ISMB 2016: BioinfoCoreWorkshop

We are holding a Bioinfo-core workshop at the 2016 ISMB meeting in Orlando, Florida. We have been given a half-day workshop track slot in the program on Monday, July 11th from 2:00-4:30 PM.

Workshop Structure

The workshop is split into 4 sessions of ~30 mins each with a required break between the first and second half of the meeting (3-3:30).

• The first slot will have 2 15 minute talks on the topic of Big Data followed by a 30 minute panel discussion. After the break we will have 2 15 minute talks about Big Compute, followed by a 30 minute panel discussion.

Workshop topics

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.

Big data

Speaker: Yury Bukhman, Great Lakes Bioenergy Research Center Time: 2:00 pm – 2:15 pm

Presentation Overview:

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.

File:Yury.pdf

Speaker: Alberto Riva, University of Florida Time:2:15 pm – 2:30 pm

Presentation Overview

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.

File:Alberto.pdf

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.

Big Compute

Speaker: Sergi Sayols Puig, Institute of Molecular Biology Mainz Time: 3:30 pm – 3:45 pm

Presentation Overview 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.

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

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.

We will have a bioinfo-core dinner the night of the workshop, Monday, at 6:30 PM. The dinner will be at Garden Grove, a restaurant in the Swan Hotel.