Poster.bib


@INPROCEEDINGS{ISBRA09-Repeats,
AUTHOR = {Michael Robinson and Camilo A. Silva and {\bf S. Masoud Sadjadi} and Guangyuan Liu and Dr. Giri Narasimhan},
TITLE = {Finding Repeats and Signatures in {DNA} Sequences Using {MPI} Clusters},
BOOKTITLE = {the 5th International Symposium on Bioinformatics Research and Applications (ISBRA09)},
YEAR = {2009},
MONTH = {May},
ADDRESS = {Nova Southeastern University, Ft. Lauderdale, Florida, USA},
ABSTRACT = {{\bf Introduction:} The extent of repeats is a striking feature of genomic
DNA sequences. For example, families of repeat sequences account for
about one half of the human genome. Finding repeats is useful in
finding defective genes and in forensic DNA fingerprinting. Techniques
to find repeats can also be used to find signatures for a pair (or a set)
of genomes. We consider the problem of finding repeats and
signatures in genomic sequences using grid-computing techniques.
\\
{\bf Methods:} The problem is clearly compute-intensive and creates costly
bottlenecks in large-scale analyses. There are a number of programs
available for finding repeats, such as the popular RepeatMasker [REF].
We have implemented an algorithm based on suffix arrays for finding
repeats, which was then ported to run on MPI clusters with dynamic
load balancing. This algorithm also searches for direct repeats and
other variants such as inverted repeats and complemented inverted
repeats. We have also implemented an algorithm that searches for
“signatures”, i.e., subsequences present in one genome but absent
from the others.
\\
{\bf Results and Conclusions:} We have successfully tested our
implementation on five strains of the bacteria Pseudomonas
aeruginosa, each containing over six million nucleotides. The MPI
cluster implementation resulted in near-optimal speedup and
balancing.
},
KEYWORDS = {Genome Sequences, Search Engine, Repeats, Signatures, Load Balancing, Fault-Tolerant, Grid Computing.},
}

@INPROCEEDINGS{FGLSAMP-Repeats,
AUTHOR = {Michael Robinson and Guangyuan Liu and Camilo A. Silva and {\bf S. Masoud Sadjadi} and Dr. Giri Narasimhan},
TITLE = {Finding Repeats and Signatures in DNA Sequences Using MPI Clusters},
BOOKTITLE = {the 16th Annual FGLSAMP EXPO},
YEAR = {2009},
MONTH = {Feb.},
ADDRESS = {University of Miami, Florida},
ABSTRACT = {One of the most striking features of genomic DNA sequences is the extent to which repeated substrings occur in the genome. The problem of identifying subsequences that are repeated or unique has many applications in Bioinformatics. A number of algorithms exist for these problems, but are compute-intensive. We implemented an algorithm based on suffix arrays for finding repeats and unique signatures, which was then ported to run on MPI clusters. It searches for single patterns in a sequence of roughly a few million bases in less than a second. We tested our data on strains of the bacteria Pseudomonas aeruginosa containing over six million nucleotides. The serial implementation completed its task averaging 30 hours for every pair of genomes. The performance of the MPI implementation was compared to that of the serial one. Effectively, the MPI implementation allowed to reduce the amount of time needed to process such tasks.
},
KEYWORDS = {Genome Sequences, Search Engine, Repeats, Signatures, Load Balancing, Fault-Tolerant, Grid Computing.},
NOTE = {(winner of the third place in the poster competition.)},
}

@INPROCEEDINGS{NCUR-BioInf-Repeats,
AUTHOR = {Michael Robinson and Guangyuan Liu and Camilo A. Silva and {\bf S. Masoud Sadjadi} and Dr. Giri Narasimhan},
TITLE = {Finding Repeats and Signatures in DNA Sequences Using MPI Clusters},
BOOKTITLE = {the 23rd National Conference on Undergraduate Research},
YEAR = {2009},
MONTH = {April},
ADDRESS = {University of Wisconsin – La Crosse, Wisconsin},
ABSTRACT = {The main characteristic of genomic data is its large size. For example, the National Institutes of Health (NIH) sequence database has a total of over 65 billion nucleotides. One of the most striking features of genomic DNA sequences is the extent to which repeated substrings occur in the genome. Families of repeat sequences account for about one third of the human genome. The problem of identifying subsequences that are either repeated or unique has many applications in Bioinformatics. Repeat sequences come in many different flavors and are responsible for different functions and diseases. Finding repeats has applications in finding defective genes, and in forensic DNA fingerprinting. It also allows us to find differences between genomes. A number of algorithms and implementations exist for these problems, but are compute-intensive. We have implemented an algorithm based on suffix arrays for finding repeats and unique signatures, which was then ported to run on MPI clusters with good results. This algorithm also searches for direct repeats and other variants such as inverted repeats and complemented inverted repeats. It searches for single patterns in a sequence of roughly a few million bases in less than a second. We tested our data on five strains of the bacteria Pseudomonas aeruginosa, which were acquired from NCBI, each containing over six million nucleotides. The serial implementation completed its task averaging 30 hours for every pair of genomes. The performance of the MPI implementation was compared to that of the serial one. Effectively, the MPI cluster implementation allowed to reduce the amount of time needed to process such tasks.
},
KEYWORDS = {Genome Sequences, Search Engine, Repeats, Signatures, Load Balancing, Faul-Tolerant, Grid Computing.},
}

@INPROCEEDINGS{Argonne-2008,
TITLE = {Application Performance Profiling and Prediction in Grid Environment},
BOOKTITLE = {the 19th Annual Argonne Symposium for Undergraduates in Science, Engineering and Mathematics},
YEAR = {2008},
MONTH = {November},
ABSTRACT = {Weather prediction can save lives and help business owners and emergency responders in the case of inclement weather.
The goal  of WRF is to improve weather prediction, especially in the case of hurricane mitigation. Optimum forecasting consists of:
Accurate and Timely Results and Precise Location Information.
Grid-Enablement is the practice of taking  existing applications that are currently configured to run on a single machine or cluster and adapting them to run on a non-homogeneous resources connected via the internet with the goal of improving its performance (execution time and resource utilization).
The expected benefits of  successful grid-enablement to WRF will be:
1) Access to a greater number of compute resources due to the utilization of more domains;
2) Faster results, by virtue of having more compute power (more power = less simulation time); and
3) Improved precision of results (more power = higher domain granularity).
The meta-scheduler is the “global” scheduler of the grid environment – above the local schedulers.  Its function is to select the best resources for a job to run on by analyzing application and target architecture characteristics to find the best match for optimal resource usage and job return time. Performance prediction provides:
1) the meta-scheduler with accurate prediction run times  -  “smarter” scheduling; and
2) at local level, improved resource allocation and local scheduling techniques as many users overestimate job execution times for precautionary reasons.
Leverage many years of experience from BSC faculty towards these goals and make personal connections that will last throughout our careers.},
KEYWORDS = {Grid Environment, Application Profiling, Prediction of Execution Time, Meta-Scheduling, WRF.},
}

@INPROCEEDINGS{LA-Grid-Summit-6-FAU-2008-10-30-BioInf-Repeats,
AUTHOR = {Camilo A. Silva and Michael Robinson and Guangyuan Liu and {\bf S. Masoud Sadjadi} and Dr. Giri Narasimhan and Hector Alejandro Durán Limón},
TITLE = {Finding Repeats and Signatures in DNA Sequences Using MPI Clusters},
BOOKTITLE = {the poster presentation session of the 6th Latin American Grid (LA Grid) Summit},
YEAR = {2008},
MONTH = {October},
ADDRESS = {Florida Atlantic University, Boca Raton, FL, U.S.A.},
ABSTRACT = {Homeland Security applications with regard to microbial detection in environmental samples are among the many other possible applications of our project.
The main characteristic of genomic data is its large size. For example, the National Institutes of Health (NIH) sequence database has a total of over 65 billion nucleotides.
One of the most striking features of genomic DNA sequences is the extent to which repeated substrings occur in the genome. In C. elegans with a genome sequence of 100.2 million nucleotides over 7,000 families of repeat sequences have been identified. Families of repeat sequences account for about one third of the human genome. Repeat sequences come in many different flavors and are responsible for different functions and diseases. Finding repeats has applications in finding defective genes, and in forensic DNA fingerprinting. It also allows us to find differences between genomes.
},
KEYWORDS = {Genome Sequences, Search Engine, Repeats, Signatures, Load Balancing, Faul-Tolerant, Grid Computing.},
PDF = {Poster/Final-PIRE_2008-2009_Poster_CamiloSilva-MichaelRobinson.pdf},
}

@INPROCEEDINGS{LA-Grid-Summit-6-FAU-2008-10-30-WRF-Portalp,
AUTHOR = {Allison Lanager and Sean Leslie and Seychelles Martinez and Elias Rodriguez and {\bf S. Masoud Sadjadi} and Hector Alejandro Durán Limón},
TITLE = {A Web-Based Portal for Hurricane Mitigation},
BOOKTITLE = {the poster presentation session of the 6th Latin American Grid (LA Grid) Summit},
YEAR = {2008},
MONTH = {October},
ADDRESS = {Florida Atlantic University, Boca Raton, FL, U.S.A.},
ABSTRACT = {The purpose of this project is to facilitate remote access to the grid enabled WRF (Weather Research and Forecasting) system, via a web based portal. The portal is used by Meteorologists and provides services facilitating the uploading of WRF configurations, modification of relevant weather variables, and the submission, tracking, and retrieval of jobs.
},
KEYWORDS = {Weather Research and Forecasting, WRF Web-Based Portal, Hurricane Mitigation, Meta-Scheduling, Grid Computing.},
PDF = {Poster/Final-PIRE_2008-2009_Poster_Allison_Sean.pdf},
}

@INPROCEEDINGS{LA-Grid-Summit-6-FAU-2008-10-30-WRF-Profiling-Intl-Exp,
TITLE = {International Experience: From 0 to 6 foreign countries in 9.5 weeks},
BOOKTITLE = {the poster presentation session of the 6th Latin American Grid (LA Grid) Summit},
YEAR = {2008},
MONTH = {October},
ADDRESS = {Florida Atlantic University, Boca Raton, FL, U.S.A.},
ABSTRACT = {Our experience was about developing new avenues as a person and in our research by reaching across cultural boundaries to really experience the meaning of a global living laboratory.  The PIRE program offered us a unique opportunity to take on technology from a different perspective than that we receive in our traditional studies.  Furthermore, forging working relationships with our international collaborators serves as a big step towards making breakthrough contributions to the research community.
Beyond the walls of research, PIRE afforded us the opportunity to develop as individuals, both professionally and personally.  We were given the opportunity to really explore the world and take on a trailblazing role in this the first year of this program.  As some what of guinea pigs, we were able to set the bar for the years to come in this program and were ambassadors for our home institutions.  The experiences we gathered here will be invaluable in the rest of our academic careers as well as our subsequent professional careers.
},
KEYWORDS = {Application Profiling, WRF, High-Performance Computing, Grid Computing},
}

@INPROCEEDINGS{LA-Grid-Summit-6-FAU-2008-10-30-WRF-Profiling-Research,
TITLE = {Application Profiling and Prediction in the Grid Environment},
BOOKTITLE = {the poster presentation session of the 6th Latin American Grid (LA Grid) Summit},
YEAR = {2008},
MONTH = {October},
ADDRESS = {Florida Atlantic University, Boca Raton, FL, U.S.A.},
ABSTRACT = {Weather prediction can save lives and help business owners and emergency responders in the case of inclement weather.
The goal  of WRF is to improve weather prediction, especially in the case of hurricane mitigation. Optimum forecasting consists of:
Accurate and Timely Results and Precise Location Information.
Grid-Enablement is the practice of taking  existing applications that are currently configured to run on a single machine or cluster and adapting them to run on a non-homogeneous resources connected via the internet with the goal of improving its performance (execution time and resource utilization).
The expected benefits of  successful grid-enablement to WRF will be:
1) Access to a greater number of compute resources due to the utilization of more domains;
2) Faster results, by virtue of having more compute power (more power = less simulation time); and
3) Improved precision of results (more power = higher domain granularity).
The meta-scheduler is the “global” scheduler of the grid environment – above the local schedulers.  Its function is to select the best resources for a job to run on by analyzing application and target architecture characteristics to find the best match for optimal resource usage and job return time. Performance prediction provides:
1) the meta-scheduler with accurate prediction run times  -  “smarter” scheduling; and
2) at local level, improved resource allocation and local scheduling techniques as many users overestimate job execution times for precautionary reasons.
Leverage many years of experience from BSC faculty towards these goals and make personal connections that will last throughout our careers.},
KEYWORDS = {Grid Environment, Application Profiling, Prediction of Execution Time, Meta-Scheduling, WRF.},
}

@INPROCEEDINGS{LA-Grid-Summit-6-FAU-2008-10-30-Pattern-Based-JFM,
AUTHOR = {Selim Kalayci and {\bf S. Masoud Sadjadi} and Gargi S. Dasgupta},
TITLE = {Pattern Based Fault-Tolerance at Workflow Management Systems},
BOOKTITLE = {the poster presentation session of the 6th Latin American Grid (LA Grid) Summit},
YEAR = {2008},
MONTH = {October},
ADDRESS = {Florida Atlantic University, Boca Raton, FL, U.S.A.},
ABSTRACT = {Complex workflows being used more often by scientists.
Grid environments are being used to utilize resources in multiple organizations.
Heterogeneity and dynamicity of the environment introduces challenges to the execution of workflows.
If not handled, these challenges may result in wasted time and resources, and basically unsuccessful execution of workflows.
Scientists need reliable tools to  successfully conduct their business.
Administrators are concerned with the utilization of resources.
},
KEYWORDS = {Workflow, Job Flow, Fault-Tolerant, Design Patterns.},
PDF = {Poster/Final-PIRE_2008-2009_Poster_Selim_Kalayci.pdf},
}

@INPROCEEDINGS{LA-Grid-Summit-5-IBM-2007-09-TGE-WRF,
AUTHOR = {{\bf S. Masoud Sadjadi} and Javier Muñoz and Diego Lopez and Javier Figueroa and Xabriel J. Collazo-Mojica and Alex Orta and Michael McFailand and David Villegas and Rosa Badia and Pat Welsh and Raju Rangaswami and Shu Shimizu and Hector A. Duran Limon},
TITLE = {Transparent Grid Enablement of {WRF} Using a Profiling, Code Inspection, and Modeling Approach},
BOOKTITLE = {the poster presentation session of the 5th Latin American Grid (LA Grid) Summit},
YEAR = {2007},
MONTH = {September},
ADDRESS = {The IBM T.J. Watson Research Center, NY, U.S.A.},
ABSTRACT = {Due to the computational requirements of the Weather Research and Forecast (WRF) numerical simulation models, a large number of computing nodes are needed to reduce the overall wall-clock time of the simulations, so that timely critical decisions can be made. In this project, we use existing and custom-designed profiling and code inspection tools to understand the runtime behavior of {WRF} on a Grid computing environment. Our goal is to produce a mathematical model to predict the allocation of computing resources, for example, the optimized number of homogenous nodes required for a hurricane path prediction simulation. We will run a number of profiling experiments with different hardware and software configurations. The data gathered through these experiments will help us formulate and validate the mathematical model. This model will enable future self-configured executions of the {WRF} code on a Grid computing environment.
},
KEYWORDS = {Grid Enablement, Grid Computing, {WRF}, Profiling, Code Inspection, Modeling.},
PDF = {Poster/TGE of WRF - Final.pdf},
}

@INPROCEEDINGS{LA-Grid-Summit-5-IBM-2007-09-WRF-Portal,
AUTHOR = {{\bf S. Masoud Sadjadi} and Steve Luis and Khalid Saleem and Donald Llopis and Javier Munoz and Diego Lopez and Javier Figueroa and David Villegas Castillo and Selim Kalayci and Pat Welsh and Shu-Ching Chen and Anthony Praino and Hugh Willoughby},
TITLE = {The {Latin American Grid (LA Grid) Weather Research and Forecast (WRF) Portal}},
BOOKTITLE = {the poster presentation session of the 5th Latin American Grid (LA Grid) Summit},
YEAR = {2007},
MONTH = {September},
ADDRESS = {The IBM T.J. Watson Research Center, NY, U.S.A.},
ABSTRACT = {The Latin American (LA) Grid Weather Research and Forecast ({WRF}) Portal is aimed to provide a comprehensive Web-based user-friendly interface for meteorologists to conduct their research and forecast, for end users to access and understand the forecast, and for system administrators to configure the underlying computing infrastructure. This way, the meteorologist will spend their time only on the science part of weather research and forecast instead of wasting their time on tedious and error-prone tasks of compiling, installing, and configuring the {WRF} code. The end users (e.g., business owners, home owners, and emergency response teams) can easily access the forecast that most relates to them and assists their understanding of how to take preventive and recovery actions accordingly. The system administrators can add or remove computational resources (e.g., clusters, supercomputers, and virtual machines) to be allocated dynamically to the different simulation tasks based on some high-level policies.  Currently, we are focusing on enabling the meteorologist to set up, automate simulations and organize data results to support ensemble runs of hurricane forecast simulations leveraging grid computing resources.
},
KEYWORDS = {Portal, {WRF}, Web, Hurricane Mitigation.},
PDF = {Poster/LA Grid WRF Portal Poster - Final.pdf},
}

@INPROCEEDINGS{LA-Grid-Summit-5-IBM-2007-09-Meta-Scheduling,
AUTHOR = {Liana Fong and {\bf S. Masoud Sadjadi} and Yanbin Liu and Ivan Rodero and David Villegas and Selim Kalayci and Norman Bobrof and Julita Corbalan},
TITLE = {The {LA Grid} Meta-Scheduling Project},
BOOKTITLE = {the poster presentation session of the 5th Latin American Grid (LA Grid) Summit},
YEAR = {2007},
MONTH = {September},
ADDRESS = {The IBM T.J. Watson Research Center, NY, U.S.A.},
ABSTRACT = {The use of local resource management systems to schedule the execution of jobs is extended through many research areas in need of high performance computing. However, while local schedulers manage the rights for a single domain, there is a need to perform a higher level scheduling of resources. A meta-scheduler, or a scheduler of schedulers, is an entity in charge of orchestrating these resources from different organizations. Different architectures have been proposed for meta-scheduling systems. In this poster, we present a hybrid approach, combining hierarchical and peer-to-peer architectures to improve fault tolerance, management and extensibility of these systems. We also define a standard protocol to allow different meta-scheduler instances to communicate using Web Services. In our experiment, three remote organizations using different scheduling technologies (namely, IBM, BSC, and FIU) interoperate using the described protocol.
},
KEYWORDS = {Grid Computing, Meta-Scheduling, LA-Grid.},
PDF = {Poster/MetaScheduling Poster - Final - IBM Conf.pdf},
}

@INPROCEEDINGS{LA-Grid-Summit-5-IBM-2007-09-Job-Flow-Management,
AUTHOR = {Gargi B Dasgupta and Liana Fong and {\bf S. Masoud Sadjadi} and Onyeka Ezenwoye and Balaji Viswanathan and Selim Kalayci and David Villegas Castillo and Norman Bobroff},
TITLE = {Fault-Tolerant Job-Flow Management in Grid Environment},
BOOKTITLE = {the poster presentation session of the 5th Latin American Grid (LA Grid) Summit},
YEAR = {2007},
MONTH = {September},
ADDRESS = {The IBM T.J. Watson Research Center, NY, U.S.A.},
ABSTRACT = {The execution of job flow applications is a reality today in scientific and enterprise domains, and the LAGrid job flow management project addresses many specific issues related to job flow management in distributed meta-brokering environments.  The central idea of the project is a two-level approach that employs job flow based service orchestration at the upper level to control coarse-grain job submissions to the resource management layer, and service choreography at the lower level, or fine-grained interaction with jobs by allocating appropriate computing and data resources.  The focus of this project is on experimentation of the span and coordination control of job flow engine and meta-scheduling functions, with respect to distributed (1) job execution, (2) failure management and (3) data handling.
},
KEYWORDS = {Grid Computing, Job Flow Management, Fault-Tolerant.},
PDF = {Poster/LA Grid Job-Flow Management Poster - Final.pdf},
}

@INPROCEEDINGS{TransparentGridEnablement-IBM-06,
AUTHOR = {{\bf S. M. Sadjadi} and J. C. Martinez and L. Atencio and T. Soldo and
TITLE = {Transparent Grid Enablement Using Transparent Shaping and GRID superscalar},
BOOKTITLE = {the poster presentation session of the IBM Technology Leadership Conference},
YEAR = {2006},
ADDRESS = {Florida International University, Miami, FL 33199},
MONTH = {October},
ABSTRACT = {
The lack of an appropriate programming model for grid computing is a major inhibitor in the emergence of grid-enabled applications, which is a focal point of the computer science and engineering portion of the project. In this project, we aim to address this issue by integrating Transparent Shaping developed at FIU, which allows introduction of static and dynamic adaptation in applications, and GRID Superscalar developed at BSC, which allows conversion of a sequential code to a parallel code ready to be run in the grid. This new programming model will include a supporting runtime and middleware that adapts execution of grid-enabled applications as a response to the changes in the grid environment (e.g., the availability of resources such as the number of available computational nodes, the available network bandwidth, and the available data storage). Development work will be carried out first at FIU by selected students and will be supervised by Masoud Sadjadi and then by Rosa M. Badia at BSC.
},
KEYWORDS = {Grid Computing, Prgramming Model, Transparent Shaping, GRID superscalar.},
PDF = {Poster/TransparentGridEnablement-Poster-Oct2006.ppt},
PS = {Poster/tge.jpg},
}

AUTHOR = {Tao Li and {\bf S. M. Sadjadi} and Charles Perng and Abdi Salahshour},
TITLE = {Data Mining for Autonomic System Management: A Case Study at FIU-SCIS},
BOOKTITLE = {Proceedings of the NON Confidential Poster at The 4th Proactive
Problem Prediction, Avoidance and Diagnosis Conference.},
YEAR = {2006},
ADDRESS = {IBM T. J. Watson Research Center, Yorktown Heights, New York},
MONTH = {April},
ABSTRACT = {
We present a case study on the Autonomic System Manager that we designed
and developed in the School of Computing and Information Sciences at
Florida International University (FIU-SCIS) as a proof of concept to the
usefulness of data mining in autonomic system management. Autonomic System
Manager is a software system that helps system and network administrators
with their complex job. It automatically monitors Net flow (network flow)
data and responds to anomalies in an adaptive fashion. The current focus of
this prototype is on network anomaly detection.  The purpose of anomaly
detection is to detect and categorize situations that deviate from the normal
everyday. As is the case with any network, some events are malicious. In order
to secure a network system effectively administrators need to use tools that
have the capability to classify malicious activities and respond to threats
in real time. The principle challenge in automatically detecting insidious
intruders is that the range of anomalous activities is huge, ranging from port
scans, denial of service attacks, ping of death, SYN flooding, UDP flooding,
worms, viruses, and disconnecting models remotely.
},
KEYWORDS = {Data mining, autonomic computing, self management, self protection,
network and system management, anomaly detection.},
}

@INPROCEEDINGS{M2-MSU-04,
AUTHOR = {Zhenxiao Yang and Zhinan Zhou and {\bf S. M. Sadjadi}},
TITLE = {M2: Middleware Support for Collaborative Adaptation},
BOOKTITLE = {The 2004 Department of Computer Science and Engineering Poster Workshop},
YEAR = {2004},
MONTH = {May},
PDF = {poster04-m2.pdf},
}

@INPROCEEDINGS{MetaSockets-DOA-02,
AUTHOR = {{\bf S. M. Sadjadi} and P. K. McKinley and E. P. Kasten},
TITLE = {MetaSockets: Run-Time Support for Adaptive Communication Services},
BOOKTITLE = {In Addendum to the Proceedings of the International Symposium on Distributed Objects and Applications (DOA)},
YEAR = {2002},