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 ‚Äď 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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