Researchers
The expertise and resources of our multidisciplinary team enable the evaluation of existing bioinformatics tools, development of bioKepler components and distributed execution patterns, and the deployment of developed modules in diverse environments. In addition, through jointly developed prototype usecases, targeted educational components and training sessions, our team demonstrates the use of bioKepler to the scientific community.
bioKepler team members have more than ten years of experience in research and development of scientific analysis software to production and working with scientists from a variety of scientific disciplines. Similarly, Co-PI Dr. Li and scientific advisors in this proposal have first-hand development and usage experience with a large set of bioinformatics tools and software.
The collaboration between the team members, engineering of bioActors, other bioKepler modules and related infrastructure will progress side-by-side with in-depth evaluation of bioinformatics tools and development of example usecases. Our engineering process will also include development of outreach components along with the preparation of educational materials and workshops. In addition, the interdisciplinary nature of the team provides leverage of various current NSF and other projects.
Leadership | |
Ilkay Altintas, Ph.D. Ilkay Altintas is the Director for the Scientific Workflow Automation Technologies Lab at the San Diego Supercomputer Center, UCSD where she also is the Deputy Coordinator for Research. She currently works on different aspects of scientific workflows in collaboration with various cross-disciplinary NSF, DOE and Moore Foundation projects. She is a co-initiator of and an active contributor to the open-source Kepler Scientific Workflow System, and the co-author of publications related to eScience at the intersection of scientific workflows, provenance, distributed computing, bioinformatics, observatory systems, conceptual data querying, and software modeling. |
Weizhong Li, Ph.D. Weizhong Li has a background in computational biology and bioinformatics. His research focuses on developing computational methods for sequence, genomic and metagenomic data analysis. Dr. Li’s role in the bioKepler project is to evaluate and provide a comprehensive list of bioinformatics tools for implementation as bioActors in bioKepler. |
Developers | |
Jianwu Wang, Ph.D. Jianwu Wang has a background in computer software and theory. His research interests include scientific workflow, distributed computing and data-intensive computing. Dr. Wang’s role in bioKepler project is to conduct research and development of distributed architecture and components for bioKepler, and their application in bioinformatics. |
Daniel Crawl, Ph.D. Daniel Crawl is the lead architect for the overall integration of distributed data parallel (DDP) execution patterns and the Kepler Scientific Workflow System. He conducts research and development of execution patterns, bioActors, and distributed directors. |
Shulei Sun Shulei Sun has a background in bioinformatics, biology, and computational biology. Her research focuses on metagenomic and genomic data analysis. Her role in bioKepler project is to provide bioinformatic support as well as to evaluate tools. |
Sitao Wu, Ph.D. Sitao Wu has a background in electric engineering. His research interests include protein structure prediction, metagenomics and genomics. Dr. Wu’s role in bioKepler project is to provide overall bioinformatics support and implement backend components for individual bioActors. |
Scientific Advisors | |
Eric Allen, Ph.D. Eric Allen researches the use of environmentally-derived genome sequence information to explore the genetic potential, ecology, and evolution of marine microbial populations. The nature of his work relies equally upon field-based collections, bioinformatics (genome assembly, annotation, and comparative analyses) and the tools of molecular ecology and genetics. |
Sheila Podell, Ph.D. Sheila Podell has an interdisciplinary background in cell and molecular biology, analytical biochemistry, and bioinformatics computer programming, including the development of new tools and algorithms for genomic and metagenomic analysis. Based on her experience as a bioinformatics coach and collaborator for wet-lab experimental biologists, her role in bioKepler is to provide real-life use case examples for workflow development. |