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In conjunction with the 5th Special Track on Grid and Cloud Computing in Biomedicine and Life Sciences Workshop, CBMS2012
June 20-22, 2012, Rome Italy


DELSA Workshop II, Supporting Ecosystems for the Life Sciences in the Beginning of the 21st Century, May 3-4, 2012, Bethesda, Washington DC.


     Introduction


This follows up our successful first meetings in this series at HPDC’11 and HPDC’10, which are well documented at ECMLS2011 and ECMLS2010. The basic motivation is as before with the dramatic important of next generation sequencers in biology and the need for corresponding increase in new algorithms and new computing systems growing more apparent. Recent workshops in the USA such as DISW2 have emphasized this and recently has prompted setting up the Data-Enabled Life Science Alliance DELSA that will aim to coordinate the community for which our proposed workshop would be a natural technical outlet.

 

Computing systems are rapidly changing with multicore, GPUs, clusters, volunteer systems, clouds, and grids offering a confusing dazzling array of opportunities. New programming paradigms such as MapReduce and Many Task Computing have joined the traditional repertoire of workflow and parallel computing for the highest performance systems. Meanwhile the Life Sciences are continuing to expand in data generated with continuing improvement in the instruments for high throughput analysis. This “fourth paradigm” (observationally driven science) is joined by complex systems or biocomplexity that can build phenomenological models of biological systems and processes. This workshop juxtaposes these trends seeking those computational methods that will enhance scientific discovery in the life sciences arena.


The purpose of this the workshop is to provide the opportunity for researchers, scientists, engineers, and students to discuss and share the latest research in parallel and distributed high performance systems applied to Life Science problems. It aims to offer an interactive environment for investigators working on novel “computational thinking” for (Systems) Biology, Bioinformatics, Biocomplexity and Cheminformatics, so that future activities and collaborations will be initiated, as well as fostering discussions about the utilization of HPDC systems in their respective research initiatives.


     Journal Special Issue


Selected papers will be published in a special issue of Journal Concurrency and Computation: Practice and Experience (CCPE).


     Student Program


We propose to build on student involvement with the first two workshops with a special student poster session followed by a panel discussing research issues in data-enabled life sciences.


     Topics of interests include (but not limited to)


  • Applications of GPU and Multicore architectures to the life sciences
  • Applications of Cloud (including MapReduce), Many Task, Grid and Parallel (High Performance) computing to the life sciences
  • Performance, Algorithms, Architectures, Tools (such as workflow) and environments for the life sciences
  • Data Management, Data Mining, Data Integration and Databases for the life sciences
  • Data Visualization (including dimension reduction) for the life sciences
  • Data Privacy and Security issues in processing and access to Life Science data
  • Biocomplexity, Complex Systems, Computational Systems Biology and Computational Biomodeling
  • Biostatistics, Biomedical Intelligence, Biomedical Databases & Information Systems
  • Computational Life Science Applications such as Alignment, Assembly, Biomedical Imagery, Drug Discovery, Computational Genomics and Proteomics
  • Text Mining, Information Extraction, and Web-mining of life science data
  • Social Networking and Virtual Organization technologies for life sciences

  •     List of related workshops


    • e-Science 2011Stockholm Sweden 5-8 December 2011
    • DISW3 Data Intensive Sciences Workshop for DELSA at SC11, November 13 2011, Seattle, USA
    • ISBB2011  International Symposium on Bioelectronics and Bioinformatics,  Suzhou, China 3-5 November
    • CMSB 2011, 9th International Conference on Computational Methods in Systems Biology, Institut Henri Poincaré, Paris, France, September 21-23, 2011
    • HiBi 2011 High Performance Computational Systems Biology) Institut Henri Poincaré, Paris, France, September 21-23, 2011
    • 11th International Workshop on Bioinformatics and Systems Biology (IBSB), Berlin Germany, 17 – 20 July 2011
    • The 12th Annual Bioinformatics Open Source Conference (BOSC 2011) Austria Center in Vienna Austria, July 15-16 2011
    • Emerging Computational Methods for the Life Sciences Workshop ECMLS2011 June 8 2011 San Jose CA
    • DISW2 NSF Data Intensive Sciences Workshop Washington DC May 16-17 2011.
    • Bioinformatics and Cloud Tracks at Bio-IT World Conference & Expo '11 April 12-14 World Trade Center Boston Mass
    • e-Science 2010 Brisbane Australia 7-10 December 2010
    • HiBi2010 (High performance computational systems Biology) workshop (September 30-Ocober 1 2010) University of Twente, The Netherlands
    • CMSB '10 — 8th Conference on Computational Methods in Systems Biology (29 Sep 2010 -  01 Oct 2010) Trento, Italy
    • DISW1 NSF Data-Intensive Sciences Workshop September 19-20 2010, Seattle Children's Research Institute.
    • The Tenth International Workshop on Bioinformatics and Systems Biology (July 25-28, 2010) IBSB2010
    • The 11th Annual Bioinformatics Open Source Conference (BOSC)
    • Emerging Computational Methods for the Life Sciences Workshop ECMLS2010 June 21 2010 Chicago, IL
    • ISBB 2009 International Symposium on Bioelectronics and Bioinformatics, December 9-11, 2009, Melbourne, Australia
    • WCMB 2009 Workshop on Computational Molecular Biology, December 9, 2009, Mysore, India
    • e-Science 2009, Oxford England 7-9 December 2009
    • SC09-sysbio, Using Clouds for Parallel Computations in Systems Biology, November 16, 2009, Portland, Oregon
    • CompMod 2009, 2nd International Workshop on Computational Models for Cell Processes, November 3, 2009, Eindhoven
    • 2009 Microsoft eScience Workshop, October 16-17, 2009, Pittsburgh, Philadelphia
    • HiBi09 - High Performance Computational Systems Biology, October 14-16, 2009, Trento, Italy
    • Workshop on Parallel Computational Biology, September 13-16, 2009, Wroclaw, Poland
    • Bioinformatics Open Source Conference, June 27-28, 2009, Stockholm, Sweden
    • BioCom 2009, Second IEEE International Workshop on BioComputing, May 26-29, 2009, Bradford, UK
    • Biocomputing @ UNM, March 27, 2009, Albuquerque, NM
    • The Ninth Annual International Workshop on Bioinformatics and Systems Biology, July 27-29, 2009, Boston, MA
    • BLSMC 2009 IEEE International Workshop on Bioinformatics and Life Science Modeling and Computing, May 26-29, 2009, Bradford, UK

        Submission Guidelines

    The papers should be prepared using the ACM proceedings style and no longer than 10 pages for full papers or 4 pages for short papers. Submitted papers will be carefully evaluated based on originality, significance to workshop topics, technical soundness, and presentation quality. Submission of the paper implies that should the paper be accepted, at least one of the authors will register and present the paper at the workshop.

    Please submit your paper to the ECMLS 2012 submission server via an EasyChair account.


        Important Dates

    Manuscript submission deadline February 25, 2012 March 9, 2012
    Acceptance notification March 26, 2012
    Camera-ready paper deadline April 16, 2012
    Workshop dates June 18-19, 2012

     

     

     



        Publication of Papers

    Full and short papers accepted for emerging computational methods for the life sciences workshop 2011 will be published by the HPDC 2012 conference proceedings by ACM in the same volume. Submitting paper implies willingness to register for the workshop and present the paper. At least one person that can be contacted about the workshop. Selected papers will be published in a special issue of Journal Concurrency and Computation: Practice and Experience.

        Workshop in HPDC 2012

    ECMLS2012 is one of the workshops held in conjunction with HPDC'12:

    Short Workshop Name Full Workshop Name
    Application Domain
    Astro-HPC 2012 Workshop on High-Performance Computing for Astronomy
    ECMLS 2012 Emerging Computational Methods for the Life Sciences Workshop
    Science Cloud 2012 Workshop on Scientific Cloud Computing
    SocMP 2012 Workshop on Social Media Processing
    Data-Intensive Processing
    DIDC 2012 Workshop on Data-Intensive Distributed Computing
    ISDP 2012 In-Situ Data Processing Technologies
    General
    LSAP 2012 Workshop on Large-scale Systems and Applications Performance
    Infrastructure
    MapReduce'12 Workshop on MapReduce and its Applications
    VTDC-2012 Workshop on Virtualization Technologies in Distributed Computing