SIH Data Bonanza at Westmead

The SIH Data Bonanza is a 2-day event that includes a series of data-intensive training workshops, Hacky Hour, and a showcase of Analytics in Healthcare. Join us and connect with fellow heath data savvy researchers. This event is hosted by the Sydney Informatics Hub, a Core Research Facility of the University of Sydney.

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Image courtesy of https://thepulse.org.au/

Free registration

This event is completely free and we welcome all staff and students from the University of Sydney to attend the SIH Data Bonanza. Registration is only required if you would like to attend our workshops. Registration links and course descriptions are available below. We encourage everyone to attend.

Time and Date

Monday 25th March, 9:00am - 5:00pm
Stream 1 - Intro to Artemis HPC and Genomics on HPC
Stream 2 - REDCap survey data capture, design and analysis
Event - SIH Hacky Hour

Tuesday 26th March, 9:00am - 5:00pm
Stream 3 - Transcriptomics in R
Event - SIH Data Analytics Showcase and Networking

Location

Westmead Education and Conference Centre (WECC)
Level 1, Education Block, Westmead Hospital
Cnr Hawkesbury Road and Darcy Road
Westmead NSW 2145

Workshops will be in various rooms on level 1 of WECC. Check the course info for the room information.

Map of level 1 WECC

Live stream:

We highly recommend you attend in person for the hands-on workshops however Zoom live streaming will be available. Details will be posted closer to the event. Please note some sessions may not be streamed due to proprietary and/or embargoed material.

Program

Monday 25th March Stream 1 Stream 2
9:00 – 10:30 am Intro to Artemis, HPC* Register
10:45 – 12:15 pm Genomics on Artemis, HPC* Register
1:00 pm – 2:30 pm Genomics on Artemis, HPC (cont.)* RedCap Surveys Register
2:45 pm – 4:15 pm Genomics on Artemis, HPC (cont.)* Survey Design Register
4:15 pm – 5 pm Hacky Hour Info
Tuesday 26th March Stream 3
9:00 – 3:15 pm Transcriptomics in R* Register
3:15 – 4:15 pm Seminar: Ingenuity Pathway Analysis and Analysis Match Register
4:15pm – 5:00 pm SIH Data and Analytics Showcase and Networking WECC L1.01 Case Study

OWN LAPTOP REQUIRED for all courses. Please contact us at sih.training@sydney.edu.au if this will be a problem.

* Please note that there are prerequisites for these courses. For the Intro to Artemis and Genomics on Artemis course, you will need to have completed an Intro to Unix course (and/or the Intro to Artemis course, which is available in the morning). For the Transcriptomics course, you will need to have completed an Intro to R/R for Reproducible Scientific Analysis course. These courses will be presented by Intersect at Westmead on the following dates:

Prerequisite courses

Intro to Unix Shell and Command Line Basics
OWN LAPTOP REQUIRED
Date: Thursday 14th March
Time: 9:30 am - 12:30 pm
Location: WECC Flexible Teaching Room 3
Click here for more info and to register for Intro to Unix.

R for Reproducible Scientific Analysis
OWN LAPTOP REQUIRED
Date: Friday 22nd March
Time: 9:30 am - 4:30 pm
Location: WECC Flexible Teaching Room 4
Click here for more info and to register for R for Reproducible Scientific Analysis.

Course Descriptions

Introduction to Artemis High Performance Computing (HPC)
Trainers: Nathaniel Butterworth, Tracy Chew, Rosemarie Sadsad
Learn about the University of Sydney’s HPC ‘Artemis’, including directory structure, software, and how to submit and monitor compute jobs using the PBS Pro scheduling software. Artemis is available at no cost to University of Sydney staff and students.

Genomics on HPC
Trainers: Tracy Chew, Rosemarie Sadsad, Darya Vanichkina
The Genomics course covering DNA sequencing analysis on Artemis aims to introduce users to running a common bioinformatics workflow on a high-performance computing cluster. Users will be introduced to the concepts of quality checking and control, reference mapping and variant calling (SNPs, Indels, and structural variants) using PBS scripts. We will work through a case study for a rare disease in humans. We will familiarize users with standard file types used in genomics and we will discuss some of the considerations that should be taken when customising pipelines to their specific analyses.

Transcriptomics in R
Trainers: Darya Vanichkina, Tracy Chew, Rosemarie Sadsad
The purpose of this workshop will be to gain practical experience in carrying out a complete analysis of human transcriptomic data. Students will learn how to map short read 100 nt paired end Illumina sequencing data to a reference genome and transcriptome and carry out quality control, differential gene expression and pathway analysis using the University’s Artemis HPC cluster and the R programming language. Previous experience with R and Unix is desirable. The workshop will provide example code for running all of the analyses.

Ingenuity Pathway Analysis and Analysis Match
Speaker: Stuart Tugendreich, PhD - Director and GPM, IPA from Redwood City, CA, USA
In this seminar, you will discover how Ingenuity Pathway Analysis (IPA) and Analysis Match - which combines the power of IPA with > 50,000 datasets processed from public sources using OmicSoft® Array Suite - can transform your research. Together, we will walk you through a case study on how you can use IPA and Analysis Match to understand biological mechanisms from your data and generate insights, including:

  • Analysing responder gene expression signatures to pinpoint significant genes and pathway
  • Comparing this analysis across a repository of processed datasets from OmicSoft Lands
  • Visualising a specific gene or genes of interest in DiseaseLand®

REDCap Surveys
Trainers: Daniele Vicari, Olya Ryjenko
Research Electronic Data Capture (REDCap) is a secure web-based database application maintained by the University of Sydney. It is ideal for collecting and managing participant data and administering online surveys, with features supporting longitudinal data collection, complex team workflows and exports to a range of statistical analysis programs. In this training session, we will cover:

  • How to build a simple data entry/survey project
  • How to choose the appropriate fileds for you data collection
  • How to collect online surveys

Survey Design
Trainer: Chris Howden, Jim Matthews
Chris has been designing and analysing surveys in the Market and Social Research Industry since 2004. This workshop is full of practical tips and guidelines on how to design, field and analyse surveys. Some of the topics considered will be; how to design a survey, line vs discrete scales, the effect of colour, optimal discrete/LIKERT scales, pros and cons of common analyses (e.g. linear and logistic regression) and optimal ways to export data.

SIH Data Analytics Showcase
Presenter: Joanna Aldridge
A brief introduction to the Sydney Informatics Hub followed by a showcase of collaborative projects between the Sydney Informatics Hub and Health partners in Analytics in Healthcare .