially I was interested in genome alignment, annotation, and the determination of conserved regions using phylogenetic methods. I contributed to the mouse, rat, chicken and fly genome sequencing consortia, and the ENCODE project. More recently I've become focused on functional genomics, which includes answering questions about the function and interaction of DNA, RNA and protein products. I'm particularly interested in applications of high-throughput sequencing to RNA biology.

I'm also interested in algorithms, statistical methodology, and mathematical foundations for computational genomics. These interests are reflected in my appointments across different departments and colleges: Mathematics, Molecular & Cell Biology, and Electrical Engineering & Computer Science. My group includes students and postdocs from Computer Science, Mathematics, Bioengineering, Molecular and Cell Biology and Statistics.