IPlant Collaborative

Ali Akoglu

Associate Professor, Electrical and Computer Engineering
Associate Professor, BIO5 Institute
Department Affiliations
Contact
(520) 621-2434

Work Summary

Ali Akoglu is an Associate Professor in the Department of Electrical and Computer Engineering and the BIO5 Institute at the University of Arizona. He received his Ph.D. degree in Computer Science from the Arizona State University in 2005. He is the site-director of the National Science Foundation (NSF), Industry-University Cooperative Research Center on Cloud and Autonomic Computing regarding the design and development of architectures for achieving self-management capabilities across the layers of cloud computing systems. Dr. Akoglu is an expert in high performance scientific computing and parallel computing with a primary focus on restructuring computationally challenging algorithms for achieving high performance on parallel hardware architectures. His research projects have been funded by the National Science Foundation, Defense Advanced Research Projects Agency, Office of Naval Research, US Air Force, NASA Jet Propulsion Laboratories, Army Battle Command Battle Laboratory, and industry partners such as Nvidia and Raytheon.

Research Interest

Ali Akoglu is an Associate Professor in the Department of Electrical and Computer Engineering and the BIO5 Institute at the University of Arizona. He received his Ph.D. degree in Computer Science from the Arizona State University in 2005. He is the site-director of the National Science Foundation (NSF), Industry-University Cooperative Research Center on Cloud and Autonomic Computing regarding the design and development of architectures for achieving self-management capabilities across the layers of cloud computing systems. Dr. Akoglu is an expert in high performance scientific computing and parallel computing with a primary focus on restructuring computationally challenging algorithms for achieving high performance on field programmable gate array (FPGA) and graphics processing unit (GPU) hardware architectures. Recently he has contributed to the scientific computing domain with: 1) design and development of novel computational methods on T-Cell Receptor (TCR) synthesis for studying the immune systems of complex organisms, which led to reducing the time scale of determining all possible ways (several trillions of sequences) in which proteins can be encoded from 62 months scale to 19 hours on a single GPU; 2) investigation of electrophysiological behavior of the heart by coupling tissue and cell models in a such a way that through physics aware programming (PAP) paradigm 3D heart simulations become parallelizable without sacrificing model accuracy, which led to reducing the time scale of such simulations from 453 hours to 1.66 seconds with a simulation accuracy of 99.9% Dr. Akoglu has been involved in many crosscutting collaborative projects with the goal of solving the challenges of bridging the gap between the domain scientist, programming environment and emerging highly-parallel hardware architectures. His research projects have been funded by the National Science Foundation, Defense Advanced Research Projects Agency, Office of Naval Research, US Air Force, NASA Jet Propulsion Laboratories, Army Battle Command Battle Laboratory, and industry partners such as Nvidia and Raytheon.

Nirav C Merchant

Director, Cyber Innovation
Director, Data Science Institute
Interim Director, Biomedical Informatics and Biostatistics Center
Primary Department
Contact
(520) 621-8379

Research Interest

Over the last two decades my work has focused on developing computational platforms and enabling technologies, primarily directed towards improving research productivity and collaboration for interdisciplinary teams and virtual organizations. The key thrust areas for my work encompass life cycle management for: 1. High throughput and automated bio sample processing systems 2. Highly scalable data and metadata management systems 3. High throughput and performance computing systemsMy recent work has been directed towards supporting pervasive computing needs for mHealth (mobile health) initiatives and health interventions, with focus on developing study management platforms that leverage cloud based telephony, messaging and video in conjunction with wearable’s and sensors.Platforms and tools developed by team are utilized in: 1. Managing samples and data for Clinically certified (CAP/CLIA) NGS pipelines 2. Large scale genotyping (million+ samples) with robotic automation 3. National Cyberinfrastructure iPlant; facilitates researchers to effectively manage their data, computation and collaborations using a cohesive computational platform 4. Health interventions and patient monitoring I firmly believe that measured adoption of emerging computational technologies and methods are essential for life scientist to successfully operate at the scale and complexity of data they are constantly encountering. This can only happen if there is continuing education and practical training focused around the use of Cyberinfrastructure and computational thinking. I have developed and taught workshops, graduate and undergraduate project based learning courses with emphasis on these topicsMy team (Bio Computing Facility) engages with the campus community at various levels ranging from multi- institutional collaborative projects, graduate and undergraduate courses for credit and special topic seminars and workshops. With emphasis on enabling digital discoveries for the life sciences.

Eric H Lyons

Associate Professor, Plant Science
Associate Professor, Agricultural-Biosystems Engineering
Advisor, CALS' Office of the Assoc Dean - Research for Cyber Initiatives in Agricultural / Life - Vet Science
Associate Professor, Genetics - GIDP
Associate Professor, BIO5 Institute
Primary Department
Department Affiliations
Contact
(520) 626-5070

Research Interest

Eric Lyons, PhD is an assistant professor at the University of Arizona School of Plant Sciences. Dr. Lyons is internationally known for his work in understanding the evolution, structure, and dynamics of genomes. Core to his research activities is the development of software systems for managing and analyzing genomic data and cyberinfrastructure for the life sciences.Dr. Lyons has published over 30 original research papers and 5 book chapters, many in collaboration with investigators from around the world. He is a frequent presenter at national and international meetings, and has been invited to teach workshops on the analysis of genomic data to plant, vertebrate, invertebrate, microbe, and health researchers.Prior to joining the faculty in the School of Plant Sciences, Dr. Lyons worked with the iPlant Collaborative developing cyberinfrastructure, and managing its scientific activities. In addition, he spent five years working in industry at biotech, pharmaceutical, and software companies. Dr. Lyons’ core software system for managing and analyzing genomic data is called CoGe, and is available for use at http://genomevolution.org