Teaching Bioinformatics Data Analysis Using Cloud Computing Technology

Genome and transcriptome sequencing have become commonplace in labs all over the world. As next generation sequencing technologies emerge, evolve, and become more affordable, researchers need to be abreast of new methodologies and tools to efficiently analyze vast amounts of data generated by these sequencing platforms.

As part of the outreach activities of the NSF-funded Plant Genome Research Resource project targeted towards curating the Medicago truncatula genome, the JCVI Plant Genomics group has been involved in organizing an annual week-long Plant Bioinformatics Workshop (started in 2009, concluded in 2014), open to researchers within and outside the USA.

The workshop covers a wide variety of topics, starting off with the basics of command-line unix for bioinformatics, and progressing on to the bioinformatics processes and analyses used to sequence, assemble and annotate a eukaryotic genome, using Medicago truncatula as a use case example. Guest instructors are invited to present on domain specific topics such as repeat analysis, small RNAs, comparative genomics, etc.

For the hands-on parts of the workshop, in-person participants (limited to 20) utilized JCVI computational resources to perform all the data analysis. Remote attendee presence was managed by WebEx conferencing, allowing for interactive audience participation. Compute resources for these participants was allocated on the Amazon Elastic Cloud Compute (EC2) infrastructure.

All workshop materials are accessible to the public via a virtual machine (VM) image hosted on the iPlant Atmosphere cloud computing environment (https://atmo.iplantcollaborative.org/application/images/899) along with the presentations and handouts on Google Drive (http://j.mp/jcvi-bioinfo-workshop). Interested users can spawn an instance of the VM image and work through the exercises at their own pace.