ISMB 2018: BioinfoCoreWorkshop

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Workshop Overview

The bioinfo-core workshop is scheduled for Saturday, July 7, 2018, from 2:00-4:00 pm in Columbus EF at the Hyatt Regency in Chicago.

The bioinformatics core workshop is a workshop by practitioners and managers of Core Facilities for all members of core facilities, including scientists, engineers, analysts, operations and management staff. In this 15th year of bringing the Core community together at ISMB, we will explore in-depth three topics relevant to bioinformatics core facilities through lightning talks that broadly explore each area followed by small-group break out discussions with insights brought back to the full audience for further discussion and knowledge share.


  • Madelaine Gogol, Stowers Institute, United States
  • Hemant Kelkar, University of North Carolina, United States
  • Alastair Kerr, University of Edinburgh, United Kingdom
  • Brent Richter, Partners HealthCare of Massachusetts General and Brigham and Women’s Hospitals, United States
  • Alberto Riva, University of Florida, United States

Part A: Strategies for Hiring, Recruiting, and Interviewing new bioinformaticians

Methods to find, interview and hire highly successful staff and bioinformaticians for a core facility. Speakers will introduce experience and challenges including finding and hiring people, interview techniques and questions and best practices for recruiting candidates

Part B: Containerization, Clouds, and Workflows

Topics to be covered include cloud infrastructure recommendations and limitations, key datasets of value hosted in the cloud, containerization technology that works and workflow tool development and results.

Part C: When good experiments go bad: Negotiating experiment quality failures

A non-exhaustive survey of methods and successes in detecting failures and exploring guidelines for terminating bad projects.

Part D: Small group discussion

During this longer session, audience members will divide into groups based on their own interests. Groups will come up with their main take away points and bring them back to the main audience for knowledge sharing and for further discussion. Topics may include all previous presentation areas as well as other areas of interest to running or working within a bioinformatics core facility such as single cell analysis or long read analysis.

Time Title Authors
2:00 PM - 2:08 PM Bioinformatics Core Staffing Sara Grimm, NIEHS, United States
2:08 PM - 2:16 PM Characteristics of a highly successful candidate and how to find them Brent Richter, Partners HealthCare, United States
2:16 PM - 2:24 PM nf-core: community-driven best-practice Nextflow pipelines Alexander Peltzer, Quantitative Biology Center, Tübingen, Germany
2:24 PM - 2:32 PM Data Science in the 21st Century: Streaming Public Data into Containerized Workflows Ben Busby, NCBI, United States
2:32 PM - 2:40 PM Shesmu - An analysis orchestration system designed for FAIR standards and the GA4GH cloud ecosystem Lars Jorgensen, OICR, Canada
2:40 PM - 2:48 PM A (Fire)Cloud-Based DNA Methylation Data Preprocessing and Quality Control Platform Divy Kangeyan, Harvard University, United States
2:48 PM - 2:56 PM Usability of Marginal Data Jyothi Thimmapuram, Purdue University, United States
2:56 PM - 3:04 PM Experimental Failures Krishna Karuturi, The Jackson Laboratory, United States
3:04 PM - 3:20 PM Small Group Discussions
3:20 PM - 4:00 PM Report to all present the insights obtained within the small group discussions