Workshops

Kubernetes Genomics Workshop

Graduate student travel funds available!  (Max reimbursement cap $700).

Workshop Attendee Limit: 20
Instructor: F. Alex Feltus, Professor Genetics and Biochemistry at Clemson University
Time and Date: Tuesday, May 19 from 1-6 pm
Target Audience:  Biologists (graduate students, post-docs, staff, faculty) or anyone in IT with basic understanding of Linux systems.
Prerequisites: Personal Laptop, Basic Linux Skills.  Interest in genomics research and/or cloud computing.

Workshop Objectives:  
This workshop will onboard users to an existing K8s cluster like Nautilus or Rodeo, teach them how to access real genomics datasets, and train participants how to build gene networks using the KINC workflow. Users will leave with the above knowledge as well as how to access the cluster they use after the workshop.

  1. Onboard users to real world Kubernetes (k8s) clusters.  This includes basic training on how to access and use a cluster after the workshop. Possible K8s systems include the Pacific Research Platform (PRP) Nautilus K8s Cluster, TACC Rodeo K8s Cluster, Cisco Container Platform (CCP) on-premise K8s clusters, and Google Cloud Platform (GCP).
  2. Train users how to push real human genomics datasets from the NIH Data Commons portal (e.g. tumor data from The Cancer Genome Atlas) to a K8s persistent storage system.
  3. Run a modern open source computational biology Nextflow workflows on real K8s systems.

 

Communication, Teamwork, and Leadership Training
for Cyberinfrastructure Professionals

Time: May 20, 2020, 1:00pm-5:00pm
Workshop Organizer & Facilitator: Dan Voss (Beaumont Health)
Email: daniel.r.voss@gmail.com
Registration: TBD

Description:  The use of cyberinfrastructure (CI) in research is becoming ubiquitous as the use of computing emerges in nearly every scientific domain. Out of necessity, many scientists have become CI-Users: individuals who need to employ advanced computation in their research, but who do not have broad expertise in CI. These CI-Users frequently request the support of CI-Professionals, who are experts in computational tools and methods. The assistance provided by CI-Professionals ranges from brief, routine interactions (e.g., providing accounts and access to CI resources and training) to in-depth, long-term collaborations (e.g., creating new computational tools or contributing to multidisciplinary research projects).

As the integration of CI in research continues, CI-Professionals find themselves tackling problems and consulting on projects that are increasingly complex and collaborative. In order to respond to these various requests, CI-Professionals need both the expertise to solve computational challenges and the professional skills to work effectively in teams with diverse backgrounds, experiences, and goals. This workshop provides professional skills training in communications, teamwork and leadership. This workshop will help prepare CI Professionals to collaborate effectively with CI Users to advance multidisciplinary, computationally-intensive research.

Format: The workshop will primarily consist of group activities designed to practice communication, teamwork and leadership skills. This workshop is part of NSF-funded training program.

Questions? Contact the workshop organizer for more information or go to colbrydi.github.io/CyberAmbassadors

IRODS Workshop

Time: Thursday, May 21 8:00-noon
Instructor: Jason Coposky
Executive Director, iRODS Consortium

iRODS is open source data management software used by research, commercial, and governmental organizations worldwide. iRODS is released as a production-level distribution aimed at deployment in mission critical environments. It virtualizes data storage resources, so users can take control of their data, regardless of where and on what device the data is stored. iRODS has been deployed in thousands of locations, across industries as diverse as oil and gas, life sciences, physical sciences, archives and records management, and media and entertainment.

This tutorial is designed to build a mental model of iRODS abstractions and how they can be applied in an automated data management context. This will include an executive overview of iRODS technology, its core competencies, policy, and capabilities and deployment patterns with a focus on existing production use cases. Attendees will begin by automating data ingest, metadata extraction, and data movement. Advanced topics will include policy composition and the relationship between iRODS policy and Capabilities.

Workshop agenda:

  • Introduction to iRODS
    • Core Competencies
    • Capabilities
    • Deployment Patterns
    • Use Cases
    • User Interfaces
  • Resource Composition
  • Policy Composition
  • Automated Ingest
  • Storage Tiering