Students:Enis

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[edit] About Me

My name is Enis Afgan. I am a Level III Ph.D. student working in the area of grid and distributed computing with a focus on grid application scheduling and accessibility. I have done a significant amount of work on enabling NCBI BLAST to execute on the grid while taking advantage of heterogeneity found in the underlying grid resources by maximizing algorithm-architecture compatibility. I have also developed a new grid language ( Application Specification Language (ASL)) used to describe applications in the grid and thus promote advances in application deployment, interface generation and job scheduling and have worked on several other projects, as shown on this page.
Outside research related activities, I like photography, spending time on a sailboat, water skiing, snow skiing, tennis, hiking, running...

My Curriculum Vitae in PDF

[edit] My Research

[edit] Long term goal

The focus of my dissertation work is grid job scheduling. Grid job scheduling can be viewed as a function of resource heterogeneity, resource and application availability, and application options. I proposed a general framework that include all of stated parameters and thus advances grid job scheduling to a new level. The goal of the framework and incorporation of all mentioned factors is to provision and present users with concrete and detailed options regarding their jobs. This, in turn, will provide more effective and efficient scheduling policies. To support these aims, the framework introduces a novel scheduling methodology that introduces new user-scheduler interaction levels and a new layer of scheduling that includes application parameter selection and parameter value optimization. Accommodating for the overall framework goals, individual components within the proposed framework allow specification of application requirements, enabling initial application registration on the grid, an application profiling system developed and customized for data analysis tools, data analysis tools geared toward job parameter optimization, and resource-job cost normalization environment enabling comparisons between resource cost provider formats. These tools act as support mechanisms for the framework as a whole to assist users with planning and scheduling their job execution on the grid. While all the components compose a large, complete framework, the focus of my work is currently in application and resource modeling and optimization of job parameters.

[edit] Affiliated projects

[edit] Dynamic BLAST

My flagship project that is a real world implementation of most of my research efforts. Dynamic BLAST is a grid enabled BLAST wrapper application that takes advantage of grid resources available on UABgrid and SURAgrid. The main purpose of Dynamic BLAST is to minimize user job turnaround time by maximizing resource utilization. It accomplishes so by not only understanding but also leveraging resource heterogeneity through job parameterization. Experiments with Dynamic BLAST show reduction in total execution time of BLAST jobs up to 50% by improving resource utilization approximately 40%. Please take a look at the papers below for more details on workings of Dynamic BLAST.

[edit] ASL

Application Specification Language (ASL) is a new grid language that has been developed and can be used by application developers and end-users to describe details of a given application. The ASL allows an individual application to be represented in the heterogeneous world of the grid by capturing its purpose, functionality and options. Through the use of ASL, application descriptions can be made available for immediate use or further advancements among applications such as application deployers, automated interface generators, job schedulers, and application-specific on-demand help provisioning tools. The ASL can also be used to describe how an application is compared and/or combined with other matching services and software. This ability to specify the composition of services can facilitate the creation of new and added functionality, as well as enabling further advancement of existing tools that can take advantage of the provided information.

[edit] AppDB

Application Performance Database (AppDB) is a repository for collecting and storing application level execution characteristics of previous application executions on the grid. Collected information can provide insight into execution relationship between application and resource, relationship between selected job parameters and execution time, relationship between values of those parameters and execution time, application scalability, application efficiency, as well as accounting information.

[edit] Grid Atlas

GridAtlas is a tool that hides and automates the process of keeping track of installation properties of any one application across resources. Because existing grid middleware (e.g., Globus Toolkit, GridWay) enables simultaneous access and invocation of application instances across grid resources, complexities involved with the installation properties on selected resources should not be left for the end-user to deal with and manage. Therefore, upon a user job submission, a job submission interface contacts GridAtlas and obtains necessary information to complement user provided information after which further steps of job submission process can take place.

[edit] UABgrid and SURAgrid

Setting up and working on distributed resource across UAB campus as well as Southeast region of the US by building UABgrid infrastructure and incorporating it with SURAgrid. I have mostly operated on maintaining CIS resources at UAB but have also closely collaborated with Academic Computing @lab at UAB and Computer Science Department at the Old Dominion University.

[edit] Publications

[edit] Journal Papers
  • Afgan E., Bangalore P., "Exploiting Performance Characterization of BLAST in the Grid", conditionally accepted to The Journal of Cluster Computing, 2009.
  • Afgan E., Bangalore P., "Dynamic BLAST – a Grid Enabled BLAST", The International Journal of Computer Science and Network Security, Volume 9, Issue 4, p.9, 2009. [PDF
[edit] Book Chapters
  • Afgan E., Bangalore P., Gray J., “A Domain-Specific Language for Describing Grid Applications”, in Software Applications: Concepts, Methodologies, Tools, and Applications, Pierre F. Tiako (Eds), IGI Global Publishers, 2009. (derived from original publication) [Publisher's Website]
  • Afgan E., Bangalore P., “A framework to assist users with planning and scheduling jobs on the grid”, in Encyclopedia of Grid Computing Technologies and Applications, Udoh E., Wang F. (Eds).
  • Afgan E., Bangalore P., Gray J., “Configuring Grid Applications from Higher Level Domain-Specific Languages”, in Designing Software-Intensive Systems: Methods and Principles, Pierre F. Tiako (Eds), IGI Global Publishers, 2008, pp. 402-438. [View on amazon.com]
[edit] Conference Proceedings
  • Bangalore P., Afgan E., "G-BLAST: A Grid Service for BLAST", 2008 International Conference on Grid Computing and Applications (GCA '08), Las Vegas, NV, July 14-17, 2008. PDF
  • Afgan E., Bangalore P., “Application Specification Language (ASL) - A Language for Describing Applications in Grid Computing”, 4th International Conference on Grid Service Engineering and Managemen (GSEM 2007), Leipzig, Germany, Sept. 24-26, 2007. PDF
  • Afgan E., Bangalore P., “Performance Characterization of BLAST on the Grid”, IEEE 7th International Symposium on Bioinformatics & Bioengineering (IEEE BIBE 2007), Boston, MA, Oct 14-17, 2007. PDF
  • Afgan E., Sathyanarayana P., Bangalore P., “Dynamic Task Distribution in the Grid for BLAST”, IEEE GrC 2006, Atlanta, GA, May 10-12, 2006. PDF
  • Afgan E., Jones W., “Design, Development and Usage of a Generic Job Submission Grid Service”, 44th ACM Southeast Conference. Melbourne, FL, March 10-12, 2006. PDF
  • Afgan E., Velusamy V., Bangalore P., “Grid Resource Broker with Application Profiling and Benchmarking”, European Grid Conference. Amsterdam, Netherlands, Feb. 14-16, 2005. PDF Poster
  • Afgan E., “Role of the Resource Broker in the Grid”. 42 nd Annual ACM Southeast Conference. Huntsville, AL, Apr. 2-3, 2004. PDF
[edit] Refereed Workshop Papers
  • Afgan E., Bangalore P., "Embarrassingly Parallel Jobs Are Not Embarrassingly Easy to Schedule on the Grid", SC08 International Conference for High Performance, Networking, Storage and Analysis - Workshop on Many-Task Computing on Grids and Supercomputers, Austin, TX, November 15-21, 2008. PDF
  • Afgan E., Bangalore P., "Experiences with developing and deploying Dynamic BLAST", Mardi Gras Conference 2008 - Workshop on Grid-Enabling Applications, New Orleans, LA, January 31-February 2, 2008. PDF
  • Afgan E., Gray J., Bangalore P., “Using Domain-Specific Modeling to Generate User Interfaces for Wizards”, MDDAUI '07 as part of MODELS 2007, Nashville, TN, Sept. 30-October 5, 2007. PDF Presentation in PDF
  • Afgan E., Bangalore P., “Computation Cost in Grid Computing Environments”, First International Workshop on the Economics of Software and Computation, Minneapolis, Minnesota, May 20, 2007. PDF
[edit] Presentations
  • Title: "A framework for efficient execution of bioinformatics applications across the grid", Presentation at MCBIOS, Mississippi State University, Starkville, MS, February 20, 2009. Presentation in PDF
  • Title: "Moving across the grid", Presentation at UAB ETLab Shared HPC Facility User Boot Camp 2008, Birmingham, AL, September 26, 2008.
  • Title: "UABgrid: Practice and Experience", Presentation at OGF22, Boston, MA, February 26, 2008. Presentation in PDF
  • Title: "Razvoj grid aplikacija – Dynamic BLAST iskustvo", Presentation at Institut Ruder Boskovic, Zagreb, Croatia, December 18, 2007. Presentation in PDF
  • Title: “Language for Describing Application Software in Grid Computing”, Alabama Academy of Science 2007 at the Tuskegee University, Tuskegee, AL, February 28-March 2, 2007. Presentation in PDF
  • Title: “UABgrid Dynamic BLAST: Searching Nucleotide and Protein Databases Using SURAgrid”, Internet 2 Meeting - Fall 2006, Chicago, IL, December 3-7, 2006. Presentation in PDF
  • Title: “Dynamic BLAST - An Approach to Dynamic Grid Application Development”, GlobusWORLD 2006, Washington, D.C., September 11-15, 2006. Presentation in PDF
  • Title: “Dynamic Task Distribution in the Grid for BLAST”, UAB Graduate Student Research Days, Birmingham, AL, March 4, 2006. Presentation in PDF
  • Title: “Extensible Resource Broker for the Globus Toolkit”, GlobusWORLD 2005, Boston, MA, Feb. 7-11, 2005. Presentation in PDF
  • Title: “Resource Brokering in a Grid Computing Environment“, ACM Mid-Southeastern Conference, Gatlinburg, TN, Nov. 11-12, 2004.
  • Title: “Adaptive Web Based Resource Broker for the Grid”, Alabama Academy of Science at the University of Montevallo, Montevallo, AL, March 17-20, 2004.
  • Title: “Role of the Resource Broker in the Grid”, ACM Mid-Southeastern Conference , Gatlinburg , TN , Nov. 21-22, 2003.
[edit] Technical Reports
  • Afgan E., Bangalore P., “Application Specification Language (ASL) ”, Technical Report, UABCIS-TR-2007-0123-1, Collaborative Computing Laboratory, University of Alabama at Birmingham, Birmingham, AL, January 23, 2007.
  • Afgan E., Bangalore P., “Effective Utilization of the Grid with the Grid Application Deployment Environment (GADE) ”, Technical Report, UABCIS-TR-2005-0601-1, Collaborative Computing Laboratory, University of Alabama at Birmingham, Birmingham, AL, June 1, 2005. PDF

[edit] Other work

[edit] Presentations/talks
  • Title: “AspectJ and Parallel Computation”, As part of the course work for CS722 (Reflective and Adaptive Systems) at UAB, October 10, 2006. Presentation in PDF
[edit] Applications/projects
  • Implementations of a basic debugger using Javassist and OpenJava. Requires Javassist and OpenJava jar files (instructions on what is required and how to get everything working are included in my implementation files).

[edit] Teaching

[edit] Tutorials

  • Jump-start Web Services: Installing Tomcat, Installing AXIS, Testing Google Web Service PDF

[edit] Spring 2009

[edit] Fall 2008

[edit] Fall 2006

[edit] May 2006

[edit] Fall 2005

[edit] Fall 2004

  • Primary TA: CS 101 - Computing Fundamentals
  • Secondary TA: CS 350 - Automata and Formal Language Theory
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