Workshop 03 (WK03): Bioinfo-core Workshop
Attention Conference Presenters - please review the Speaker Information Page available here.
Monday, July 11, 2:00 pm – 4:30pm
Charlie Whittaker, The Koch Institute at MIT, Cambridge, United States
Jian-Liang (Jason) Li, Sanford Burnham Prebys Medical Discovery Institute, Orlando, United States
Madelaine Gogol, Stowers Institute, Kansas City, United States
The workshop will address "The practical experience of big data and big compute". Members of core facilities will share their experience and insights via presentation and panel discussion.
Speaker: Yury Bukhman, Great Lakes Bioenergy Research Center
Time: 2:00 pm – 2:15 pm
The Computational Biology Core of the Great Lakes Bioenergy Research Center supports mostly academic labs at the University of Wisconsin, Michigan State University and other universities. With a variety of experiment types, they are challenged to manage and analyze disparate data and metadata in a diverse academic environment. Details of these data challenges and solutions will be discussed.
Speaker: Alberto Riva, University of Florida
Time:2:15 pm – 2:30 pm
The Bioinformatics Core of the ICBR provides bioinformatics services to the large and diverse scientific community of the University of Florida. Routine handling of projects covering a vast spectrum of biological and biomedical research requires a flexible and powerful data infrastructure. Implementation details of a software development environment (Actor) for reliable, reusable, reproducible analysis pipelines will be discussed, as well as insights on managing big data projects in a core setting.
Speaker: Big Data Panel
Time: 2:30 pm – 3:00 pm
Moderator: Madelaine Gogol, Stowers Institute for Medical Research
Panel Speaker: Yury Bukhman, Great Lakes Bioenergy Research Center
Panel Speaker: Alberto Riva, University of Florida
Panel Speaker: Hua Li, Stowers Institute for Medical Research
Panel Speaker: Jyothi Thimmapuram, Purdue University
The presenters, panelists, and attendees will explore practical experience with “big data” as well as use of public datasets in a panel discussion. Topics may include accuracy of annotation, trust of data, raw versus processed, data validation, and QC.
Coffee Break (3:00-3:30 pm)
Speaker: Sergi Sayols Puig, Institute of Molecular Biology Mainz
Time: 3:30 pm – 3:45 pm
With a variety of computing infrastructures available, building robust, transferable pipelines can increase utilization of compute resources. NGS analysis pipelines implemented as docker containers and deployed on a variety of compute platforms – (cluster, supercomputer, or workstation) will be discussed.
Speaker: Jingzhi Zhu, The Koch Institute at MIT
Time: 3:45 pm – 4:00 pm
Experiences transitioning a Bioinformatics core from a local to a cloud-based compute solution will be discussed, including the motivation, performance, cost, and issues with deploying bioinformatics pipelines to Amazon EC2 instances.
Speaker: Big Compute Panel
Time: 4:00 pm – 4:30 pm
Moderator: Brent Richter, Partners HealthCare
Panel Speaker: Sergi Sayols Puig, Institute of Molecular Biology Mainz
Panel Speaker: Jingzhi Zhu, The Koch Institute at MIT
Panel Speaker: Sara Grimm, NIEHS
Panel Speaker: TBA
The presenters, panelists, and attendees will discuss how people manage to stay on top of compute requirements for their own sites in a panel discussion. Major hurdles to overcome and the compromises needed for success will be discussed. We may also touch on experiences with containers and portable computing.