Workshops and Tutorials

Workshops & Tutorials – Titles, Organizers and Summary
InCoB 2016 Singapore, 21-23 September 2016

An introduction to transcriptomics and cancer genomics: tools, databases and workflows

21st September 2016 (Wednesday), 1700 – 1900 hrs

Jonathan GOKE (Genome Institute of Singapore, A*STAR, Singapore)
Anders Jacobsen SKANDERUP (Genome Institute of Singapore, A*STAR, Singapore)
Yu GUO (Genome Institute of Singapore, A*STAR, Singapore)

Summary

High-throughput next-generation sequencing (NGS) data has become an integral component in most fields of biology research. In this workshop we will give two distinct guided tours on how to effectively leverage NGS data for transcriptomics and cancer genomics research, respectively. In the first part, we will present a research case study on the analysis of differential expression and alternative splicing using RNA-Seq data. We will use this case study to introduce fundamental concepts of experimental design for transcriptomics studies (differential expression, splicing, single cell gene expression), and to give an overview of commonly used software, tools, and workflows. In the second part, we will introduce and motivate the use of whole genome sequencing in cancer research. We will present efficient and robust computational algorithms and workflows to identify cancer mutations and cancer genes from hundreds of tumor genomes. Specifically, we will highlight common sources of errors in tumor DNA data and how we can leverage statistical models to deal with noise in the data.

Prerequisites

  • Prior knowledge in computational biology recommended. No additional equipment required.

Garuda Platform: Re-imagining connectivity in biology and medicine

21st September 2016 (Wednesday), 1700 – 1900 hrs

Vipul Gupta, Scientist, The Systems Biology Institute, Tokyo.
Nikos Tsorman, Technical Lead, The Systems Biology Institute, Tokyo.

Summary

With the explosion of data in different dimensions of drug discovery, biomedicine and healthcare, a key challenge is the ability to connect the disparate data sources, discover the right analytics tools for a specific analysis and navigate through inter-operable analytics to provide executable insights. Garuda is an open, community-driven, platform that provides a framework to discover, connect & navigate through different applications on devices as well as in the cloud. Through this workshop, we will provide an overview of the Garuda platform, the alliance eco-system and a brief demonstration of the platform in action together with its various components. The demonstration is specifically designed to cater to an array of audience from different backgrounds with a goal towards re-imagining connectivity and integrated analytics in biomedical research, healthcare and beyond.

Please go to http://bit.ly/garudaInCoB2016 for updates on the workshop.

Agenda

  • A short introduction to Garuda- 20mins + 5 min QA. (Vipul Gupta)
  • Garuda in action: A Case Study- 20mins + 5 min QA.
  • Break – 10 mins.
  • Garuda hands-on – 30 mins (Vipul/Nikos)
  • Open discussions – 30mins.

Decoding causative mutations: finding SNPs in a sea of sequenced data

21st September 2016 (Wednesday), 1700 – 1900 hrs

Lloyd Low (Centre for Bioinformatics, Perdana University, Malaysia)
Kenneth Ban (Yong Loo Lin School of Medicine, National University of Singapore, Singapore)

Summary

The next generation sequencing (NGS) technology revolution took off around 2005 and ended Sanger sequencing dominance in the marketplace. The revolution is still ongoing and there has been a rapid decline in the cost of sequencing since the introduction of NGS technologies. With sequencing getting cheaper, personal genomics is no longer just a dream. If you have always wondered how it is possible to search massive amount of sequenced data to find and prioritize disease-causing variants then this workshop is for you.

Prerequisites

  • An introductory knowledge of genetics and familiarity with Linux.
  • Bring your own laptop for the practical session.
  • Suitable for those working with NGS data.

Exploring idiosyncratic analytical issues in proteomics data via networks

21st September 2016 (Wednesday), 1700 – 1900 hrs

Wilson Wen Bin Goh (Tianjin University, National University of Singapore)

This workshop has been CANCELLED.