Newsletter: Spring 2008
Greetings from the Chair
Welcome to the Spring 2008 edition of the UNO Computer Science Department web Newsletter. We wish to keep the department's friends and alumni up-to-date with regard to activities and events within the department. Computer Science is a field that evolves very rapidly and our department changes as it keeps current with technology and with the art of computing. We hope you find interesting the news you read in the newsletter. Also we encourage input from our readers. Feel free to offer suggestions for the newsletter. Let us know if you would like to be included in our mailing list. Alumni can view the general UNO alumni webpage.
Best wishes from the Department, and now please read on.
Mahdi Abdelguerfi
Professor & Chair
Katrina Notes
This is the first Newsletter since the cataclysm of Katrina. A brief summary of events post-Katrina may interest alumni and friends of the Department.
Just like the entire citizenry of greater New Orleans, every department member was affected in his or her own way. Of course, many evacuated immediately before the storm. Some people had enormous damage to their residences and had to find alternative living quarters. Some lost their homes. Some were spared that. Some were lucky. Some faculty and staff were in a Katrina diaspora and spent Fall 2005 in other cities. Others were able to return to the Metro area in the weeks following the storm itself. Some lived in FEMA trailers on UNO campus itself.
The University itself was seriously damaged. Being located on the south shore of Lake Pontchartrain, the campus caught the full brunt of wind, rain, and flying debris. The MATH and CERM buildings, where our offices are, suffered significant but not ruinous damage from the storm, largely in the form of water damage that entered from above. The entire campus was immediately closed, and barely reopened in time for the Spring 2006 semester.
UNO was the only area university that salvaged a Fall 2005 semester. Six weeks after Katrina, the University reopened for classes, but not on our Lakefront campus. Using a combination of on-line courses, and satellite campuses, primarily the Jeff Center on N. Causeway Blvd., the university was able to service approximately 7,000 enrollees. The Computer Science Department was a full participant in this effort. The arrangement was a strain for students and faculty alike. But, illustrating the great will of the community of New Orleanians, and their love of this remarkable city, it was achieved.
Campus reopened, just barely, in January 2006 for a spring semester. One "classroom" was a large tent pitched just north of the University Center. The Computer Science Department, and its equipment, were all largely functioning. Progress has been slow, but the Department and the University have rebounded remarkably well. Nonetheless, as the New Year started this January, the MATH building was still without a functioning elevator. Enrollments in the University are markedly lower, now down to about 12,000 each semester, versus the 17,000 that were enrolled the week that Katrina struck.
Some UNO faculty have departed, for one reason or another. Computer Science junior faculty members Dr. Bin Fu and Dr. Yixin Chen decided to pursue their careers at other institutions. Dr. Fred Hosch and Mr. Sal Tillis have since decided to retire. But in Fall 2007 we added new faculty member, Dr. Chris Summa, and in January 2008 we added new faculty member Dr. Dongxiao Zhu.
Again, just like the entire citizenry of greater New Orleans, for some in the Department, life has largely returned to normal. But for some, there still remain daily tribulations of repairing homes and lives and lifestyles that were upended by Katrina.
New Faculty: Dr. Christopher Summa and Dr. Dongxiao Zhu
Dr. Christopher Summa joined the Department of Computer Science at the University of New Orleans as an Assistant Professor in August of 2007. Dr. Summa received a B.S. in Biochemistry and a B.A. in Russian from the Pennsylvania State University and his Ph.D. in Biochemistry and Molecular Biophysics from the University of Pennsylvania. Dr. Summa was a three-year NSF Postdoctoral Fellow in Bioinformatics at Stanford University School of Medicine before joining the department.
The fields of Bioinformatics and Computational Biology depend heavily on the use of computational tools to understand fundamental problems in Biology and Biochemistry. Dr. Summa's research focuses on protein structure/function relationships, protein structure prediction, and protein design and engineering. These research areas lie at the interface between biochemistry, chemistry, physics, computer science, bioinformatics, computational biology, molecular biology, and bioengineering.
As a graduate student, focusing on protein design and its computational aspects, Dr. Summa worked on the design, analysis, and characterization of di-metal binding proteins, implemented a suite of computer programs for computational protein design, and designed and produced a water-soluble variant of the integral membrane protein phospholamban. He also designed and implemented a potential function that has shown promise in the field of ab initio protein structure prediction.
At Stanford, Dr. Summa participated in CASP5 as an ab initio protein structure predictor and has been working on the derivation, testing, and optimization of potential functions for use in ab initio protein structure prediction and in near-native protein model refinement. He participated in the CASP7 refinement experiment using potentials he developed at Stanford, and is also working on design of symmetric self-assembling protein systems, continuing a line of research he began in graduate school.
In his own words, Dr. Summa says:
My family and I arrived in New Orleans this past summer, and, having survived the hot weather during the month of August, I must say that both my family and I are VERY happy with our new environment. We've found the city and its people to be welcoming of new transplants, and also a very interesting and vibrant place to live. At UNO, I've found the faculty and staff in the CSCI Department to be very supportive and helpful, the importance of which is difficult to understate for a new faculty member. I've also enjoyed the opportunity to interact with faculty in the Chemistry and Biology Depts., and hope to collaborate with some of my colleagues in these departments in the future.
My research is now moving forward, and the general themes are similar, though not exactly the same, as my graduate and postdoctoral research. I maintain an interest in bioinformatics and computational biology methods development, and the applications of these computational tools to biological problems such as cellular signaling networks and protein structure prediction.
UNO has impressed me thus far as a University that is moving beyond the sum of its parts, with designs to foster still more cross-disciplinary scholarship than already exists, and I'm thrilled by the idea that I may get to play a small role in that forward movement.
Dr. Dongxiao Zhu joins UNO's Computer Science Department effective January 2007. Dr. Zhu received a M.A. degree in Statistics from the University of Michigan, Ann Arbor (2005) and a Ph.D. degree in Bioinformatics from the Electrical Engineering and Computer Science Department of the University of Michigan, Ann Arbor (2006). Before joining UNO's Computer Science Department, he has been with Stowers Institute for Medical Research since June, 2006, where he holds a primary appointment as Biostatistician. He also holds a secondary appointment with the University of Kansas Medical Center, Department of Biostatistics as an Assistant Professor.
Dr. Zhu's methodology research interests fall in many aspects of bioinformatics and biostatisitcs. Dr. Zhu's bioinformatics research interest area includes: computational and statistical methods for analyzing genome-wide data, biological network inference, comparative genomics and biological sequence analysis. Dr. Zhu's applied statistics research interest area includes: applied multivariate analysis, statistical inference and computing, machine learning. In addition, Dr. Zhu actively collaborates with biomedical researchers to apply appropriate computational and statistical techniques to solve real-world biomedical problems.
In his own words, Dr. Zhu says:
It is my pleasure to join computer science department of the University of New Orleans. I was born in Jinan, the capital city of Shandong province, China, it is also called "spring city". I spent my first 25 years in Jinan and Beijing, the latter is capitol city of China: family, friends, loves, pains, studies, scientific research etc. I then moved to United States to pursue my career. After exploring a number of academic fields, I finally chose to develop my career in the exciting field of bioinformatics and computational biology.
I earned my M.A. in statistics (2005) and Ph.D. in bioinformatics (2006) from the University of Michigan, Ann Arbor. After graduation I joined Stowers Institute for Medical Research to assume an industry-like job as biostatistician. Driven by strong motivation for research, I also obtained an academic appointment as assistant professor with University of Kansas Medical Center.
In Jan 2008, one year and half after my graduation, I finally went back to my beloved academia to enjoy free life style that it has to offer. As a seafood lover, I feel so blessed to be so much close to the ocean. In my future years at UNO computer science, I hope to continue and expand my research programs to the cutting edge of bioinformatics and biostatistics. I passionately believe in that scientific research gives me the opportunity to understand, learn and mold young minds for a larger cause - the betterment of both science and humankind.
Infrastructure Changes
The Department of Computer Science is fully independent, with its own email and printing facilities and a dedicated wireless network. The network infrastructure and the servers in the data center were recently upgraded. The department network is now powered by thirteen Cisco 3750 series gigabit switches, with fifteen state-of-the-art servers running web, E-mail, database, file, application, and directory services. The servers have 2 to 4 Sparc IIIi or AMD Opteron dual core processors, 8 to 32 gigabytes of RAM and over 6TB of storage space.
The latest addition to the computing power is a 32 node Beowulf cluster (in addition to the front end). Each node has dual AMD Opteron 2.4 gigahertz processors with 4 gigabytes of RAM and 73GB, 10,000 RPM ULTRA320 SCSI hard disks. The cluster network is gigabit and the nodes share a 1.8TB disk array. The department is expecting a 47+TB disk array to be shared with the LONI group. This disk array is a result of a joint research venture known as PETASHARE between the department and four other universities (LSU-Baton Rouge, Louisiana Tech, ULL and Tulane).
The department has 10 computer labs that are distributed by function as follows: 2 instructional/teaching labs, 2 public labs open 24/7, and 6 dedicated research labs. Each research lab is supervised by one or more faculty members and is dedicated to a research topic. Workstations in the instructional and teaching labs have AMD Opteron processors with 2GB of RAM and 80GB SATA hard drives. The research labs contain high-end workstations ranging in price from $3,500 to $12,500 (this includes a 50% educational discount). The resources available on the research lab workstations are dual or quad core processors with 4-16GB of RAM and from 250GB to 2TB of disk space. Many machines have high-end graphics capabilities, such as dual NVIDIA 8800GTX and 5500FX cards and large flat panel LCD displays ranging from 19 to 30 inches.
Faculty Grants
The Naval Research Laboratory (NRL) at Stennis Space Center in Mississippi is awarding Dr. Abdelguerfi a contract for research into Mining Large Spatio-Temporal Data Sets over Spatial Networks. The $307,037 research contract is effective August 23, 2007.
UNO's Computer Science Department has received funding in the amount of $43,228 from the National Security Agency (NSA). This Information Assurance (IA) related project is led by Professor Golden Richard and includes Drs. Vassil Roussev, Jaime Nino, and Mahdi Abdelguerfi.
Dr. Golden G. Richard III was recently awarded an NSF Cyber grant for research into next-generation file carving. The 260K grant is three years in duration and funds Lodovico Marziale, a Ph.D. student working in digital forensics. One of the most important software techniques in digital forensics is file carving, which uses a database of characteristics about commonly encountered file types to search physical disks for files of these types. File carving is a particularly powerful technique because files can be retrieved from raw disk images, regardless of the type of file system, even if file metadata has been destroyed. File carving can find data associated with deleted files, in slack space, swap files, and data "hidden" outside the file system. The goal is to identify the starting and ending locations of files in the disk images and "carve" (copy) sequences of bytes into regular files so their value as evidence can be measured.
Dr. Stephen Winters-Hilt, recently obtained the prestigious "Career Transition Award For Informatics" from the National Institutes of Health (NIH). The $486,000 award, provides almost half a million dollars to cover expenses associated with experiments, post doc/student wages, travel, etc., over the next three years.
Students of Note: Mr. Paul Flowers and Ms. Angela Kay Hernandez
Mr. Paul Flowers has been awarded with Ph.D. Student Fellowship in Information Assurance. He will work in Dr. Golden G. Richard III on digital forensics and information assurance. In his own words, he says:
I am a native of Memphis, TN, with New Orleans being our adopted home for over 25 years. Married to a most gracious woman and blessed with three wonderful children. My son has graduated from UNO with a degree in Education and has started his teaching career. One of my daughters has graduated from UNO and is pursuing her Master's in Mathematics. My other daughter attends UNO with a concentration in Computer Science. My father was a teacher and carrier for the U.S. Postal Service and my late mother was a teacher and assistant principal in the Memphis City school system.
I am very grateful for the encouragement, kindness, fellowship, humor and patience exhibited by the professors that taught me at UNO: Dr. Shengru Tu, Dr. Frederick Hosch, Dr. Mahdi Abdelguerfi and especially the professor that guided me in my thesis research, Dr. Golden Richard. My extensive academic studies at UNO in pursuit of my Master's degree has empowered me with the knowledge and ability to continue my studies in computer science and endeavor to obtain my doctorate degree. I believe the opportunity of working with such dedicated teachers in the area of Information Assurance will be very interesting, challenging and rewarding.
New Ph.D. Student, Ms. Angela Kay Hernandez, Recipient of Ph.D. fellowship. In her own words, she says:
I am originally from the suburbs of Memphis,and have been in New Orleans for 2 years. I graduated in the Spring from the university with a B.S. in Biological Sciences and a minor in Psychology. I worked on undergraduate research while working on my undergraduate degree with Dr. Martin O'Connell, and my final semester with the Pontchartrain Institute for Environmental Sciences. Currently, I am working in the Research Institute at Children's Hospital on nanopore research under the direction of Dr. Stephen Winters-Hilt. I feel honored to be the recipient of such a prestigious award, and appreciate everyone's support that helped me in achieving this goal.