Best Paper Award at ASAP 2009
Posted on Friday, July 03, 2009 at 2:01 PM by Bertil Schmidt
The paper: Y. Liu, B. Schmidt, D.L. Maskell: MSA-CUDA: "Multiple Sequence Alignment on Graphics Processing Units with CUDA" has won the Best Paper Award at the 20th IEEE International Conference on Application-specific Systems, Architectures and Processors (ASAP 2009) in Boston, MA
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Taipan and SHREC available
Posted on Thursday, June 18, 2009 at 9:41 AM by Bertil Schmidt
The Taipan software for de-novo assembly from short-read data (such as Illumina) is now availabe at: http://taipan.sourceforge.net. Details about the algorithm and a performance comparison to Velvet and Edena can be found in:
B. Schmidt, R. Sinha, B. Beresford-Smith, S. Puglisi: "A Fast Hybrid Short Read Fragment Assembly Algorithm", Bioinformatics, DOI: 10.1093/bioinformatics/btp374, in press
SHREC is a new method for correcting sequencing errors in short-read data (such as Illumina) based on suffix tries.Details about the algorithm can be found in:
J. Schroder, H. Schroder, S. Puglisi, R. Sinha, B. Schmidt: "SHREC: A short-read error correction method", Bioinformatics, DOI: doi:10.1093/bioinformatics/btp379, in press
Edited on: Friday, July 03, 2009 1:59 PMPosted in (RSS)
CUDASW++ paper and software available
Posted on Wednesday, May 06, 2009 at 1:41 PM by Bertil Schmidt
The CUDASW++ software for protein sequence database scanning on CUDA-enabled GPUs is now available for download at: http://cudasw.sourceforge.net/. The performancce of CUDASW++ is close to 10 GCUPS on a GTX 280 (single-GPU version), and upto 16 GCUPS on a GTX 295 (dual GPU version). Details can be found in the paper:
Y. Liu, D. Maskell, B. Schmidt: "CUDASW++: optimizing Smith-Waterman sequence database searches for CUDA-enabled graphics processing units", BMC Research Notes 2009, 2:73
Edited on: Wednesday, May 06, 2009 1:53 PMPosted in (RSS)
Research Fellow and PhD Postions available
Posted on Monday, December 29, 2008 at 2:15 PM by Bertil Schmidt
I am currently looking for 1 Research Fellow and 1 Ph.D. Student to do research in my newly funded project "Development of Scalable Bioinformatics Algorithms and Tools for Emerging Sequencing Technologies".
Please contact me by email if you are interested.
Edited on: Monday, December 29, 2008 2:16 PMPosted in (RSS)
Call for Papers: ICCS 2009 Workshop
Posted on Monday, September 22, 2008 at 2:31 PM by Bertil Schmidt
CALL
FOR PAPERS:
Workshop
on Using
Emerging Parallel Architectures for Computational Science
held
in conjunction with the
International
Conference on Computational Science (ICCS 2009),
Baton Rouge, Louisiana, May 25-27, 2009
The computing landscape has undergone significant transformation with the emergence of more powerful processing elements such as GPUs, FPGAs, Cell B.E., multi-cores, etc. On the multi-core front, Moore's Law has transcended beyond the single processor boundary with the prediction that the number of cores will double every 18 months. Going forward, the primary method of gaining processor performance will be through parallelism. Multi-core technology has visibly penetrated the global market. Accordingly to the latest Top500 lists the HPC landscape has evolved from supercomputer systems into large clusters of dual or quad-core processors. Furthermore, GPUs, FPGAs and heterogeneous multi-cores have been shown to be formidable computing alternatives, where certain classes of applications witness more than one order of magnitude improvement over their GPP counterpart. Therefore, future computational science centers will employ resources such as FPGAs, GPUs and Cell architectures to serve as co-processors to offload appropriate compute intensive portions of applications from the servers.
This workshop provides a forum for exploring the capabilities of emerging parallel architectures to accelerate computational science applications. Papers are being sought on a wide variety of topics related to the field of using emerging parallel architectures for computational science including but not limited to:
- Application studies on emerging architectures such as GPUs, FPGAs and Cell B.E.
- Parallel algorithms and methodologies on emerging architectures
- Languages, models, tools, and compilation techniques for emerging architectures
- Hybrid computer systems consisting of a combination of GPUs, FPGAs, etc.
- Use of emerging architectures in clusters, grids and supercomputers
Submission Guidelines:
Authors are invited to submit manuscripts reporting original, unpublished research and recent developments. All accepted oral papers will be printed in the conference proceedings published by Springer-Verlag in the Lecture Notes in Computer Science series. The submitted paper must be camera-ready and formatted according to the rules of LNCS (for LNCS formatting information see http://www.springeronline.com/sgw/cda/frontpage/0,10735,5-164-2-72376-0,00.html ). Submission implies the willingness of at least one of the authors to register and present the paper. PostScript and source versions of your paper must be submitted electronically through the ICCS paper submission system: http://www.iccs-meeting.org/iccs2009/papers/upload.php (choosing the "Using Emerging Parallel Architectures for Computational Science" workshop). Note that papers must not exceed ten pages in length, when typeset using the LNCS format. A paper without figures can be around 5500 words maximally.
Important Dates:
- Full paper submission: December 20, 2008
- Acceptance notification: February 2, 2009
- Camera ready papers: February 15, 2009
- Early registration opens: February 2, 2009
- Early registration ends: March 15, 2009
Workshop Co-Chairs:
- Bertil Schmidt, Nanyang Technological University, Singapore, asbschmidt@ntu.edu.sg , http://www3.ntu.edu.sg/home/asbschmidt/
- Douglas Maskell, Nanyang Technological University, Singapore, asdouglas@ntu.edu.sg , http://www3.ntu.edu.sg/home/asdouglas/
Program Committee:
- Michael Huebner (Univeristy of Karlsruhe, Germany)
- Manfred Schimmler (University of Kiel, Germany)
- David Luebke (NVIDIA, USA)
- Simon See (SUN Microsystems)
- Neil Bergmann (University of Queensland, Australia)
- Philip Leong (Chinese University of Hong Kong, Hong Kong)
- Heiko Schroder (RMIT, Australia)
- Alexandros Stamatakis (LMU Munich, Germany)
- Dominique Lavenier (IRISA, France)
- Tarek El-Ghazawi (George Washington University, USA)
- Jaroslaw Zola (Iowa State Uni, USA)
- Michela Taufer (University of Delaware, USA)
- Rick Goh (IHPC, Singapore)
- Scott Emrich (University of Notre Dame, USA)
- Ananth Kalyanaraman (Washington State University, USA)
- Shi Haixiang (NTU, Singapore)
- Gerrit Voss (Fraunhofer Institute, Germany and NTU, Singapore)
- Weiguo Liu (NTU, Singapore)
- Malcolm Low (NTU, Singapore)
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NVIDIA Professor Partnership Award
Posted on Thursday, September 18, 2008 at 12:38 PM by Bertil Schmidt
My research group has just been awarded an NVIDIA Professor Partnership for GPU-enabled genomics research. This is a highly competitive award and so far has only been awarded to professors based in US and Europe.
Edited on: Thursday, September 18, 2008 12:39 PMPosted in (RSS)
Workshop at ICCS 2009
Posted on Friday, September 12, 2008 at 11:20 AM by Bertil Schmidt
We will be organizing a Workshop titled "Using Emerging Parallel Architectures for Computational Science" at the ICCS 2009 conference in Baton Rouge, Louisiana, USA.
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Invited talk at GridAsia 2008
Posted on Monday, July 28, 2008 at 1:26 PM by Bertil Schmidt
I will be giving an invited talk at the GridAsia 2008 meeting about "GPU-accelerated Grid Computing for Bioinformatics Applications"
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Ph.D. Positions available!
Posted on Tuesday, July 15, 2008 at 2:55 PM by Bertil Schmidt
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Bertil's Contact
Posted on Tuesday, July 15, 2008 at 2:54 PM by Bertil Schmidt
School of Computer Engineering,
Nanyang Technological University,
N4, Nanyang Avenue, Singapore 639798
Tel:+65 6790 6107
Email: asbschmidt{at}ntu.edu.sg
Map: link to map
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