Teaching

Cyber Carpentry: Data Life-Cycle Training with the Datanet Federation Consortium

Published in North Carolina, Chappel Hill, 2018

This two-week workshop provided doctoral students and post-doctoral researchers with an overview of best data management practices, data science tools, and concrete steps and methods for performing end-to-end data intensive computing and data life-cycle management. Training will prepare participant to facilitate and promote reproducible science and data reuse. As part of this workshop, my role as one of the lead instructor is to teach the basic concepts of reproducible research using software containers. The tutorial for running Cybercarpentry workshop's containers can be found here

CyVerse AstroContainers Workshop

Published in CyVerse, 2018

Container technologies such as Docker and Singularity let scientists easily share, reuse, and scale all types of computational analyses. The CyVerse AstroContainers Workshop series are two-day hands-on workshops designed for astronomers to learn how to create, use, and deploy containers across a variety of compute systems (your computer, CyVerse, local HPC, etc). Our inaugural workshop will focus on Docker and Singularity. We will use a blend of practical theories and hands-on exercises for small groups to deploy tools and workflows they bring to the workshop. As part of this workshop, my role as one of the lead instructor is to teach the basic concepts of reproducible research using software containers here

CyVerse Container Camp: Container Technology for Scientific Research

Published in CyVerse, 2018

CyVerse Container Camp is an intense three-day hands-on workshop to learn how to create, use, and deploy containers across a variety of compute systems (your computer, local HPC, cloud compute environments, and national resources). We will use blend of practical theory and hands-on exercises where small groups deploy tools and workflows they bring to the workshop. Outcomes: Theory and application of container technology, how to containerize an application, how to use other containerized applications, how to build/deploy containerized workflows and how to scale out your computation: From Laptop to Cloud to HPC. As part of this workshop, my role as one of the lead instructor is to teach the basic concepts of reproducible research using software containers here

WQ-MAKER: A Flexible, scalable genome annotation pipeline on Jetstream cloud

Published in CyVerse, 2017

In this webinar, I presented WQ-MAKER, a customized version of MAKER with a Work Queue-based distributed computing framework designed to run MAKER on multiple virtual machines on the Jetstream cloud. We'll show how to run WQ-MAKER on a test dataset starting from setting up a Jetstream account along with some of the accessory scripts (Ansible playbooks and custom scripts) and a few apps developed to manage the computation and progress. Performance numbers for various genomes annotated using WQ-MAKER will be discussed. The tutorial for this webinar is online at and a publication describing WQ-MAKER is here here.

Evolinc – Identification and Evolutionary Analysis of lncRNA

Published in CyVerse, 2016

In this webinar, I along with Andrew Nelson presented Evolinc, a two-part set of apps in the CyVerse Discovery Environment (DE). Evolinc-I is designed to make long non-coding RNA (lncRNA) identification easy and reproducible, regardless of the system. Evolinc-II compares such lncRNAs to determine whether they are conserved at the genomic or transcriptomic level in various species. This information is helpful in curating lncRNA populations and identifying promising candidates for functional analysis. The tutorial for running Evolinc can be found here and the paper describing the Evolinc can be found here