Forschung

Research

Research Interests:

High-performance Computing in Bioinformatics
Resource Management in Dynamic and Distributed Real-Time Systems
Operating Systems

Publications:

Journal Articles / Book Chapters

J. Lichtenberg, K. Kurz, X. Liang, R. Al-ouran, L. Neiman, L. J Nau, J. D Welch, E. Jacox, T. Bitterman, K. Ecker, L. Elnitski, F. Drews, S. S. Lee, L. R. Welch, “Concurrent Bioinformatics Software For Discovering Genome-wide Patterns and Word Based Genomic Signatures”, BMC Bioinformatics , 11 (Suppl 12):S6doi:10.1186/1471-2105-11-S12-S6, 2010.

F. Drews, J. Lichtenberg, and L. Welch, "Scalable Parallel Word Search in Multicore/Multiprocessor Systems", Special Issue for the Journal of Supercomputing on “Scalability of Data Management Applications and Systems”, Springer DOI: 10.1007/s11227-009-0308-3, 2010.

J. Lichtenberg, A. Yilmaz, J. D. Welch, K. Kurz, X. Liang, F. Drews, K. Ecker, S. S. Lee, M. Geisler, E. Grotewold, L. R. Welch, “The Word Landscape of the Non-Coding Segments of the Arabidopsis thaliana Genome”, BMC Genomics, 10:463, 2009.

Jens Lichtenberg, Edwin Jacox, Josiah Seaman, Xiaoyu Liang, Mary Q Yang, Frank Drews, Stephen Lee, Klaus Ecker, Laura Elnitski, and Lonnie Welch, Word-based Characterization of Promoters involved in Human DNA-repair Pathways, BMC Genomics, Vol 10(Suppl1): S18, DOI: 10. 1186/1471-2164-10-S1-S18, 2009.

D. Gu, L. Welch, F. Drews, K. Ecker, Characterizing Robustness in Dynamic Real-Time Systems, Journal of Systems and Software, Volume 80, Issue 7, 1005-1014, 2007.

C. Cavanaugh, F. Drews, L. Welch, Dynamic Resource Management in Distributed Real-Time Systems (Editorial, Journal of Systems and Software, Volume 80, Issue 7, 933-937, 2007.

D. Juedes, F. Drews, D. Gu, L. Welch, K. Ecker and S. Schomann, “Approximation algorithm for periodic real-time tasks with workload-dependent running-time functions,” Journal of Real-time Systems, 34(3):173-194, November 2006.

F. Drews, K. Ecker, O. Kao and S. Schomann, Strategies for Workload Balancing in Cluster-Based Image Databases, In Parallel Processing Letters, World Scientific, Vol. 14, No. 1, pp. 33 - 43, March 2004

U. Rerrer, O. Kao, and F. Drews, Extending the Divisible Task Model for Workload Balancing in Clusters, in Parallel Computing: Software Technology, Algorithms, Architectures and Applications, G. Joubert, W. Nagel, F. Peters, W. Walter, Elsevier, ISBN 0444516891, 219 – 224, 2004.
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Conference Publications

M. Yuan, J. Baker, W. Meilander, Lev Neiman, F. Drews, “An Efficient Associative Processor Solution to an Air Traffic Control Problem”, accepted for publication in Proceedings of the 24th IEEE International Parallel and Distributed Processing Symposium (IPDPS 2010), 2010

M. Yuan, J. Baker, F. Drews, W. Meilander, “Efficient Implementation of Air Traffic Control Using the ClearSpeed CSX600 System”, in Proceedings of the 21st IASTED International Conference on Parallel and Distributed Computing and Systems (PDCS’09), 2009.

K. Kurz, L. Nau, F. Drews, and L. Welch, “An Open Source Framework for Bioinformatics Word Enumeration and Scoring”, In Proceedings of the Bioinformatics Open Source Conference (BOSC 2009), 2009.

L. Welch, J. Lichtenberg, F. Drews, “The WORDIFIER Pattern for Functional and Regulatory Genomics”, In Proceedings of the Bioinformatics Open Source Conference (BOSC 2009), 2009.

J. Lichtenberg, F. Drews, L. Elnitski, E. Grotewold, E. Jacox, K. Kurz, S. S. Lee, X. Liang, P. Morris, C. Nelson, E. Stockinger, J. D. Welch, S. Wyatt, A. Yilmaz, and L. R. Welch. “Identification of Regulatory Landscapes in Genomes: Strategies and Case Studies”, Proceedings of the Ohio Collaborative Conference on Bioinformatics (OCCBIO’09), IEEE Computer Society Press, 2009.

F. Drews, W. Leal, P. K. Srinivasan, Enabling Uniform CPU Allocation in the Presence of System Dynamics: Implementation and Experimental Evaluation, In Proceedings of the 2008 International Conference on Embedded Systems and Applications (ESA'08), Las Vegas, NV, 2008.

F. Drews, E. Petri, J. Lichtenberg, and L. Welch, Scalable Parallel Word Search in Multi-Core/Multiprocessor Systems , Proceedings of The 2008 International Conference on Bioinformatics and Computational Biology (BIOCOMP'08), Las Vegas, July, 2008.

K. Ecker, F. Drews, QoS-based Management of Multiple Shared Resource in Dynamic Real-Time Systems, In Proceedings of the 20th IEEE International Parallel & Distributed Processing Symposium, 2006.

F. Drews, K. Ecker, J. Lichtenberg, QoS-based Management of Multiple Shared Resources in Dynamic Real-Time Systems, in CIRM 2006 Symposium on Scheduling Algorithms for new Emerging Applications, 2006.

D. Gu, F. Drews, and L. Welch, “Robust Task Allocation for Dynamic Distributed Real-time Systems Subject to Multiple Environmental Parameters,” The 25th International Conference on Distributed Computing Systems, June 2005.

H. Zhao, D. Gu, L. Welch, F. Drews, Stable Allocations in Distributed Real-time Systems with Multiple Environmental Parameters and Replicable Applications," 13^th International Workshop on Parallel and Distributed Real-time Systems, April 2005.

R. Judd, F. Drews, D. Lawrence, D. Juedes, B. Leal, J. Deshpande, and L. Welch
QoS-based Resource Allocation in Dynamic Real-Time Systems, Proceedings of the 24th American Control Conference (ACC 2005), pp. 1745-1751, 2005.

Klaus Ecker, Andrej Chernyk, Frank Drews, Continuous Mode Changes in Real-Time Systems, In Proceedings of the 3-rd International Conference on Parallel Computing Systems, Colima, Mexico, September 19-22, 2004.

Eric Aber, Frank Drews, Dazhang Gu, David Juedes, Andrew Lenharth, David Parrott, Lonnie Welch, Hang Zhao, David Fleeman, “Experimental Comparison of Heuristic and Optimal Resource Allocation Algorithms for Maximizing Allowable Workload in Dynamic, Distributed Real-Time Systems,” WTR 2004 - 6th Brazilian Workshop on Real-Time Systems, May 2004.

David Juedes, Frank Drews, and Lonnie Welch, Workload Functions: A New Paradigm for Real-time Computing, In Proceedings of the 10th IEEE Real-Time and Embedded Technology and Applications Symposium RTAS2004, 2004.

A. Bruening, F. Drews, M. Hoefer, O. Kao, and U. Rerrer, Towards Quality of Service Based Resource Management for Cluster-Based Image Retrieval Systems, In Proceedings of the 2004 International Conference on Algorithmic Mathematics and Computer Science (AMCS'04), Las Vegas, 2004.

William Leal, Frank Drews, Chang Liu, Lonnie Welch, “Toward Model-Based Verification of Adaptive Allocation Managers,” Workshop on Model-based Development of Embedded Systems, May 2004.

F. Drews, L.Welch, D. Juedes, D. Fleeman, A. Bruening, K. Ecker and M. Hoefer, "Utility-Function based Resource Allocation for Adaptable Applications in Dynamic Distributed Real-Time Systems," 12^th International Workshop on Parallel and Distributed Real-time Systems, April 2004.

David Juedes, Frank Drews, Lonnie Welch, and David Fleeman, “Heuristic Resource Allocation Algorithms for Maximizing Allowable Workload in Dynamic, Distributed Real-Time Systems,” 12^th International Workshop on Parallel and Distributed Real-time Systems, April 2004.

D. Gu, F. Drews and L. Welch, “A Characterization of Task Allocation Problems for Distributed Real-time Systems,” Parallel and Distributed Computing and Systems (PDCS), July 2004.

U. Rerrer, O. Kao, and F. Drews, Extending the Divisible Task Model for Workload Balancing in Clusters, In Proceedings of Conference on Parallel Computing (ParCo 2003), published 2004.

D. Parrott, D. Fleeman, L. Welch, D. Chelberg, C. Bruggeman, F. Drews and Z. Tan, “Autonomous Satellite Systems Operating in Dynamic, Real-Time Environments.” International Conference of Artificial Intelligence, Las Vegas, Nevada, June 2003.

D. Chelberg, F. Drews, D. Fleeman, L. Welch, J. Marquart and B. Pfarr, “Obtaining the Greatest Scientific Benefit from Observational Platforms by Consideration of the Relative Benefit of Observations,” International Conference on Space Mission Challenges for Information Technology (SMC-IT), Pasadena, CA, July 2003.

K. Ecker, F. Drews, D. Juedes, L. Welch, D. Chelberg, D. Fleeman. and D. Parrott, “An Optimization Framework for Dynamic, Distributed Real-Time Systems,” in Proceedings of the 11th International Workshop on Parallel and Distributed Real-Time Systems, Nice, France, April 2003.

F. Drews and L. Welch, An Architecture and a General Optimization Framework for Resource Management in Dynamic, Distributed Real-Time Systems, IEEE International Workshop on Object-oriented Real-time Dependable Systems, Capri, Italy, Oct. 2003.

F. Drews, K. Ecker, O. Kao and U. Rerrer, Extending the Divisible Task Model for Load Balancing in Parallel and Distributed Systems, In Proceedings of The 2003 International Conference on Parallel and Distributed Processing Techniques and Applications (PDPTA 2003), CSREA Press, 2003, Vol. 1 pp. 493-497.

S. Schomann, F. Drews, and O. Kao, Evolutionary Algorithms for Scheduling in the Extended LogGP Model, in Proceedings of The 2003 International Conference on Parallel and Distributed Processing Techniques and Applications (PDPTA 2003), CSREA Press 2003, Vol. 1 pp. 286-292.

F. Drews, K. Ecker, O. Kao and S. Schomann, Simulated Annealing Strategy for Workload Balancing in Parallel Image Databases, Proceedings of the International Conference on Parallel and Distributed Processing Techniques and Applications (PDPTA), Special Session on Parallel and Distributed Retrieval of Multimedia Data, CSREA Publishing, pp. 734-740, 2002

F. Drews, Scheduling and Performance Prediction of I/O intensive Tasks in parallel Time-Sharing Systems, in Proceedings of the International Conference on Parallel and Distributed Processing Techniques and Applications (PDPTA 2001), CSREA Publishing, June 25-28 2001.

F. Drews, O. Kao, Randomized Block Size Scheduling Strategy for Cluster-Based Image Databases, Proceedings of the International Conference on Parallel and Distributed Processing Techniques and Applications (PDPTA 2001), CSREA Publishing, pp. 2116-2123, 2001.

O. Kao, G. Steinert, F. Drews, Scheduling Aspects for Image Retrieval in Cluster-Based Image Databases, Proceedings of the IEEE/ACM International Symposium on Cluster Computing and the Grid (CCGrid 2001), 2001, pp 329-336, IEEE Society Press.

Other Publications

F. Drews, K. Ecker, K. Kurz, S. S. Lee, X. Liang, J. Lichtenberg, J. Welch, L. Welch (2008) WordSeeker, “ A High Performance Bioinformatics Pipeline for Computational Regulatory Genomics”, OPBC, 2008.

J. Lichtenberg, E. Jacox, J. Welch, K. Kurz, M. Yang, K. Ecker, F. Drews, L. Elnitski, and L. Welch, Word-based characterization of promoters from human DNA-repair pathways, in Genome Informatics, 2008.

F. Drews, D. Juedes, L. Welch, and K. Ecker, An Approximation Algorithm for Periodic Real-Time Tasks with Workload-Dependant Running Times, In Dagstuhl Seminar Proceedings No. 04231, Schloss Dagstuhl, International Conference and Research Center for Computer Science, Germany, 2004

F. Drews, Incorporating Multitasking into a Static Scheduling Model, Schloss Dagstuhl, International Conference and Research Center for Computer Science,
Dagstuhl Seminar Report, 2002

Grants:

A Customized, Fully Automated Sequencing and Analysis Pipeline for the Illumina Sequencing Machine
Ohio Agricultural Research and Development Center
November 2010 – February 2011
$ 8,926.72

Role:	My role in this project is that of Principal Investigator (100%)



Description:	The Center for Scientific Computing (CSC) at Ohio University will design, develop, and deploy a customized, fully-automated sequencing and analysis pipeline for the Ilumina sequencing machine. The software will be deployed at the Ohio Agricultural Research and Development Center (OARDC)

Ohio Bioinformatics Consortium
Ohio Board of Regents
July 2008 - June 2013
$ 4,475,000.00

Role:	My role in this project is that of Co-Principal Investigator (25%) with Dr. Lonnie Welch as Principal Investigator and Dr. Sarah Wyatt as Co-Principal Investigator.



Description:	This proposal led by Ohio University and powered by the resources of the Ohio Supercomputer Center and the Ralph Regula School of Computational Science is aimed at positioning the state as a national leader in the emerging field of bioinformatics. The Ohio Consortium for Bioinformatics will receive $4.475 million from the Ohio Board of Regents for student scholarships.

Biomimetic Aerial Robotic Transformer
Air Force Research Laboratory Campus Challenge Competition
December 2007 – December 2008
$ 150,000.00

Role:	My role in this project is that of Co-Lead Investigator in Cybertronics (with Dr. Matolak; Dr. Jim Zhu is the Principal Investigator). My responsibility was the development of a concept for a Quality-of-Service-based on-board resource management architecture that enables the ART to operate autonomously in highly dynamic and unpredictable environments.



Description:	The Campus Challenge problem solving competition is an effort sponsored by the Air Force Research Laboratory’s Munitions Directorate. The purpose of the competition is to “solicit innovative, potentially paradigm-shifting ideas that have the potential, upon maturity, to successfully address specific real-world problems of interest to the Air Force research community”. The ultimate goal is to devise an “efficient, transformable, unmanned Aerial Robotic Transformer (ART) that is both air and ground mobile”. This competition is divided into four phases: Letters of Intent, White Papers, Proposal Submissions and Campus Challenge Winner Selection. After proceeding to phase 2, we were singled out and awarded this grant to create a Development Plan describing how the Air Force could most efficiently realize the ideas presented in our white paper.

A Minor Program in Computation Sciences
National Science Foundation (NSF) Subcontract
August 2008 – September 2008
$ 5,000.00

Role:	My role in this project is that of an NSF Subcontractor (Dr. Steven Gordon, Ohio Supercomputing Center is the Principal Investigator of the NSF grant through which the subcontract was awarded).

Description:	The contract provided support for one month during Summer 2008 for the development of an online “Parallel Computing” course offered through the Ralph Regula School of Computational Sciences. A number of developed modules were integrated into CS 412/512 “Parallel Computing I” (see Part II – Section B).

Bringing Together the Cell and the Computer: A Proposal for a Research Program in Bioinformatics
Ohio University 1804 Research Fund
July 2005 – June 2006
$ 36,000.00

Role:	My role in this project is that of an Co-Principal Investigator with Dr. Lonnie R. Welch, Dr. David Juedes, Dr. Allan Showalter, Dr. Ahmed Faik, Dr. Sarah Wyatt (Department of Environmental and Plant Biology), Dr. John Kopchik, David Wight (Edison Biotechnology Institute), and Dr. Winfried Just (Department of Mathematics). My responsibilities included the supervision and mentoring of the graduate students hired under this grant.


Description:	This proposal seeks support for a collaborative effort between The Department of Environmental and Plant Biology, Edison Biotechnology Institute, The Department of Chemical Engineering, and The School of Electrical Engineering and Computer Science. This grant provided funding for 3 graduate students for the development of bioinformatics software tools.

Research and Development Activities:

Research in Bioinformatics:

Development of high-performance software to find exceptional motifs in genomic sequences. Collaboration with the National Institute of Health (NIH), The Ohio State University, Ohio Supercomputing Center (OSC), 2007- to date.

Development of a Real-time Air Traffic Control System using SIMD COTS technology

Collaboration between Ohio University, Kent State, and Worldscape Inc. (2006-to date).

QoS-based Resource Management

Collaboration between Ohio University and The Ohio State University. Development of algorithms for QoS-based resource management; development of (RT-)CORBA-based resource management middleware architectures and components. Design and development of a QoS-based Resource Management Subsystem and Integration into the Linux 2.6 Kernel (2004-to date).

NASA HART (Hierarchical Adaptive Resource Management) Project:

Development of QoS-based resource management algorithms and a resource management middleware architecture for NASA’s future generation earth observing satellites (2002-2004).

Cluster-Computing

Design and implementation of a resource management middleware for a cluster-based image retrieval system (1999-2002)

Professional Activities

Editorial

Associate Editor/Member of the Editorial Board, IASTED/ACTA Press International Journal of Computational Bioscience, 2008.

Guest Editor, Journal of Systems and Software, Special Issue on Resource Management for Real-Time and Distributed Systems, 2006.

Conference Activities, Committee Memberships and Other Professional Service

Member of the Organizing Committee – Bioinformatics Open Source Conference (BOSC 2009) held in conjunction with the 17th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB) 2009.

Program Committee Member - The 2009 IEEE International Joint Conference on Computational Sciences and Optimization (CSO 2009)

Program Co-Chair – The Second IEEE International Symposium on Applied Computing and Computational Sciences (ACCS 2009)

Program Committee Member – 4th Ohio Collaborative Conference on Bioinformatics and its Applications in the Life Sciences (OCCBIO 2009).

Exhibitor – “Wordseeker – A Software to find Exceptional Motifs in Genomic Sequences”, Supercomputing 2008 (SC’08), 2008. Collaboration with the Ohio Supercomputing Center (OSC).

General Chair – 16th IEEE International Parallel and Distributed Processing Symposium (IPDPS 2008) International Workshop on Parallel and Distributed Real-Time Systems, Miami, FL, 2008.

Program Chair – 15th IEEE International Parallel and Distributed Processing Symposium (IPDPS 2007) International Workshop on Parallel and Distributed Real-Time Systems, Long Beach, CA, 2007.

Program Committee Member – IEEE Real-Time and Embedded Technology and Applications Symposium 2007 (RTAS 2007).

Program Committee Member – IEEE International Symposium of Object-oriented Real-Time Computing 2007 (ISORC 2007).

Publication Chair – 1st Ohio Collaborative Conference on Bioinformatics and its Applications in the Life Sciences (OCCBIO 2006), Ohio University, June 2006.

Invited Session Organizer – "Soft and Firm Real-Time Systems” at the 14th IEEE IPDPS International Workshop on Parallel and Distributed Real-Time Systems (WPDRTS2005), Rhodes Island, Greece, 2006.

Program Committee Member – IEEE Real-Time Systems Symposium 2006 (RTSS 2006).

Invited Session Organizer – "Scheduling and Resource Management in Parallel and Distributed Real-time Systems” at the 13th IEEE IPDPS International Workshop on Parallel and Distributed Real-Time Systems (WPDRTS2005), Denver, Colorado, 2005.

Publicity Chair – 12th IEEE International Parallel and Distributed Processing Symposium (IPDPS 2004) International Workshop on Parallel and Distributed Real-Time Systems (WPDRTS2004), 2004.

Dissertation: Compile-time Scheduling in Multiprocessor Systems (7/2002)