UAB CIDay 2008

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Second Annual UAB Cyberinfrastructure (CI) Day

August 21, 2008 Cudworth Hall Auditorium


Cyberinfrastructure (CI) Advances from a national, regional, state and campus perspective.


8:00 - 9:00 Registration & Refreshments

Session 1 David L Shealy, Session chair

9:00 – 9:05 Welcome, Sheila Sanders, Vice President for Information Technology, UAB

9:05 – 10:00 caBIG, an Open Platform for Interoperable Biomedical Informatics Mark Adams, caBIG (ppt, pdf)

10:00 – 10:20 Coffee Break

Session 2 David L Shealy, Session chair

10:20 – 10:50 Supporting Transformative Research through Regional Cyberinfrastructure (CI), Gary Crane, SURA (ppt, pdf)

10:50 – 11:20 HPC and Network Offerings from the Alabama Supercomputer Authority, David Young, CSC (ppt, pdf)

11:20 – 11:50 Cyberinfrastructure for Research Teams, John-Paul Robinson, UAB HPC Services (ppt, pdf)

11:50 – noon Questions & Answers

Session 3

Noon – 1:30 Poster Session of Selected UAB Cyberinfrastructure Users, Cudworth Hall 140

  • Viral Bioinformatics Resource Facility, Elliott Lefkowitz (Dept of Microbiology, UAB)

and Chris Upton (University of Victoria, BC)

  • Dynamic BLAST – an Effective and Efficient BLAST Wrapper for the Grid, Enis Afgan (Student, Dept of CIS, UAB) and Purushotham Bangalore (Dept of CIS, UAB)
  • Web-Enabled Grid Authentication, John-Paul Robinson (HPCS, UAB), Jill Gemmill, Pravin Joshi, Purushotham Bangalore, YiYi Chen, Silbia Peechakara, Song Zhou, Prahalad Achutharo (pdf)
  • Research Computing Support and Infrastructure Services: Powering Statistical Genetics in the Grid Using GRIDway to Automate R-Based Workflows, John-Paul Robinson (HPCS, UAB) and Poornima Pochana (HPCS, UAB) (pdf)
  • Grid Tastes Better with gRAVI: Developing caGRID Services in the Cloud Using the Introduce Toolkit and gRAVI, John-Paul Robinson (HPCS, UAB) and Christie Bellah (HPCS, UAB) (pdf)
  • Powering Statistical Genetics with the Grid: Using GridWay to Automate R-based Workflows, John-Paul Robinson (HPCS, UAB) and Poornima Pochana (HPCS,UAB) (pdf)
  • Hole Patching in Unstructured Mesh using NURBS Surfaces, Amitesh Kumar (Student, ME), Dough Ross, Dr. Yasushi Ito, Dr. Alan Shih (Advisor, ME)
  • Geometry Design, Mesh Generation and Wind Field Simulation, Kevin Nord (Student, ME) and Dr. Alan Shih (Advisor, ME)
  • Validation of Turbulent Transition Models, Prapanj Ganeshan Radhamony (Student, ME), Kshitij D Neroorkar, Dr. Gary Cheng (Advisor, ME)
  • Geometry and Mesh Generation Template System for Unmanned Aerial Vehicles (UAVs), Blair Farley (Student, ME) and Dr. Alan Shih (Advisor, ME)

Bio-Sketches of Speakers

R. Mark Adams, Ph.D. Dr. Mark Adams has been in the field of bioinformatics for more than 15 years with extensive experience in the design and implementation of large-scale informatics systems, including regulated systems for use in clinical trials and the management of high-throughput laboratory processes. His theoretical work has encompassed abstract mathematical and computational analysis of molecular genetic and protein structure. Additionally, his scientific work has resulted in many patent applications, with several patents granted. As a biotechnology executive Dr. Adams has extensive experience in the strategic leadership and management of scientific and technical teams, having managed teams of up to 50 biologists and computer scientists designing and implementing high-throughput molecular biology and bioinformatics systems. In his role as vice-president of a public biotechnology company, Dr. Adams served on the executive committee, chartered with creating and executing a strategic plan for cancer pharmacogenomics. Dr. Adams has experience in the development and management of large government contracts and federal health research activities, with an emphasis on developing community focused collaborative research and informatics programs. He is currently the Booz Allen Program Manager of the National Cancer Institute cancer Biomedical Informatics Grid (caBIG) project. Dr. Adams is an active member of the field of bioinformatics where he speaks and publishes frequently. He is currently an editor of the Journal of Applied Analytics in Consulting, and a past editor of Briefings in Bioinformatics.

Gary Crane Gary Crane is the Director of Information Technology Initiatives for the Southeastern Universities Research Association (SURA). Gary is responsible for the development of SURA’s information technology projects and programs (, including SURAgrid, a regional grid development initiative that includes partnerships with IBM and Dell that are facilitating the acquisition of high performance computing systems by SURA members and a partnership with AT&T that is providing national academic regional optical network operators with access to low cost fiber optic facilities. Gary holds B.S.E.E. and M.B.A. degrees from the University of Rochester.

David Young, Ph.D. Dr. David Young provides software applications support to users of the Alabama Supercomputer Center. He has a Ph.D. in Chemistry from Michigan State University as well as degrees in Computational Mathematics and Business. Dr. Young's first book "Computational Chemistry; A Practical Guide for Applying Techniques to Real World Problems" has been a best seller in its field. His second book titled "Computational Drug Design; Things That All Drug Designers Should Know" is expected to be published late in 2008.

John-Paul Robinson John-Paul Robinson is a grid systems architect deeply engaged in the development of UAB and regional research Cyberinfrastructure. His is currently involved in the development of HPC resources for UABgrid, applications support for caBIG, and is serving as co-Chair of the SURAgrid Governance Committee. He has broad experience in systems integration projects for the academic and medical environments over the past 15 years. John-Paul holds a B.S. degree in Computer Science from Jacksonville State University.

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