AWS partner event: HPC in Healthcare and Life Sciences

Ellexus CEO and founder Dr Rosemary Francis will be giving a joint presentation with the Sanger Institute at the upcoming Amazon Web Services conference for Healthcare and Life Sciences involved in HPC.

The talk is titled: ‘Accelerating cloud-based genomics pipelines through I/O profiling for analysis of over 3,000 whole genome pairs.’

Rosemary will present alongside Keiran Raine, Principal Bioinformatician in the The Cancer, Ageing and Somatic Mutation Group at The Sanger Institute Wellcome Trust.

The talk

The cgpbox project encapsulates the core Cancer Genome Project analysis pipeline in an easy to use Docker image for cloud deployment. This is primarily for use within the PanProstate Project, which aims to analyse more than 3,000 whole genome pairs.

To begin, Keiran will outline the work being undertaken at The Sanger Institute to optimise and containerise the pipeline for collaboration and easy deployment in the cloud. Rosemary will then present the results of profiling the I/O patterns with tools from Ellexus when running the pipeline on AWS. She will show in detail how this was used to shape the choice of storage architecture in the cloud.

The presenters

Keiran’s work is primarily focused on development and coordination of infrastructure to support the scientific staff within the group. He has worked on on the development of laboratory management systems for high throughput capillary sequencing. More recently he has been involved in the ICGC/TCGA PanCancer Analysis of Whole Genomes projects’ technical working group, and subsequently that of ICGC PanProstate and ICGC ARGO.

Rosemary obtained her PhD in Computer Architecture from the Cambridge University Computer Lab after studying computer science with maths and bioinformatics. After working in the chip design industry, Rosemary founded Ellexus to help manage application dependencies and I/O patterns in scientific computing. Ellexus is now the I/O profiling company, working with HPC around the world such as ARM and The Sanger Institute.

The event

The AWS conference will be held on 5 December at the British Film Institute in London.

The event will include a keynote talk from Peter Froman, VP of Population Genomics at Illumina, on global data sharing of genomics information. Other talks will be given by AWS, Intel, Univa and Congenica, on subjects such as the challenges of processing whole genome sequencing and security in life sciences.