CUDA-MEME software available
Posted on Thursday, October 15, 2009 at 12:30 PM by Bertil Schmidt
The CUDA-MEME software for motif finding with the MEME algorithm on CUDA-compatible GPUs is availble at: http://sites.google.com/site/yongchaosoftware/Home/cuda-meme. The paper describing CUDA-MEME has also been accepted for publication:
Y. Liu, B. Schmidt, W. Liu, D. Maskell: "CUDA-MEME: Accelerating Motif Discovery in Biological Sequences Using CUDA-enabled Graphics Processing Units", Pattern Recognition Letters, in press, doi:10.1016/j.patrec.2009.10.009
Edited on: Thursday, November 05, 2009 6:13 PMPosted in (RSS)
2nd WEPA Workshop at ICCS2010
Posted on Thursday, September 24, 2009 at 6:11 PM by Bertil Schmidt
We will be organizing the "2nd Workshop on Emerging Parallel Architectures (WEPA)" at the ICCS 2010 conference in Amsterdam The Netherlands.
Edited on: Thursday, November 05, 2009 6:14 PMPosted in (RSS)
New Elsevier Science Journal of Computational Science is alive!
Posted on Friday, September 18, 2009 at 9:07 AM by Bertil Schmidt
Am on the Editorial Baord of the new JoCS journal! Check: http://www.elsevier.com/locate/jocs. and consider submitting a paper.
Edited on: Thursday, September 24, 2009 5:42 PMPosted in (RSS)
Ph.D. Position
Posted on Friday, July 10, 2009 at 3:10 PM by Bertil Schmidt
I am currently looking for a Ph.D. Student to do research in the project "Development of Scalable Bioinformatics Algorithms and Tools for Emerging Sequencing Technologies". - focussing on Algortihm Design for Solexa/Illumina read data. (expected starting date is January 2010)
Please contact me by email if you are interested.
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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, 25(17) pp. 2279-2280, 2009
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, 25(17) pp. 2157-2163, 2009
Edited on: Thursday, August 20, 2009 4:20 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 2010 Workshop (WEPA)
Posted on Monday, September 22, 2008 at 2:31 PM by Bertil Schmidt
Call
for Papers: 2nd
Workshop on using
Emerging Parallel Architectures (WEPA)
held
in conjunction with the International
Conference on Computational Science (ICCS 2010),
Amsterdam, The Netherlands, May 31 - June 2, 2010
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 Elsevier Science in the open-access Procedia Computer Science series (on-line and CD). The submitted paper must be camera-ready and formatted according to the rules of Procedia Computer Science (for formatting information see for Latex and for MSword). 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 2010 paper submission system: http://www.iccs-meeting.org/iccs2010/papers/upload.php.
Please, note that papers must not exceed ten pages in length, when typeset using the Procedia format.
Important Dates:
- Full paper submission: January 01, 2009
- Acceptance notification: February 15, 2010
- Camera ready papers: March 1, 2010
- Early registration opens: February 15, 2010
- Early registration ends: March 31, 2010
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:
- Vipin Chaudhary (Uni Buffalo, USA)
- John Paul Walters (USC, USA)
- Scott Emrich (Uni Notre Dame, USA)
- Witold Rudnicki (Uni Warsaw, Poland)
- Arpith Jacob (Washington Uni in St Louis, USA)
- Mathieu Giraud (INRIA, France)
- Rob Farber (PNNL, USA)
- Stan Scott (Queens Uni Belfast, UK)
- Chris Clarke (Uni Bath, UK)
- Manfred Schimmler (University of Kiel, Germany)
- Simon See (SUN Microsystems)
- Neil Bergmann (University of Queensland, Australia)
- Heiko Schroder (RMIT, Australia)
- Alexandros Stamatakis (TU Munich, Germany)
- Dominique Lavenier (IRISA, France)
- Jaroslaw Zola (Iowa State Uni, USA)
- Ananth Kalyanaraman (Washington State Uni, 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)