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Workshop [clear filter]
Wednesday, June 2
 

9:00am CDT

Workshop: Doing Genomics in the Cloud: From Repository to Result (Session 1)
Computational genomics has become a core toolkit in the study of biological systems at the molecular level. To run genomics workflows, a researcher needs access to advanced computer systems including compute, storage, memory, and networks to move and mine huge genomics datasets. The Cloud provides scalable compute solutions to run workflows. In this workshop, we will demonstrate how one can create a compute cluster in the Cloud using Kubernetes and run containerized genomics workflows. The Cloud workflows will include pulling high-throughput DNA datasets from the NCBI-SRA data repository, performing reference genome mapping of SRA RNAseq datasets, and building a gene co-expression network.

Target audience: Undergrads, Grad students, Post-Docs, Faculty, IT professionals. This workshop is limited to 40 participants.

We recognize and thank the following companies that contributed resources to make this workshop possible: Praxis AI LLC, Cisco, and c-Light.

Speakers
avatar for Dr. F. Alex Feltus

Dr. F. Alex Feltus

Professor, Genetics and Biochemistry Department, Clemson University
Dr. F. Alex Feltus received a B.Sc. in Biochemistry from Auburn University in 1992, served two years in the Peace Corps in the Fiji Islands, and then completed advanced training in biomedical sciences at Vanderbilt and Emory.  He has performed research in artificial intelligence... Read More →
MK

Meenakshi Kaushik

Kubernetes and AI/ML, Cisco
CM

Cole McKnight

Cloud Architect, Clemson University


Wednesday June 2, 2021 9:00am - 12:00pm CDT
Workshop Room A

10:00am CDT

Workshop: Intermediate perfSONAR Tips and Tactics (Morning Sessions)
This interactive workshop will cover several intermediate level perfSONAR topics, including MaDDash setup and configuration, command line testing and troubleshooting, and automated provisioning with Ansible, along with Q&A time for each topic. Audience participation is encouraged!

The workshop is divided up into four sessions. A short break is planned between sessions with a one-hour break for lunch.

Wednesday, June 2, 10:00 AM
Session 1: Command line testing and troubleshooting (45 minutes, including Q&A)
Session 2: MaDDash setup and configuration (45 minutes, including Q&A)
Wednesday, June 2, 1:00 PM
Session 3: PWA and testing frequency? (45 minutes, including Q&A)
Session 4: Ansible provisioning (75 minutes, including Q&A)

Speakers
avatar for Doug Southworth

Doug Southworth

Network Systems Analyst, International Networks @ Indiana University
Doug Southworth joined the International Networks @ Indiana University team in 2018 and is primarily responsible for network performance analysis and troubleshooting of their three NSF funded 100Gb international Research and Education links. Southworth is also involved in the development... Read More →



Wednesday June 2, 2021 10:00am - 12:00pm CDT
Workshop Room B

1:00pm CDT

Workshop: Intermediate perfSONAR Tips and Tactics (Afternoon Sessions)
This interactive workshop will cover several intermediate level perfSONAR topics, including MaDDash setup and configuration, command line testing and troubleshooting, and automated provisioning with Ansible, along with Q&A time for each topic. Audience participation is encouraged!

The workshop is divided up into four sessions. A short break is planned between sessions with a one-hour break for lunch.

Wednesday, June 2, 10:00 AM
Session 1: Command line testing and troubleshooting (45 minutes, including Q&A)
Session 2: MaDDash setup and configuration (45 minutes, including Q&A)
Wednesday, June 2, 1:00 PM
Session 3: PWA and testing frequency? (45 minutes, including Q&A)
Session 4: Ansible provisioning (75 minutes, including Q&A)

Speakers
avatar for Doug Southworth

Doug Southworth

Network Systems Analyst, International Networks @ Indiana University
Doug Southworth joined the International Networks @ Indiana University team in 2018 and is primarily responsible for network performance analysis and troubleshooting of their three NSF funded 100Gb international Research and Education links. Southworth is also involved in the development... Read More →



Wednesday June 2, 2021 1:00pm - 3:15pm CDT
Workshop Room B

1:00pm CDT

Workshop: Doing Genomics in the Cloud: From Repository to Result (Session 2)
Computational genomics has become a core toolkit in the study of biological systems at the molecular level. To run genomics workflows, a researcher needs access to advanced computer systems including compute, storage, memory, and networks to move and mine huge genomics datasets. The Cloud provides scalable compute solutions to run workflows. In this workshop, we will demonstrate how one can create a compute cluster in the Cloud using Kubernetes and run containerized genomics workflows. The Cloud workflows will include pulling high-throughput DNA datasets from the NCBI-SRA data repository, performing reference genome mapping of SRA RNAseq datasets, and building a gene co-expression network.

Target audience: Undergrads, Grad students, Post-Docs, Faculty, IT professionals. This workshop is limited to 40 participants.

We recognize and thank the following companies that contributed resources to make this workshop possible: Praxis AI LLC, Cisco, and c-Light.

Speakers
avatar for Dr. F. Alex Feltus

Dr. F. Alex Feltus

Professor, Genetics and Biochemistry Department, Clemson University
Dr. F. Alex Feltus received a B.Sc. in Biochemistry from Auburn University in 1992, served two years in the Peace Corps in the Fiji Islands, and then completed advanced training in biomedical sciences at Vanderbilt and Emory.  He has performed research in artificial intelligence... Read More →
MK

Meenakshi Kaushik

Kubernetes and AI/ML, Cisco
CM

Cole McKnight

Cloud Architect, Clemson University


Wednesday June 2, 2021 1:00pm - 4:00pm CDT
Workshop Room A
 
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