WEPA 2010: Extended Deadline
Posted on Wednesday, December 30, 2009 at 10:52 AM by Bertil Schmidt
Due to several requests we have extended the submission deadline of the 2nd Workshop on using Emerging Parallel Architectures (WEPA 2010) to 8th January 2010.
Posted in (RSS)
New Tesla S1070 cluster
Posted on Monday, December 21, 2009 at 1:15 PM by Bertil Schmidt
A new NVIDIA Tesla S1070 Cluster has been successfully installed in my lab. It contains 2 Tesla S1070 quad-GPUs and 8 AMD quad-core CPUs connected by a high-speed Infinband switch.
Posted in (RSS)
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.
Posted in (RSS)
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
Posted in (RSS)
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)