ISMB 2019: BioinfoCoreWorkshop

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Workshop Overview

The bioinfo-core workshop is scheduled for Monday, July 22, 2019, from 10:15 to 12:40 pm at the Congress Center in Basel.

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 16th year of bringing the Core community together at ISMB, we will explore topics relevant to bioinformatics core facilities through lightning talks and demos followed by small-group break out discussions with insights brought back to the full audience for further discussion and knowledge sharing.

Organizers:

  • 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: Technologies and Analytical Methods

Machine Learning and AI in a core.

Part B: Communication and Training

Communication and project management tools and training offered by cores.

Part C: Small group discussion

During this hour-long 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.

Part D: Pipeline Demos

Demos of nextflow and snakepipes.

Time Title Authors
10:15 AM - 10:22 AM Transitioning bioinformatics core to support biomedical AI/ML research - lessons learned Yang Fann, NIH, United States
10:22 AM - 10:30 AM
10:30 AM - 10:38 AM
10:38 AM - 10:42 AM
10:42 AM - 10:50 AM Improving project management and tracking with Asana and Toggl Sara Brin Rosenthal, UCSD, United States
10:50 AM - 10:58 AM Bioinformatics training (in the context of a core) Radhika Khetani, Harvard School of Public Health, United States
10:58 AM - 11:06 AM Development of bioinformatics workshop by a core facility Alberto Riva, University of Florida
11:06 AM - 11:40 AM Small Group Discussions
11:40 AM - 12:05 PM Small Group Reports
12:05 PM - 12:20 PM snakePipes, a set of pipelines for analysing common NGS datasets (ChIP-seq, ATAC-seq, RNA-seq, etc.) Devon Ryan, Max Planck Institute, Germany
12:20 PM - 12:35 PM nf-core - A community effort to collect a curated set of pipelines built using Nextflow (https://nf-co.re/). Harshil Patel, The Francis Crick Institute, United Kingdom