I currently have one PhD scholarship starting in January 2009 available!

Furthermore, there are PhD scholarships available through SINGA. The SINGA scholarship gives you the opportunity to work with me as well as IHPC.

Research Interests

• High Performance Computing
• Bioinformatics
• Reconfigurable Computing
• GPGPU
• Heterogeneous Mutlicores

Research Background

New high performance computing challenges emerge daily. Each problem raises questions as to

• What algorithms and data structures to use?
• How to exploit parallelism?
• Which computer architectures will minimize the execution time?

My group is working on solutions to emerging high performance computing problems on hybrid parallel computer architectures with a very low price-performance ratio. Such architectures can provide the flexibility to speedup a wide range of algorithms at both fine-grained and coarse-grained parallel levels.

Examples for the fine-grained parallel level are

• reconfigurable architectures (FPGA)
• graphics architectures (GPU)
• heterogeneous multi-core architectures (in particular the Cell BE).

Examples of coarse-grained parallel and distributed architectures include

• PC clusters
• Compuational Grids (based on the BOINC middleware)

We are currently investigating the use of this infrastructure to support advanced algorithms and applications in serveral different domain. Some examples are described in the follwoing.

1. Bioinformatics

Algorithms and Systems for New Sequencing Technologies (such as Solexa/Illimuna):

Next generation, rapid, low-cost genome sequencing promises to address a broad range of genetic analysis applications. One of the ambitious goals for these technologies is to produce a complete human genome in a reasonable time frame for US$100,000, and eventually US$1,000. In order to do this, throughput must be increased dramatically. This is achieved by carrying out many parallel reactions. Although the read-length is short (currently around 35 base-pairs for Solexa/Illumina), the overall throughput is enormous, each run producing up to several hundreds of million reads and billions of base-pairs of sequence data. Therefore, computational methods for analyzing and managing the massive numbers of the short reads produced by these platforms, is urgently needed. In particular existing assembly tools and algorithms have been designed and optimized for shotgun sequencing. Since new sequencing technologies are using much shorter reads these approaches cannot be applied for assembly next-generation sequencing technologies (in particular the characterization of sequencing errors is different).

We are currently working on the design of efficient assembly algorithms on high performance computers for new sequencing technologies.

Partners: Shi Haixiang (NTU), Bryan Beresford-Smith (NICTA), Jan Schroeder (Kiel Uni), Heiko Schroder (RMIT), Simon Puglisi (RMIT), Ranjan Sinha (Melbourne Uni),

Pandemic Control System.

Recent occurrences of pandemics like the SARS or the Avian Influenza clearly display the threat and seriousness of global diseases. The steadily growing globalization makes it difficult to contain pandemics to a certain region. Therefore, pandemic control is of highest importance to human health. Unfortunately, the segmented nature of viruses is very conducive for genetic shift and their rapid spread across various genera augments genetic drift. For instance, the H5N1 outbreak in Hong Kong in 1997 has demonstrated the ability of an avian virus to jump from birds to humans directly. This project investigates a new approach to pandemic control by constantly monitoring molecular evolution at both macro level (within the group of viruses) and micro level (within the group of strains). The goal is to facilitate prediction of how viruses are evolving in spatial, temporal, and host dimension, and therefore, allows for fast and efficient responses to new outbreaks as well as their diagnosis. In order to achieve high-quality predictions, computational analysis of these viruses is required at gene and at genome level. However, corresponding algorithms suffer high runtimes due to their high computational complexities as well as the large datasets involved. Therefore, it is necessary to develop IT solutions that use suitable algorithms and take advantage of high performance technologies.

Partners: D.T. Singh (Genvea Biosciences)

Related Publication: D.T. Singh, R.Trehan, B. Schmidt, T. Bretschneider: "Comparative Phyloinformatics of Virus Genes at Micro and Macro Levels in a Distributed Computing Environments", BMC Bioinformatics, Vol. 9:S23, 2008

2. Simulation

Computational simulation of complex systems is of highest importance to R&D in science and engineering. Examples of areas that require extensive simulation include the engineering design of modern aircrafts, development of new materials (such as Carbon-Nano-Tubes) and drugs as well as climate prediction. Most of these simulations are highly compute-intensive. Examples include computational electrodynamics modeling techniques (such as FMM) and molecular dynamics simulations for protein docking. However, in order to achieve highly accurate simulations large input data sets are required. This, in turn leads to prohibitive runtimes of such simulations on traditional computer architectures. The purpose of this project is to investigate and evaluate the suitability of new classes of emerging high performance architectures (such as FPGAs, GPUs and Cell BE) for engineering simulations.

Partners: Liu Weiguo (NTU), G. Alleon (EADS), P.K. Kolatkar (GIS), Francis Nai (PhD Student)

Related Publication: W. Liu, B. Schmidt, G. Voss, W. Mueller-Wittig: "Accelerating Molecular Dynamics simulations using Graphics Processing Units with CUDA", Computer Physics Communications, in press, doi:10.1016/j.cpc.2008.05.008

3. Data Mining and Database Searching

Data Mining is increasingly used in science and engineering to extract information from the enormous data sets generated by modern experimental and observational methods. The process of finding statistically overrepresented patterns in a data set can be divided into three phases: model specification, model evaluation, and search. Model specification includes the selection of a suitable analysis method from a whole range of available algorithms. Utilized algorithms are usually iterative optimization methods such as Expectation Maximization (EM), Gibbs Sampling or evolutionary algorithms. In order to avoid getting trapped into local minima, a large number of starting points or populations have to be tested. This, in turn, can be highly compute-intensive depending on the size of the data set, the model representation and objective function. Using high performance computers for this task allows the application of more complex model representations and objective functions to data mining methods on larger input data sets. An example is the hybrid parallel EM algorithms for the identification of Transcription Factor Binding Sites (TFBS) in genomic sequences, which we have recently developed.

Other examples that we are currently working on are fast searching of large genomic databases using BLAST and BLAST-like tools.

Partners: Liu Weiguo (NTU), D. Maskell (NTU), V. Brusic (Harvard). M. Rajapakse (I2R), H. Schroder (RMIT)

Related Publications:

• C. Chen, B. Schmidt, W. Liu, W. Mueller-Wittig: "GPU-MEME: Using Graphics Hardware to Accelerate Motif Finding in DNA Seqeunces", PRIB 2008, Lecture Notes in Bioinformatics, Springer, to appear
• H. Zhang, B. Schmidt, W. Mueller-Wittig: "Accelerating BLASTP on the Cell Broadband Engines", PRIB 2008, Lecture Notes in Bioinformatics, Springer, to appear
• M. Rajapakse, B. Schmidt, F. Lin, V. Brusic: "Predicting peptides binding to MHC class II molecules using multi-objective evolutionary algorithms", BMC Bioinformatics, 2007, 8:459

Edited Books and Book Chapters

1. B. Schmidt, C. Chen, W. Liu, W. Mitchell: "PheGee@Home: A Grid-based Tool for Comprative Genomics", Handbook of Research on Compuational Grid Technologies for Life Science, Biomedicine and Healthcare, to appear
2. J. Rajapakse, B. Schmidt, G. Volkert, Proceedings of the 2nd IAPR Workshop on Pattern Recognition in Bioinformatics (PRIB 2007), Lecture Notes in Bioinformatics, Springer, LNCS Volume 4774, 2007 (ISBN: 978-3-540-75285-1)
3. B. Schmidt, W. Liu, C. Chen: "Hierarchical Grid Computing for High Performance Bioinformatics", in Grids for Bioinformatics and Computational Biology, Wiley & Sons Book Series on Bioinformatics, 2007 (ISBN: 978-0-471-78409-8)
4. B. Schmidt, H. Schroeder: "Special-Purpose Computing for Biological Sequence Analysis", in Parallel Computing in Bioinformatics and Computational Biology, Wiley Book Series on Parallel and Distributed Computing, John Wiley & Sons, New York, 2005 (ISBN: 0-471-71848-3)
5. F.K. Fuss, S. L. Chia, S.S. Venkatraman, S.M. Krishnan, B. Schmidt, Proceedings of the International BioEngineering Conference 2004 (IBEC 2004), Singapore 2004 (ISBN: 981-05-1946-X)
6. B. Schmidt, M. Schimmler, H. Schroeder: "High-Speed Cryptography", in: Embedded Cryptographic Hardware: Methodologies & Architectures, Nova Science Publishers, 2004 (ISBN: 1-59454-012-8)

Journals

1. A. Wirawan, B. Schmidt, H. Zhang, C.K. Kwoh: "High Performance Protein Sequence Database Scanning on the Cell B.E. Processor", Scientific Programming, accepted for publication
2. A. Wirawan, C.K. Kwoh, T.H. Nim, B. Schmidt: "CBESW: Sequence Alignment on the Playstation 3" BMC Bioinformatics, Vol. 9:377, 2008 (Impact factor: 3.493)
3. T. Oliver, Y.Y. Leow, B. Schmidt: "Integrating FPGA Acceleration into HMMer", Parallel Computing, Vol. 34, No. 11, pp.681-691, 2008 (Impact factor: 0.825)
4. W. Liu, B. Schmidt, G. Voss, W. Mueller-Wittig: "Accelerating Molecular Dynamics simulations using Graphics Processing Units with CUDA", Computer Physics Communications, Vol. 179, No. 9, pp. 634-641, 2008 (Impact factor: 1.842)
5. D.T. Singh, R.Trehan, B. Schmidt, T. Bretschneider: "Comparative Phyloinformatics of Virus Genes at Micro and Macro Levels in a Distributed Computing Environments", BMC Bioinformatics, Vol. 9:S23, 2008 (Impact factor: 3.493)
6. A. Singh, C. Chen, W. Liu, W. Mitchell, B. Schmidt: "A Hybrid Computational Grid Architecture for Comparative Genomics", IEEE Transactions on Information Technology in Biomedicine, Vol. 12, No. 2, pp. 218-225, March 2008 (Impact factor: 1.436)
7. T. Oliver, B. Schmidt, Y. Jacop, D. Maskell: "High-Speed Biological Sequence Analysis with Hidden Markov Models on Reconfigurable Platforms", IEEE Transactions on Information Technology in Biomedicine, in press, doi:10.1109/TITB.2007.904632 (Impact factor: 1.436)
8. M. Rajapakse, B. Schmidt, F. Lin, V. Brusic: "Predicting peptides binding to MHC class II molecules using multi-objective evolutionary algorithms", BMC Bioinformatics, 2007, 8:459 (Impact factor: 3.493)
9. W. Liu, B. Schmidt, G. Voss, W. Mueller-Wittig, "Streaming Algorithms for Biological Sequence Alignment on GPUs", IEEE Transactions on Parallel and Distributed Systems, Vol. 18, No. 9, pp. 1270-1281, 2007 (Impact factor: 1.146)
10. F. Lin,, H. Schroeder, B. Schmidt.: "Solving the Bottleneck Problem in Bioinformatics Computing: an Architectural Perspective", Journal of VLSI Signal Processing Systems, Springer, Vol. 48, No. 3, pp185-188, 2007 (Impact factor: 0.449)
11. W. Liu, B. Schmidt, W. Mueller-Wittig: "Performance Analysis of General-Purpose Computation on Commodity Graphics Hardware: A Case Study Using Bioinformatics", Journal of VLSI Signal Processing Systems, Springer, Vol. 48, No. 3, pp. 209-221, 2007 (Impact factor: 0.449)
12. J.P. Walters, X. Meng, V. Chaudhary T. Oliver, Y.Y Leow, B. Schmidt, D. Nathan J. Landman: "MPI-HMMER-Boost: Distributed FPGA Acceleration", Journal of VLSI Signal Processing Systems, Springer, Vol. 48, No. 3, pp. 223-238, 2007 (Impact factor: 0.449)
13. B. Schmidt: "A Survey of Desktop Grid Applications for E-Science", International Journal of Web and Grid Services, Vol. 3. No. 3, pp. 354-368, 2007 (Impact factor: -)
14. M. Schimmler, B. Schmidt, H.-W. Lang, S. Heithecker: "An Area-Efficient Bit-Serial Integer and GF(2n) Multiplier", Microelectronic Engineering, Vol. 82, No. 2, pp. 253-259, February 2007. (Impact factor: 1.503)
15. M. Rajapakse, G.L. Zhang, K.N. Srinivasan, B. Schmidt, N. Petrovsky, V. Brusic: "PREDNOD, a prediction server for peptide binding to the H-2g7 haplotype of the nonobese diabetic mouse", Autoimmunity, Vol. 39 No. 8, pp. 645-650, December 2006 (Impact factor: 2.887)
16. C. Chen, B. Schmidt: "Constructing Large Suffix Trees on a Computational Grid", Journal of Parallel and Distributed Computing, Vol. 66, No. 12, pp.1512-1523, December 2006 (Impact factor: 0.574)
17. W. Liu, B. Schmidt: "A Parallel Pattern-based System for High Performance Computational Biology", IEEE Transactions on Parallel and Distributed Systems, Vol. 17, No. 8, pp. 750-763, August 2006 (Impact factor: 1.146)
18. T. Oliver, B. Schmidt, D. Maskell, D. Nathan, R. Clemens: "High-speed multiple sequence alignment on a reconfigurable platform", International Journal of Bioinformatics Research and Applications, Vol. 2, No. 4, pp. 394-406, 2006 (Impact factor: -)
19. Z. Du, F. Lin, B. Schmidt: "Accomplishments and Challenges in High Performance Computing for Computational Biology", Current Bioinformatics, Vol. 1, No. 2, pp. 185-195, May 2006 (Impact factor: 1.226)
20. W. Liu, B. Schmidt: "Mapping of Hierarchical Parallel Genetic Algorithms for Protein Folding onto Computational Grids", IEICE Transactions on Information and Systems, E89-D(2):589-596, February 2006 (Impact factor: 0.245)
21. T. Oliver, B. Schmidt, D. Nathan, R. Clemens, D. Maskell: "Using reconfigurable hardware to accelerate multiple sequence alignment with ClustalW", Bioinformatics, Vol. 21, No. 16, pp. 3431-3432, 2005. (Impact factor: 5.039)
22. T. Oliver, B. Schmidt, D. Maskell: "Reconfigurable Architectures for Bio-sequence Database Scanning on FPGAs", IEEE Transactions on Circuits and Systems II, Vol. 52, No. 12, pp. 851-855, 2005 (Impact factor: 1.104)
23. C. Chen, B. Schmidt: "An Adaptive Grid Implementation of DNA Sequence Alignment", Future Generation Computer Systems, Vol. 21, No. 7, pp. 988-1003, 2005 (Impact factor: 1.095)
24. T. Liu, B. Schmidt: "Parallel RNA Secondary Structure Prediction using Stochastic Context-Free Grammars", Concurrency and Computation: Practice and Experience, Vol. 17, No. 14, pp. 1669-85, 2005 (Impact factor: 1.154)
25. B. Schmidt, M. Schimmler: "A Bit-Serial Floating-Point Unit for a massively parallel system on a chip", Journal of Parallel Algorithms and Architectures, Vol. 19, No. 2-3, pp. 79-96, 2004 (Impact factor: -)
26. B. Schmidt, M. Schimmler, H. Schroeder: "A massively parallel architecture for public-key cryptography", International Journal of Computer Research, accepted for publication in 2004. (Impact factor: -)
27. B. Schmidt, F. Lin, A. Laud, Y. Santoso: "Development of Distributed Bioinformatics Applications with GMP", Concurrency and Computation: Practice and Experience, Vol. 16, pp. 945-959, 2004 (Impact factor: 1.154)
28. B. Schmidt, H. Schroeder, M. Schimmler: "A hybrid architecture for bioinformatics", Future Generation Computer Systems, No. 18, pp. 855-862, 2002 (Impact factor: 1.095)
29. B. Schmidt, H. Schroeder: "A hybrid Architecture for Multimedia Processors", Computing and Informatics, Vol. 20, No. 9, pp. 225-244, 2001. (Impact factor: 0.349)
30. B. Schmidt, M. Schimmler, H. Schroeder: "Tomographic Image Reconstruction on the Instruction Systolic Array", Computing and Informatics, Vol. 20, No. 1, pp. 27-42, 2001. (Impact factor: 0.349)
31. B. Schmidt, M. Schimmler: "KPROC - An Instruction Systolic Architecture for Parallel Prefix Applications", Parallel and Distributed Computing Practices, Vol. 3, No. 2, 2000. (Impact factor: -)
32. B. Schmidt, H. Schroeder, M. Schimmler: "A Morphological Approach to Hough Transform on the Instruction Systolic Array", Computers and Artificial Intelligence, Vol. 18, No. 6, pp. 541-557, 1999. (Impact factor: 0.349)

Conferences

1. C. Chen, B. Schmidt, W. Liu, W. Mueller-Wittig: "GPU-MEME: Using Graphics Hardware to Accelerate Motif Finding in DNA Seqeunces", PRIB 2008, Springer, Lecture Notes in Bioinformatics, Vol. 5265, pp.448-459, 2008.
2. H. Zhang, B. Schmidt, W. Mueller-Wittig: "Accelerating BLASTP on the Cell Broadband Engines", PRIB 2008, Springer, Lecture Notes in Bioinformatics, Vol. 5265, pp. 460-470, 2008.
3. N.T. Hieu, C.K. Kwoh. A. Wirawan, B. Schmidt: "Applications of Heterogeneous Structure of Cell Broadband Engine Architecture for Biological Database Similarity Search", 2nd International Conference on Bioinformatics and Biomedical Engineering (iCBBE2008), IEEE Press, pp. 5-8 (2008)
4. W. Liu, B. Schmidt, G.Voss, W. Mueller-Wittig: "Molecular Dynamics Simulations on Commodity GPUs With CUDA" 14th IEEE International Conference on High Performance Computing (HiPC 2007), Goa, India, Springer, LNCS, Vol. 4873
5. M.Y.H. Low, W. Liu, B. Schmidt, "A Parallel BSP Algorithm for Irregular Dynamic Programming", 7th International Symposium on Advanced Parallel Processing Technologies (APPT 2007), Springer, LNCS Vol. 4847, pp. 151-160, 2007
6. A. Wirawan, B. Schmidt, C.K. Kwoh: "Parallel DNA Sequence Alignment on the Cell Broadband Engine",7th International Conference on Parallel Processing and Applied Mathematics (PPAM 2007), Gdansk, Poland, Springer, LNCS Vol. 4967, pp. 1249-1256, 2008
7. L.A. Aung, D. Maskell, T. Oliver, B. Schmidt: "C-based Design Methodology for FPGA Implementation of ClustalW MSA", Pattern Recognition in Bioinformatics (PRIB 2007), Springer LNCS Vol. 4774, pp. 11-18, 2007
8. R. Trehan, D.T. Singh, B. Schmidt: "Phylogenetic Analysis of Neuraminidase Genes of H5N1 Isolates using HPC technologies", 9th International Conference on e-Health Networking, Application and Services (IEEE Healthcom 2007), IEEE Press, pp. 285-288, 2007
9. C. Chen, A. Singh, W. Mitchell, B. Schmidt: "Phenotype Genotype Exploration on a Desktop GPU Grid", 3rd International Workshop on Grid Computing and Applications, World Scientific, pp.154-165, 2007
10. W. Liu, W. Mueller-Wittig, B. Schmidt: "Performance Predictions for General-Purpose Computation on GPUs", International Conference on Parallel Processing (ICPP 2007), XiAn, China, IEEE Press, 2007
11. T. Oliver, Y.Y. Leow, B. Schmidt: "High Performance Database Searching with HMMer on FPGAs", 6th IEEE International Workshop on High Performance Computational Biology (HiCOMB 2007), Long Beach, CA, IEEE Press, 2007.
12. J. Feng, S. Chakraborty, B. Schmidt, W. Liu, U.D. Bordoloi: "Fast Schedulability Analysis Using Commodity Graphics Hardware", 13th IEEE International Conference on Embedded and Real-Time Computing Systems and Applications (RTCSA 2007), IEEE Press, pp.400-408, 2007
13. W. Liu, B. Schmidt, G. Voss, W. Mueller-Wittig: "GPU-ClustalW: Using Graphics Hardware to Accelerate Multiple Sequence Alignment", 13th IEEE International Conference on High Performance Computing (HiPC 2006), Bangalore, India, Springer, LNCS Vol. 4297, pp. 363-374, 2006.
14. A. Wirawan, B. Schmidt: "Parallel Discovery of Transcription Factor Binding Sites", IEEE Asia Pacific Conference on Circuits and Systems (APCCAS 2006), Singapore, IEEE Press, 2006
15. T. Oliver, B. Schmidt, J. Yanto, D. Maskell: "Accelerating the Viterbi Algorithm for Profile Hidden Markov Models using Reconfigurable Hardware", International Conference on Computational Science (ICCS 2006), Reading, UK, Springer-Verlag, LNCS Vol. 3991, Part I, pp. 522-529, 2006
16. M. Rajapakse, B. Schmidt, V. Brusic: "Multi-Objective Evolutionary Algorithm for Discovering Peptide Binding Motifs", 4th European Workshop on Evolutionary Computation and Machine Learning in Bioinformatics (EvoBIO 2006), Budapest, Hungary, Springer, LNCS Vol. 3907, pp. 149-158, 2006
17. W. Liu, B. Schmidt, G. Voss, A. Schroeder, W. Mueller-Wittig: "Bio-Sequence Database Scanning on a GPU", 5th IEEE International Workshop on High Performance Computational Biology (HiCOMB 2006), Rhode Island, Greece, IEEE Press, 2006
18. M. Rajapakse, B. Schmidt, V. Brusic: "Pareto-Optimal Motif for Predicting Peptide Binders", 16th International Conference on Genomic Informatics (GIW 2005), Yokohama, Japan, 2005
19. G. Voss, A. Schröder, W. Müller-Wittig, B. Schmidt: "Using Graphics Hardware to Accelerate Biological Sequence Analysis", IEEE Tencon 2005, Melbourne, Australia, 2005
20. W. Liu, B. Schmidt: "Mapping of Hierarchical Parallel Genetic Algorithms for Protein Folding onto Computational Grids", IEEE Tencon 2005, Melbourne, Australia, 2005.
21. J. Yanto, T. Oliver, B. Schmidt, D. Maskell: "Biological Sequence Analysis with Hidden Markov Models on an FPGA", 10th Asia-Pacific Computer Systems Architecture Conference (ACSAC 2005), Singapore, Springer-Verlag LNCS Vol. 3740, 2005.
22. C. Chen, B. Schmidt: "Parallel Construction of Large Suffix Trees on a PC Cluster", Euro-Par 2005, Lisbon, Portugal, Springer-Verlag LNCS Vol. 3648, 2005.
23. M. Rajapakse, L. Wyse, B. Schmidt, V. Brusic: “Deriving Matrix of Peptide-MHC Interactions in Diabetic Mouse by Genetic Algorithmâ€?, 6th International Conference on Intelligent Data Engineering and Automated Learning (IDEAL 2005), Brisbane, Australia, LNCS, Springer, 2005
24. T. Oliver, B. Schmidt, D. Nathan, R. Clemens, D. Maskell: "Multiple Sequence Alignment on an FPGA", 11th International Conference on Parallel and Distributed Systems (ICPADS 2005), IEEE Computer Society Press, Fukuoka, Japan, 2005
25. T. Oliver, B. Schmidt, D. Maskell, A.P. Vinod: "A Reconfigurable Architecture for Scanning Biosequence Databases", 2005 IEEE International Symposiumon Circuits and Systems (ISCAS 2005), Kobe, Japan, IEEE Computer Society Press, 2005
26. W. Liu, B. Schmidt: "A Case Study on Pattern-based Systems for High Performance Computational Biology", 4th IEEE International Workshop on High Performance Computational Biology (HiCOMB 2005), Denver, CO, IEEE Press, 2005
27. T. Oliver, B. Schmidt, D. Maskell: "Hyper Customized Processors for Bio-Sequence Database Scanning on FPGAs", 13th ACM International Symposium on Field-Programmable Gate Arrays (FPGA 2005), Monterrey, CA, 2005.
28. T. Liu, B. Schmidt: "Optimal local alignment in RNA secondary structures", BioMED 2005, Innsbruck, Austria, 2005.
29. W. Liu, B. Schmidt: "A Tunable Coarse-Grained Parallel Algorithm for Irregular Dynamic Programming Applications", 11th Annual International Conference on High Performance Computing (HiPC 2004), Bangalore, India, Springer, LNCS Vol. 3296, 2004.
30. C.X. Chen, B. Schmidt: "Load Balancing for Hierarchical Grid Computing: A Case Study", 11th Annual International Conference on High Performance Computing (HiPC 2004), Bangalore, Springer, LNCS Vol. 3296, 2004.
31. W. Liu, B. Schmidt: "A Generic Parallel Pattern-based System for Bioinformatics", Euro-Par 2004, Pisa, Italy, Springer, LNCS Vol. 3149, 2004
32. C.S.S. Tan, B. Schmidt: "Combining message-passing and inter-process communication in SMP-hybrid cluster for efficient parallel medical image analysis", APPLICATIONS OF DIGITAL IMAGE PROCESSING XXVII, Denver, CO, Proceedings of SPIE Vol. #5558, 2004
33. T. Oliver, B. Schmidt: "High Performance Biosequence Database Scanning on Reconfigurable Platforms", 3rd IEEE International Workshop on High Performance Computational Biology (HiCOMB 2004), Santa Fe, NM, IEEE Press, 2004
34. T. Liu, B. Schmidt: "Parallel RNA Sequence-Structure Alignment", 3rd IEEE International Workshop on High Performance Computational Biology (HiCOMB 2004), Santa Fe, NM, IEEE, 2004
35. C.X. Chen, B. Schmidt: "Performance Analysis of Computational Biology Applications on Hierarchical Grid Systems", 4th IEEE/ACM International Symposium on Cluster Computing and the Grid (CCGrid 2004), Chicago, IL, IEEE, 2004.
36. C.X. Chen, B. Schmidt: "Computing Large-Scale Alignments on a Multi-Cluster", IEEE International Conference on Cluster Computing (Cluster 2003), Hong Kong, 2003.
37. W. Liu, B. Schmidt: "Parallel Design Pattern for Computational Biology and Scientific Computing", IEEE International Conference on Cluster Computing (Cluster 2003), Hong Kong, 2003
38. M. Schimmler, B. Schmidt, S. Heithecker: "An Area-Efficient Bit-Serial Integer Multiplier", The 2003 International Conference on VLSI (VLSI'03), Las Vegas, NV, 2003
39. M. Schimmler, B. Schmidt, H.-W. Lang: "Design of a Bit-serial Floating-Point Unit for a Fine-Grained Parallel Processor Array", The 2003 International Conference on Parallel and Distributed Processing Techniques and Applications (PDPTA'03), Las Vegas, NV, 2003
40. B. Schmidt, F. Lin, A. Laud, Y. Santoso: "Parallel Detection of Regulatory Elements with gMP", 2nd IEEE International Workshop on High Performance Computational Biology (HiCOMB 2003), Nice, France, IEEE Press, 2003
41. L. Wang, W. Cai, B. Schmidt, B.S. Lee, W. Jie: "Biogrid Computing Platform: Parallel computing for protein alignment analysis", HPC Asia 2002, Bangalore, India, 2002
42. H. Schröder, B. Schmidt, J. Zhu: “A new approach to protein structure predictionâ€?, The International Conference on Bioinformatics (InCoB 2002), Bangkok, Thailand, 2002
43. B. Schmidt, M. Schimmler, W. Adi: "Area efficient modular arithmetic for mobile security", The 2002 International Conference on Wireless Networks (ICWN'02), Las Vegas, NV, 2002
44. B. Schmidt, H. Schroeder, M. Schimmler: "Massively Parallel Solutions for Molecular Sequence Analysis", IEEE International Workshop on High Performance Computational Biology (HiCOMB 2002), Ft Lauderdale, FL, IEEE Press, 2002
45. B. Schmidt, H. Schroeder: "Massively Parallel Sequence Analysis with Hidden Markov Models", International Conference on Scientific & Engineering Computation (IC-SEC 2002), Singapore, World Scientific, 2002
46. L. Wang, W. Cai, B. Schmidt, B.S. Lee, W. Jie: "Replica Selection Framework for Bio-Grid Computing", International Conference on Scientific & Engineering Computation (IC-SEC 2002), Singapore, World Scientific, 2002
47. H. Schroeder, B. Schmidt: "Image Processing Algorithms for on-board Computing", 3rd International Conference on Information, Communications & Signal Processing (ICICS'01), Singapore, 2001
48. L.S. Chin, H. Schroeder, B. Schmidt: "Parallel Volume Rendering using Slice Orientation", 3rd International Conference on Information, Communications & Signal Processing (ICICS'01), Singapore 2001
49. B. Schmidt, H. Schroeder, M. Schimmler: "Protein Sequence Comparison on the Instruction Systolic Array", 6th International Conference on Parallel Computing Technologies (PaCT'01), Novosibirsk, Russia, Springer-Verlag LNCS Vol. 2127, 2001
50. B. Schmidt, H. Schroeder, M. Schimmler: "Scanning Biosequence Databases on a Hybrid Parallel Architecture", Euro-Par 2001, Manchester, UK, Springer LNCS Vol. 2150, 2001.
51. B. Schmidt, H. Schroeder, T. Srikanthan: "A SIMD Solution to Biosequence Database Scanning", Parallel Computing 2001 (ParCo 2001), Naples, Italy, Imperial College Press, 2001.
52. L.S. Chin, B. Schmidt, H. Schroeder: "Volume Rendering Using the Instruction Systolic Array Concept", Asia-Pacific Conference on Computational Mechanics, Sydney, Australia, 2001
53. B. Schmidt: "Design of a Parallel Accelerator for Volume Rendering", Euro-Par 2000, Munich, Germany, Springer LNCS Vol. 1900, pp. 1095-1104, 2000.
54. B. Schmidt, H. Schroeder: "Volume Visualisation on a Hybrid Parallel Architecture", 7th Australasian Conference on Parallel and Real-Time Systems (PART 2000), Sydney, Australia, Springer, 2000.
55. B. Schmidt, M. Schimmler: "A Parallel Accelerator Architecture for Multimedia Video Compression", Euro-Par 1999, Toulouse, France, Springer LNCS Vol. 1685, 1999.
56. B. Schmidt, M. Schimmler, H. Schroeder: "Long Operand Arithmetic on Instruction Systolic Computer Architectures and its Application for RSA Cryptography", Euro-Par 1998, Southampton, UK, Springer-Verlag LNCS Vol. 1470, 1998
57. B. Schmidt, M. Schimmler, H. Schroeder: "The Instruction Systolic Array in Tomographic Image Reconstruction Applications", 5th Annual Australasian Conference on Parallel and Real-time Systems (PART 1998), Adelaide, Australia, Springer, 1998
58. B. Schmidt, M. Schimmler, H. Schroeder: "Morphological Hough Transform on the Instruction Systolic Array", Euro-Par 1997, Passau, Germany, Springer LNCS Vol. 1300, 1997
59. U. Mahlmeister, B. Schmidt, G. Sommer: "Preattentive Colour Features by Steerable Filters", 17th DAGM Symposium Pattern Recognition (DAGM'95), Bielefeld, Germany, Springer, 1995

ACADEMIC QUALFICATIONS:

Ph.D. in Computer Science

• 1999, Loughborough University (UK), Thesis title: "Algorithm Design on the Instruction Systolic Array", Advisor: Prof. Dr. Heiko Schroeder

Diplom-Informatiker

• 1995, Major: Computer Science, Minor: Mathematics, University of Kiel (Germany) - Award for the "Best Degree in Computer Science in 1995", Thesis advisor: Prof. Dr. Gerald Sommer

ACADEMIC EXPERIENCE:

Nayang Technological University:

• 07/2008 - present: Associate Professor, School of Computer Engineering
• 05/2001 - 12/2006: Assistant Professor, School of Computer Engineering
• 01/2006 - 12/2006: Programme Director, M.Sc. in Bioinformatics
• 05/2003 - 05/2005: Deputy Director, BioMedical Engineering Research Center (BMERC)
• 09/1999 - 04-/2201: Research Fellow, School of Computer Engineering

University of Melbourne:

• 01/2008 - 06/2008: Senior Researcher, NICTA VRL

University of New South Wales:

• 01/2007 - 08/2007: Associate Professor, Computer Engineering and Information Technology (Asia Campus)

University of Karlsruhe (Karlsruhe Institute of Technology):

• 10/1998 - 03/1999: Research Associate, Institute of Applied Informatics and Formal Description Methods (AIFB) under the guidance of Prof. Hartmut Schmeck

RWTH Aachen:

• 09/1997 - 09/1998: Research Associate, Department of Computer Science under the guidance of Prof. Juraj Hromkovic

INDUSTRIAL EXPERIENCE:

• 01/1996 - 08/1997: Software Engineer, ISATEC Soft-und Hardware GmbH (Kiel, Germany), Parallelization of scientific computing applications on Systola1024 (image and signal processing, FFT, medical image reconstruction, cryptography, and multimedia video compression)

Professional Consultation

• Progeniq Pte Ltd, Singapore, "BLAST on FPGAs", "Speech Recognition on FPGAs", "Ray Tracing on SGI RASC RC100", "Development of biological sequence analysis applications on FPGAs"
• Matrixview Ltd, Singapore, Evaluation of computational platforms for real-time medical imaging compression
• Helixense Pte Ltd, Singapore Development of a software system for bioinformatics applications on PC clusters
• Siemens AG, Munich, Germany, Design of an embedded system for H.263 video compression

AWARDS AND HONORS:

• Award for the best degree in Computer Science at University of Kiel in 1995
• Nominated for the Excellence in Teaching Award for contributions in teaching at Nanyang Technological University in 2005
• Best Paper Award "Systems Category", Fraunhofer Institute (IGD in Darmstadt) in 2007, Paper title "GPU-ClustalW: Using Graphics Hardware to Accelerate Multiple Sequence Alignment"
• NVIDIA Professor Partnership Award, 2008-09

LIST OF PUBLICATIONS

Edited Books and Book Chapters

1. B. Schmidt, C. Chen, W. Liu, W. Mitchell: "PheGee@Home: A Grid-based Tool for Comprative Genomics", Handbook of Research on Compuational Grid Technologies for Life Science, Biomedicine and Healthcare, to appear
2. J. Rajapakse, B. Schmidt, G. Volkert, Proceedings of the 2nd IAPR Workshop on Pattern Recognition in Bioinformatics (PRIB 2007), Lecture Notes in Bioinformatics, Springer, LNCS Volume 4774, 2007 (ISBN: 978-3-540-75285-1)
3. B. Schmidt, W. Liu, C. Chen: "Hierarchical Grid Computing for High Performance Bioinformatics", in Grids for Bioinformatics and Computational Biology, Wiley & Sons Book Series on Bioinformatics, 2007 (ISBN: 978-0-471-78409-8)
4. B. Schmidt, H. Schroeder: "Special-Purpose Computing for Biological Sequence Analysis", in Parallel Computing in Bioinformatics and Computational Biology, Wiley Book Series on Parallel and Distributed Computing, John Wiley & Sons, New York, 2005 (ISBN: 0-471-71848-3)
5. F.K. Fuss, S. L. Chia, S.S. Venkatraman, S.M. Krishnan, B. Schmidt, Proceedings of the International BioEngineering Conference 2004 (IBEC 2004), Singapore 2004 (ISBN: 981-05-1946-X)
6. B. Schmidt, M. Schimmler, H. Schroeder: "High-Speed Cryptography", in: Embedded Cryptographic Hardware: Methodologies & Architectures, Nova Science Publishers, 2004 (ISBN: 1-59454-012-8)

Journals

1. A. Wirawan, B. Schmidt, H. Zhang, C.K. Kwoh: "High Performance Protein Sequence Database Scanning on the Cell B.E. Processor", Scientific Programming, accepted for publication
2. A. Wirawan, C.K. Kwoh, T.H. Nim, B. Schmidt: "CBESW: Sequence Alignment on the Playstation 3" BMC Bioinformatics, Vol. 9:377, 2008 (Impact factor: 3.493)
3. T. Oliver, Y.Y. Leow, B. Schmidt: "Intgrating FPGA Acceleration into HMMer", Parallel Computing, Vol. 34, No. 11, pp.681-691, 2008 (Impact factor: 0.825)
4. W. Liu, B. Schmidt, G. Voss, W. Mueller-Wittig: "Accelerating Molecular Dynamics simulations using Graphics Processing Units with CUDA", Computer Physics Communications, Vol. 179, No. 9, pp. 634-641, 2008 (Impact factor: 1.842)
5. D.T. Singh, R.Trehan, B. Schmidt, T. Bretschneider: "Comparative Phyloinformatics of Virus Genes at Micro and Macro Levels in a Distributed Computing Environments", BMC Bioinformatics, Vol. 9:S23, 2008 (Impact factor: 3.493)
6. A. Singh, C. Chen, W. Liu, W. Mitchell, B. Schmidt: "A Hybrid Computational Grid Architecture for Comparative Genomics", IEEE Transactions on Information Technology in Biomedicine, Vol. 12, No. 2, pp. 218-225, March 2008 (Impact factor: 1.436)
7. T. Oliver, B. Schmidt, Y. Jacop, D. Maskell: "High-Speed Biological Sequence Analysis with Hidden Markov Models on Reconfigurable Platforms", IEEE Transactions on Information Technology in Biomedicine, in press, doi:10.1109/TITB.2007.904632 (Impact factor: 1.436)
8. M. Rajapakse, B. Schmidt, F. Lin, V. Brusic: "Predicting peptides binding to MHC class II molecules using multi-objective evolutionary algorithms", BMC Bioinformatics, 2007, 8:459 (Impact factor: 3.493)
9. W. Liu, B. Schmidt, G. Voss, W. Mueller-Wittig, "Streaming Algorithms for Biological Sequence Alignment on GPUs", IEEE Transactions on Parallel and Distributed Systems, Vol. 18, No. 9, pp. 1270-1281, 2007 (Impact factor: 1.146)
10. F. Lin,, H. Schroeder, B. Schmidt: "Solving the Bottleneck Problem in Bioinformatics Computing: an Architectural Perspective", Journal of VLSI Signal Processing Systems, Springer, Vol. 48, No. 3, pp185-188, 2007 (Impact factor: 0.449)
11. W. Liu, B. Schmidt, W. Mueller-Wittig: "Performance Analysis of General-Purpose Computation on Commodity Graphics Hardware: A Case Study Using Bioinformatics", Journal of VLSI Signal Processing Systems, Springer, Vol. 48, No. 3, pp. 209-221, 2007 (Impact factor: 0.449)
12. J.P. Walters, X. Meng, V. Chaudhary T. Oliver, Y.Y Leow, B. Schmidt, D. Nathan J. Landman: "MPI-HMMER-Boost: Distributed FPGA Acceleration", Journal of VLSI Signal Processing Systems, Springer, Vol. 48, No. 3, pp. 223-238, 2007 (Impact factor: 0.449)
13. B. Schmidt: "A Survey of Desktop Grid Applications for E-Science", International Journal of Web and Grid Services, Vol. 3. No. 3, pp. 354-368, 2007 (Impact factor: -)
14. M. Schimmler, B. Schmidt, H.-W. Lang, S. Heithecker: "An Area-Efficient Bit-Serial Integer and GF(2n) Multiplier", Microelectronic Engineering, Vol. 82, No. 2, pp. 253-259, February 2007. (Impact factor: 1.503)
15. M. Rajapakse, G.L. Zhang, K.N. Srinivasan, B. Schmidt, N. Petrovsky, V. Brusic: "PREDNOD, a prediction server for peptide binding to the H-2g7 haplotype of the nonobese diabetic mouse", Autoimmunity, Vol. 39 No. 8, pp. 645-650, December 2006 (Impact factor: 2.887)
16. C. Chen, B. Schmidt: "Constructing Large Suffix Trees on a Computational Grid", Journal of Parallel and Distributed Computing, Vol. 66, No. 12, pp.1512-1523, December 2006 (Impact factor: 0.574)
17. W. Liu, B. Schmidt: "A Parallel Pattern-based System for High Performance Computational Biology", IEEE Transactions on Parallel and Distributed Systems, Vol. 17, No. 8, pp. 750-763, August 2006 (Impact factor: 1.146)
18. T. Oliver, B. Schmidt, D. Maskell, D. Nathan, R. Clemens: "High-speed multiple sequence alignment on a reconfigurable platform", International Journal of Bioinformatics Research and Applications, Vol. 2, No. 4, pp. 394-406, 2006 (Impact factor: -)
19. Z. Du, F. Lin, B. Schmidt: "Accomplishments and Challenges in High Performance Computing for Computational Biology", Current Bioinformatics, Vol. 1, No. 2, pp. 185-195, May 2006 (Impact factor: 1.226)
20. W. Liu, B. Schmidt: "Mapping of Hierarchical Parallel Genetic Algorithms for Protein Folding onto Computational Grids", IEICE Transactions on Information and Systems, E89-D(2):589-596, February 2006 (Impact factor: 0.245)
21. T. Oliver, B. Schmidt, D. Nathan, R. Clemens, D. Maskell: "Using reconfigurable hardware to accelerate multiple sequence alignment with ClustalW", Bioinformatics, Vol. 21, No. 16, pp. 3431-3432, 2005. (Impact factor: 5.039)
22. T. Oliver, B. Schmidt, D. Maskell: "Reconfigurable Architectures for Bio-sequence Database Scanning on FPGAs", IEEE Transactions on Circuits and Systems II, Vol. 52, No. 12, pp. 851-855, 2005 (Impact factor: 1.104)
23. C. Chen, B. Schmidt: "An Adaptive Grid Implementation of DNA Sequence Alignment", Future Generation Computer Systems, Vol. 21, No. 7, pp. 988-1003, 2005 (Impact factor: 1.095)
24. T. Liu, B. Schmidt: "Parallel RNA Secondary Structure Prediction using Stochastic Context-Free Grammars", Concurrency and Computation: Practice and Experience, Vol. 17, No. 14, pp. 1669-85, 2005 (Impact factor: 1.154)
25. B. Schmidt, M. Schimmler: "A Bit-Serial Floating-Point Unit for a massively parallel system on a chip", Journal of Parallel Algorithms and Architectures, Vol. 19, No. 2-3, pp. 79-96, 2004 (Impact factor: -)
26. B. Schmidt, M. Schimmler, H. Schroeder: "A massively parallel architecture for public-key cryptography", International Journal of Computer Research, accepted for publication in 2004. (Impact factor: -)
27. B. Schmidt, F. Lin, A. Laud, Y. Santoso: "Development of Distributed Bioinformatics Applications with GMP", Concurrency and Computation: Practice and Experience, Vol. 16, pp. 945-959, 2004 (Impact factor: 1.154)
28. B. Schmidt, H. Schroeder, M. Schimmler: "A hybrid architecture for bioinformatics", Future Generation Computer Systems, No. 18, pp. 855-862, 2002 (Impact factor: 1.095)
29. B. Schmidt, H. Schroeder: "A hybrid Architecture for Multimedia Processors", Computing and Informatics, Vol. 20, No. 9, pp. 225-244, 2001. (Impact factor: 0.349)
30. B. Schmidt, M. Schimmler, H. Schroeder: "Tomographic Image Reconstruction on the Instruction Systolic Array", Computing and Informatics, Vol. 20, No. 1, pp. 27-42, 2001. (Impact factor: 0.349)
31. B. Schmidt, M. Schimmler: "KPROC - An Instruction Systolic Architecture for Parallel Prefix Applications", Parallel and Distributed Computing Practices, Vol. 3, No. 2, 2000. (Impact factor: -)
32. B. Schmidt, H. Schroeder, M. Schimmler: "A Morphological Approach to Hough Transform on the Instruction Systolic Array", Computers and Artificial Intelligence, Vol. 18, No. 6, pp. 541-557, 1999. (Impact factor: 0.349)

Conferences

1. C. Chen, B. Schmidt, W. Liu, W. Mueller-Wittig: "GPU-MEME: Using Graphics Hardware to Accelerate Motif Finding in DNA Seqeunces", PRIB 2008, Springer, Lecture Notes in Bioinformatics, Vol. 5265, pp.448-459, 2008.
2. H. Zhang, B. Schmidt, W. Mueller-Wittig: "Accelerating BLASTP on the Cell Broadband Engines", PRIB 2008, Springer, Lecture Notes in Bioinformatics, Vol. 5265, pp. 460-470, 2008.
3. N.T. Hieu, C.K. Kwoh. A. Wirawan, B. Schmidt: "Applications of Heterogeneous Structure of Cell Broadband Engine Architecture for Biological Database Similarity Search", 2nd International Conference on Bioinformatics and Biomedical Engineering (iCBBE2008), IEEE Press, pp. 5-8 (2008)
4. W. Liu, B. Schmidt, G.Voss, W. Mueller-Wittig: "Molecular Dynamics Simulations on Commodity GPUs With CUDA" 14th IEEE International Conference on High Performance Computing (HiPC 2007), Goa, India, Springer, LNCS, Vol. 4873
5. M.Y.H. Low, W. Liu, B. Schmidt, "A Parallel BSP Algorithm for Irregular Dynamic Programming", 7th International Symposium on Advanced Parallel Processing Technologies (APPT 2007), Springer, LNCS Vol. 4847, pp. 151-160, 2007
6. A. Wirawan, B. Schmidt, C.K. Kwoh: "Parallel DNA Sequence Alignment on the Cell Broadband Engine",7th International Conference on Parallel Processing and Applied Mathematics (PPAM 2007), Gdansk, Poland, Springer, LNCS Vol. 4967, pp. 1249-1256, 2008
7. L.A. Aung, D. Maskell, T. Oliver, B. Schmidt: "C-based Design Methodology for FPGA Implementation of ClustalW MSA", Pattern Recognition in Bioinformatics (PRIB 2007), Springer LNCS Vol. 4774, pp. 11-18, 2007
8. R. Trehan, D.T. Singh, B. Schmidt: "Phylogenetic Analysis of Neuraminidase Genes of H5N1 Isolates using HPC technologies", 9th International Conference on e-Health Networking, Application and Services (IEEE Healthcom 2007), IEEE Press, pp. 285-288, 2007
9. C. Chen, A. Singh, W. Mitchell, B. Schmidt: "Phenotype Genotype Exploration on a Desktop GPU Grid", 3rd International Workshop on Grid Computing and Applications, World Scientific, pp.154-165, 2007
10. W. Liu, W. Mueller-Wittig, B. Schmidt: "Performance Predictions for General-Purpose Computation on GPUs", International Conference on Parallel Processing (ICPP 2007), XiAn, China, IEEE Press, 2007
11. T. Oliver, Y.Y. Leow, B. Schmidt: "High Performance Database Searching with HMMer on FPGAs", 6th IEEE International Workshop on High Performance Computational Biology (HiCOMB 2007), Long Beach, CA, IEEE Press, 2007.
12. J. Feng, S. Chakraborty, B. Schmidt, W. Liu, U.D. Bordoloi: "Fast Schedulability Analysis Using Commodity Graphics Hardware", 13th IEEE International Conference on Embedded and Real-Time Computing Systems and Applications (RTCSA 2007), IEEE Press, pp.400-408, 2007
13. W. Liu, B. Schmidt, G. Voss, W. Mueller-Wittig: "GPU-ClustalW: Using Graphics Hardware to Accelerate Multiple Sequence Alignment", 13th IEEE International Conference on High Performance Computing (HiPC 2006), Bangalore, India, Springer, LNCS Vol. 4297, pp. 363-374, 2006.
14. A. Wirawan, B. Schmidt: "Parallel Discovery of Transcription Factor Binding Sites", IEEE Asia Pacific Conference on Circuits and Systems (APCCAS 2006), Singapore, IEEE Press, 2006
15. T. Oliver, B. Schmidt, J. Yanto, D. Maskell: "Accelerating the Viterbi Algorithm for Profile Hidden Markov Models using Reconfigurable Hardware", International Conference on Computational Science (ICCS 2006), Reading, UK, Springer-Verlag, LNCS Vol. 3991, Part I, pp. 522-529, 2006
16. M. Rajapakse, B. Schmidt, V. Brusic: "Multi-Objective Evolutionary Algorithm for Discovering Peptide Binding Motifs", 4th European Workshop on Evolutionary Computation and Machine Learning in Bioinformatics (EvoBIO 2006), Budapest, Hungary, Springer, LNCS Vol. 3907, pp. 149-158, 2006
17. W. Liu, B. Schmidt, G. Voss, A. Schroeder, W. Mueller-Wittig: "Bio-Sequence Database Scanning on a GPU", 5th IEEE International Workshop on High Performance Computational Biology (HiCOMB 2006), Rhode Island, Greece, IEEE Press, 2006
18. M. Rajapakse, B. Schmidt, V. Brusic: "Pareto-Optimal Motif for Predicting Peptide Binders", 16th International Conference on Genomic Informatics (GIW 2005), Yokohama, Japan, 2005
19. G. Voss, A. Schröder, W. Müller-Wittig, B. Schmidt: "Using Graphics Hardware to Accelerate Biological Sequence Analysis", IEEE Tencon 2005, Melbourne, Australia, 2005
20. W. Liu, B. Schmidt: "Mapping of Hierarchical Parallel Genetic Algorithms for Protein Folding onto Computational Grids", IEEE Tencon 2005, Melbourne, Australia, 2005.
21. J. Yanto, T. Oliver, B. Schmidt, D. Maskell: "Biological Sequence Analysis with Hidden Markov Models on an FPGA", 10th Asia-Pacific Computer Systems Architecture Conference (ACSAC 2005), Singapore, Springer-Verlag LNCS Vol. 3740, 2005.
22. C. Chen, B. Schmidt: "Parallel Construction of Large Suffix Trees on a PC Cluster", Euro-Par 2005, Lisbon, Portugal, Springer-Verlag LNCS Vol. 3648, 2005.
23. M. Rajapakse, L. Wyse, B. Schmidt, V. Brusic: "Deriving Matrix of Peptide-MHC Interactions in Diabetic Mouse by Genetic Algorithm", 6th International Conference on Intelligent Data Engineering and Automated Learning (IDEAL 2005), Brisbane, Australia, LNCS, Springer, 2005
24. T. Oliver, B. Schmidt, D. Nathan, R. Clemens, D. Maskell: "Multiple Sequence Alignment on an FPGA", 11th International Conference on Parallel and Distributed Systems (ICPADS 2005), IEEE Computer Society Press, Fukuoka, Japan, 2005
25. T. Oliver, B. Schmidt, D. Maskell, A.P. Vinod: "A Reconfigurable Architecture for Scanning Biosequence Databases", 2005 IEEE International Symposiumon Circuits and Systems (ISCAS 2005), Kobe, Japan, IEEE Computer Society Press, 2005
26. W. Liu, B. Schmidt: "A Case Study on Pattern-based Systems for High Performance Computational Biology", 4th IEEE International Workshop on High Performance Computational Biology (HiCOMB 2005), Denver, CO, IEEE Press, 2005
27. T. Oliver, B. Schmidt, D. Maskell: "Hyper Customized Processors for Bio-Sequence Database Scanning on FPGAs", 13th ACM International Symposium on Field-Programmable Gate Arrays (FPGA 2005), Monterrey, CA, 2005.
28. T. Liu, B. Schmidt: "Optimal local alignment in RNA secondary structures", BioMED 2005, Innsbruck, Austria, 2005.
29. W. Liu, B. Schmidt: "A Tunable Coarse-Grained Parallel Algorithm for Irregular Dynamic Programming Applications", 11th Annual International Conference on High Performance Computing (HiPC 2004), Bangalore, India, Springer, LNCS Vol. 3296, 2004.
30. C.X. Chen, B. Schmidt: "Load Balancing for Hierarchical Grid Computing: A Case Study", 11th Annual International Conference on High Performance Computing (HiPC 2004), Bangalore, Springer, LNCS Vol. 3296, 2004.
31. W. Liu, B. Schmidt: "A Generic Parallel Pattern-based System for Bioinformatics", Euro-Par 2004, Pisa, Italy, Springer, LNCS Vol. 3149, 2004
32. C.S.S. Tan, B. Schmidt: "Combining message-passing and inter-process communication in SMP-hybrid cluster for efficient parallel medical image analysis", APPLICATIONS OF DIGITAL IMAGE PROCESSING XXVII, Denver, CO, Proceedings of SPIE Vol. #5558, 2004
33. T. Oliver, B. Schmidt: "High Performance Biosequence Database Scanning on Reconfigurable Platforms", 3rd IEEE International Workshop on High Performance Computational Biology (HiCOMB 2004), Santa Fe, NM, IEEE Press, 2004
34. T. Liu, B. Schmidt: "Parallel RNA Sequence-Structure Alignment", 3rd IEEE International Workshop on High Performance Computational Biology (HiCOMB 2004), Santa Fe, NM, IEEE, 2004
35. C.X. Chen, B. Schmidt: "Performance Analysis of Computational Biology Applications on Hierarchical Grid Systems", 4th IEEE/ACM International Symposium on Cluster Computing and the Grid (CCGrid 2004), Chicago, IL, IEEE, 2004.
36. C.X. Chen, B. Schmidt: "Computing Large-Scale Alignments on a Multi-Cluster", IEEE International Conference on Cluster Computing (Cluster 2003), Hong Kong, 2003.
37. W. Liu, B. Schmidt: "Parallel Design Pattern for Computational Biology and Scientific Computing", IEEE International Conference on Cluster Computing (Cluster 2003), Hong Kong, 2003
38. M. Schimmler, B. Schmidt, S. Heithecker: "An Area-Efficient Bit-Serial Integer Multiplier", The 2003 International Conference on VLSI (VLSI'03), Las Vegas, NV, 2003
39. M. Schimmler, B. Schmidt, H.-W. Lang: "Design of a Bit-serial Floating-Point Unit for a Fine-Grained Parallel Processor Array", The 2003 International Conference on Parallel and Distributed Processing Techniques and Applications (PDPTA'03), Las Vegas, NV, 2003
40. B. Schmidt, F. Lin, A. Laud, Y. Santoso: "Parallel Detection of Regulatory Elements with gMP", 2nd IEEE International Workshop on High Performance Computational Biology (HiCOMB 2003), Nice, France, IEEE Press, 2003
41. L. Wang, W. Cai, B. Schmidt, B.S. Lee, W. Jie: "Biogrid Computing Platform: Parallel computing for protein alignment analysis", HPC Asia 2002, Bangalore, India, 2002
42. H. Schröder, B. Schmidt, J. Zhu: "A new approach to protein structure prediction", The International Conference on Bioinformatics (InCoB 2002), Bangkok, Thailand, 2002
43. B. Schmidt, M. Schimmler, W. Adi: "Area efficient modular arithmetic for mobile security", The 2002 International Conference on Wireless Networks (ICWN'02), Las Vegas, NV, 2002
44. B. Schmidt, H. Schroeder, M. Schimmler: "Massively Parallel Solutions for Molecular Sequence Analysis", IEEE International Workshop on High Performance Computational Biology (HiCOMB 2002), Ft Lauderdale, FL, IEEE Press, 2002
45. B. Schmidt, H. Schroeder: "Massively Parallel Sequence Analysis with Hidden Markov Models", International Conference on Scientific & Engineering Computation (IC-SEC 2002), Singapore, World Scientific, 2002
46. L. Wang, W. Cai, B. Schmidt, B.S. Lee, W. Jie: "Replica Selection Framework for Bio-Grid Computing", International Conference on Scientific & Engineering Computation (IC-SEC 2002), Singapore, World Scientific, 2002
47. H. Schroeder, B. Schmidt: "Image Processing Algorithms for on-board Computing", 3rd International Conference on Information, Communications & Signal Processing (ICICS'01), Singapore, 2001
48. L.S. Chin, H. Schroeder, B. Schmidt: "Parallel Volume Rendering using Slice Orientation", 3rd International Conference on Information, Communications & Signal Processing (ICICS'01), Singapore 2001
49. B. Schmidt, H. Schroeder, M. Schimmler: "Protein Sequence Comparison on the Instruction Systolic Array", 6th International Conference on Parallel Computing Technologies (PaCT'01), Novosibirsk, Russia, Springer-Verlag LNCS Vol. 2127, 2001
50. B. Schmidt, H. Schroeder, M. Schimmler: "Scanning Biosequence Databases on a Hybrid Parallel Architecture", Euro-Par 2001, Manchester, UK, Springer LNCS Vol. 2150, 2001.
51. B. Schmidt, H. Schroeder, T. Srikanthan: "A SIMD Solution to Biosequence Database Scanning", Parallel Computing 2001 (ParCo 2001), Naples, Italy, Imperial College Press, 2001.
52. L.S. Chin, B. Schmidt, H. Schroeder: "Volume Rendering Using the Instruction Systolic Array Concept", Asia-Pacific Conference on Computational Mechanics, Sydney, Australia, 2001
53. B. Schmidt: "Design of a Parallel Accelerator for Volume Rendering", Euro-Par 2000, Munich, Germany, Springer LNCS Vol. 1900, pp. 1095-1104, 2000.
54. B. Schmidt, H. Schroeder: "Volume Visualisation on a Hybrid Parallel Architecture", 7th Australasian Conference on Parallel and Real-Time Systems (PART 2000), Sydney, Australia, Springer, 2000.
55. B. Schmidt, M. Schimmler: "A Parallel Accelerator Architecture for Multimedia Video Compression", Euro-Par 1999, Toulouse, France, Springer LNCS Vol. 1685, 1999.
56. B. Schmidt, M. Schimmler, H. Schroeder: "Long Operand Arithmetic on Instruction Systolic Computer Architectures and its Application for RSA Cryptography", Euro-Par 1998, Southampton, UK, Springer-Verlag LNCS Vol. 1470, 1998
57. B. Schmidt, M. Schimmler, H. Schroeder: "The Instruction Systolic Array in Tomographic Image Reconstruction Applications", 5th Annual Australasian Conference on Parallel and Real-time Systems (PART 1998), Adelaide, Australia, Springer, 1998
58. B. Schmidt, M. Schimmler, H. Schroeder: "Morphological Hough Transform on the Instruction Systolic Array", Euro-Par 1997, Passau, Germany, Springer LNCS Vol. 1300, 1997
59. U. Mahlmeister, B. Schmidt, G. Sommer: "Preattentive Colour Features by Steerable Filters", 17th DAGM Symposium Pattern Recognition (DAGM'95), Bielefeld, Germany, Springer, 1995

RESEARCH GRANTS:

External Research Grants

• "NVIDIA Professor Partnership Award" for GPU-enabled Genomics, Source: NVIDIA Corporation, Amount and Period: US$25,000 (2008-09), Role: Principle Investigator
• "Dynamic Reconfigurable Computing: The next generation high performance computing platform for embedded applications", Source: MOE AcRF Tier 2 (Ministry of Education), Amount and Period: S$527,695 (2007-10), Role: Co-Principle Investigator
• "Development of a Grid System with Applications to Large-Scale Bio and Nanomaterial-systems, Source: A-Star (Agency for Science, Technology and Research), Amount and Period: S$297,145 (2005-08), Role: Principle Investigator
• "Hybrid Computing", Source: ISAVISION GmbH, Amount and Period: S$200,000 (2000-2003), Role: Principle Investigator

University Research Grants:

• "Algorithms and Architectures for Emerging High Performance Computing Applications", Type: Group Seed Funding Scheme Award (UNSW), Amount: S$80,000 (2007-08), Role: Joint Principle Investigator (together with Oliver Diessel)
• " Using a PlayStation3 Cluster for Biological Sequence Analysis", Type: Small Research Grant Award (UNSW), Amount: S$9,000 (2007-08), Role: Principle Investigator
• "GPGPU Grid", Type: Equipment Grant, NTU Office of Research (2005-06), Amount: S$16,000, Role: Principle Investigator
• "Ph.D. scholarships", Type: Research Student Scholarship, NTU, Amount and Period: approx. S$100,000 (2005-10), Role: Supervisor
• "DNA Chip Design Program", Type: ER-Lab Research Program Grant, NTU, Amount and Period: S$40,000 (2005-07), Role: Co-Principle Investigator

PROFESSIONAL SERVICE

Professional Associations

• Senior Member, IEEE and IEEE Computer Society

Editorial Service

• B. Schmidt, D.A. Bader, S. Aluru, Editors, Proceedings of the Seventh IEEE International Workshop on High Performance Computational Biology (HiCOMB 2008), IEEE Computer Society Press, Miami, FL, April 2008
• Guest Editor, The Journal of VLSI Signal Processing Systems (Springer), Special Issue on Computing Architectures and Acceleration for Bioinformatics Algorithms, Vol. 48, No. 3, 2007
• Guest Editor, International Journal of Web and Grid Services, Special Issue on Selected paper from CCGrid Workshop on Grid Testbeds, Vol. 3, No. 3, 2007
• J. Rajapakse, B. Schmidt, G. Volkert, Proceedings of the 2nd IAPR Workshop on Pattern Recognition in Bioinformatics (PRIB 2007), Lecture Notes in Bioinformatics, Springer, LNCS Volume 4774

Organizing Committees

• Workshop Chair, "Using Emerging Parallel Architectures for Computational Science", held at the International Conference on Computational Science 2009 (ICCS 2009), Baton Rouge, Louisiana
• Workshop Co-Chair, 2008 BIRC Workshop on Protein Structure and Function Prediction, Oct, 25th, 2008, Singapore
• Program Chair, 7th IEEE International Workshop on High Performance Computational Biology (HiCOMB 2008), Miami, FL
• Program Co-Chair, 2nd IAPR Workshop on Pattern Recognition in Bioinformatics (PRIB 2007), Singapore
• Technical Co-Chair, 3rd IAPR Workshop on Pattern Recognition in Bioinformatics (PRIB 2008), Melbourne, Australia
• Scientific Organizing Committee, World Wide Work Flow Grid Workshop (W4G 2007), Singapore, 5-7 June 2007
• Workshop Organizer, International Workshop on Grid Testbeds, held in conjunction with ACM/IEEE CCGrid 2006, Singapore, May, 16-19, 2006
• Track Chair, IEEE International Conference in Biomedical and Pharmaceutical Engineering 2006 (ICBPE2006), Singapore, December 11-14, 2006
• Workshops Chair, 6th ACM/IEEE Symposium on Cluster Computing and the Grid (CCGrid 2006), Singapore, May 16-19, 2006.
• Program Vice-Chair, 7th NTU-SGH Symposium, Singapore, August 11-12, 2005
• Cyberchair, 11th Annual International Conference on High Performance Computing (HiPC 2004), Bangalore, India, December 19-22, 2004
• Publicity Chair, The 2004 IEEE International Conference on Cluster Computing (Cluster 2004), San Diego, CA, September 20-23, 2004
• Exhibits/Sponsorship Chair, 1st International BioEngineering Conference 2004 (IBEC 2004), Singapore, September 8-10, 2004.
• Topic Vice-Chair, Euro-Par 2003, Klagenfurt, Austria, August 26-29, 2003

Program Committee Memberships

• 3rd Workshop on Parallel Computational Biology (PBC 2009), Wroclaw, Poland, September 13-16, 2009.
• 2009 IEEE Congress on Evolutionary Computation (IEEE CEC 2009) - Special Session on "Evolutionary Computation in Bioinformatics and Computational Biology", Trondheim, Norway
• 8th IEEE International Workshop on High Performance Computational Biology (HiCOMB 2009), Rome, Italy
• 6th ACS/IEEE International Conference on Computer Systems and Applications (AICCSA 2008), Doha, Qatar, March 31 - April 4, 2008
• 14th Annual International Conference on High Performance Computing (HiPC 2007), Goa, India, December 18-21, 2007
• 10th International Conference on e-Health Networking, Applications and Services (IEEE Healthcom 2008), Singapore, July, 7-9, 2008
• 9th International Conference on e-Health Networking, Applications and Services (IEEE Healthcom 2007), Taipei, Taiwan, June, 19-22 2007
• 21st IEEE International Parallel & Distributed Processing Symposium (IPDPS 2007), Long Beach, California, March 26-30, 2007
• 2007 IEEE International Symposium on Bioinformatics and Life Science Computing (BLSC07), Niagara Fall, Ontario, Canada
• Parallel Bio-Computing (PBC 2007) Workshop, Gdansk, Poland, September 9-12, 2007
• 2006 Workshop on Pattern Recognition in Bioinformatics (PRIB 2006), Hong Kong, 20-24 August, 2006
• IEEE Workshop on Biomedical Computations on the Grid (BioGrid 2007), jointly held with IEEE/ACM Symposium on Cluster Computing and the Grid (CCGrid 07), Rio de Janero, Brazil, May 14-17, 2007
• IEEE Workshop on Biomedical Computations on the Grid (BioGrid 2006), jointly held with IEEE/ACM Symposium on Cluster Computing and the Grid (CCGrid 06), Singapore, May 16-19, 2006
• IEEE Workshop on High-Performance Computing in Medicine and Biology (HiPCoMB 2006), April 18-20, 2006, Vienna, Austria, held in conjunction with 20th International Conference on Advanced Information Networking and Applications (AINA 2006)
• IEEE Workshop on High-Performance Computing in Medicine and Biology (HiPCoMB 2005), July 20-22, 2005, Fukuoka, Japan, held in conjunction with 11th International Conference on Parallel and Distributed Systems (ICPADS 2005)
• 4th IASTED International Conference on Biomedical Engineering (BioMED 2006), Innsbruck, Austria, February 15-17, 2006,
• 5th IASTED International Conference on Biomedical Engineering (BioMED 2007), Innsbruck, Austria, February, 14-16, 2007,
• 6th IASTED International Conference on Biomedical Engineering (BioMED 2008), Innsbruck, Austria, February, 14-16, 2008
• 1st IEEE International Conference on e-Science and Grid Computing (E-Science 2005) December 5-8, 2005, Melbourne, Australia
• 2nd IEEE International Conference on e-Science and Grid Computing (E-Science 2006) , December 4-6, 2006, Amsterdam, Netherland

Journal Reviewing

• IEEE Transactions on Information Technology in Biomedicine
• IEEE Transactions on Computers
• IEEE Transactions on Nanobiosciences
• IEEE Transactions on Circuits and Systems II
• IEEE/ACM Transactions on Computational Biology and Bioinformatics
• IEEE Computer Magazine
• IEEE Transactions on Parallel and Distributed Computing
• Journal of Computational Biology
• Bioinformatics
• Parallel Computing
• Journal of Parallel and Distributed Computing
• Computer Physics Communications
• Comparative and Functional Genomics
• Virus Genes
• Pattern Recognition Letters
• Journal of Real-Time Imaging

Lecturer and Course Coordinator

• "Discrete Mathematics" (XMTH1040 at UNSW, SC109, B.Eng. in Computer Engineering at NTU

1. Spring 2007, Class size = 12
2. Spring 2004, Class size = 485
3. Spring 2003, Class size = 551
4. Spring 2002, Class size = 537

• "Algorithms for Bioinformatics" (BI6106, M.Sc. in Bioinformatics)

1. Fall 2008, Class Size = 30
2. Fall 2006, Class Size = 40
3. Fall 2005, Class size = 36
4. Fall 2004, Class size = 35
5. Fall 2003, Class size = 57

• "High Performance Computing for Bioinformatics" (BI6121, M.Sc. in Bioinformatics)

1. Spring 2006, Class size = 16
2. Spring 2005, Class size = 12

Publications on Learning and Teaching Methods

Tutor

• Digital Circuits and Systems (CPE 201): Fall 2008
• Logic Design (SC102): Fall 2001, Fall 2002, Fall 2003, Fall 2004
• Mathematics I (SC104): Fall 2004
• Discrete Mathematics (SC109): Spring 2001, Spring 2002, Spring 2003, Spring 2004
• Algorithms (SC203): Fall 2001, Fall 2002, Fall 2003
• Discrete Mathematics and Algorithms (CPE204): Fall 2005
• Software Engineering (CPE207): Spring 2005, Fall 2006
• at University of Karlsruhe: Computer Networks (Winter 1998)
• at RWTH Aachen: Algorithms (Spring 1998), Introduction to Computer Science (Fall 1997)
• at University of Kiel: Computer Science for Engineers (Spring 1993)

Laboratories

• Digital Circuits and Systems (CPE201): Fall 2008
• Software Engineering (CPE207): Spring 2005, Spring 2006, Fall 2006
• at University of Kiel: Computer Vision (Spring 1995)

INDIVIDUAL GUIDANCE

Researchers (as members of my research team):

Graduated Ph.D. Students (as major advisor):

• Weiguo Liu, Dissertation: "Parallel and Distributed Algorithms for Computational Biology", External examiners: Prof. David Bader (Georgia Tech), Prof. Thomas Ludwig (University of Heidelberg) - Based on his strong results Liu Weiguo got awarded the prestigious Lee Kuan Yew Postdoctoral Fellowship (LKY PDF) for three years
• Chunxi Chen, Dissertation: "Computational Genomics on the Grid", External examiners: Prof Ming Li (University of Waterloo), Prof. Hans-Werner Lang (University of Applied Science Flensburg)

Current Ph.D. Students:

• Liu Yongchao
• Menaka Rajapakse, joint supervision with Vladimir Brusic (Harvard Medical School) and Lin Feng (NTU)
• Adrianto Wirawan, joint supervision with Kwoh Chee Keong (NTU)
• Chen Yupeng, joint supervision with Douglas Maskell (NTU)
• Francis Nai, joint supervision with P.K.Kolatkar (GIS)

TEACHING ACTVITIES

Lecturer and Course Coordinator

• "Discrete Mathematics" (XMTH1040 at UNSW, SC109, B.Eng. in Computer Engineering at NTU)

1. Spring 2007, Class size = 12
2. Spring 2004, Class size = 485
3. Spring 2003, Class size = 551
4. Spring 2002, Class size = 537

• "Algorithms for Bioinformatics" (BI6106, M.Sc. in Bioinformatics)

1. Fall 2008, Class Size = 30
2. Fall 2006, Class Size = 40
3. Fall 2005, Class size = 36
4. Fall 2004, Class size = 35
5. Fall 2003, Class size = 57

• "High Performance Computing for Bioinformatics" (BI6121, M.Sc. in Bioinformatics)

1. Spring 2006, Class size = 16
2. Spring 2005, Class size = 12

Tutorials

• Digital Circuits and Systems (CPE 201): Fall 2008
• Logic Design (SC102): Fall 2001, Fall 2002, Fall 2003, Fall 2004
• Mathematics I (SC104): Fall 2004
• Discrete Mathematics (SC109): Spring 2001, Spring 2002, Spring 2003, Spring 2004
• Algorithms (SC203): Fall 2001, Fall 2002, Fall 2003
• Discrete Mathematics and Algorithms (CPE204): Fall 2005
• Software Engineering (CPE207): Spring 2005, Fall 2006
• at University of Karlsruhe: Computer Networks (Winter 1998)
• at RWTH Aachen: Algorithms (Spring 1998), Introduction to Computer Science (Fall 1997)
• at University of Kiel: Computer Science for Engineers (Spring 1993)

Laboratories

• Digital Circuits and Systems (CPE 201): Fall 2008
• Software Engineering (CPE207): Spring 2005, Spring 2006, Fall 2006
• at University of Kiel: Computer Vision (Spring 1995)