SIH Training

2018 Upcoming Events and Training Sessions

A number of training sessions have been scheduled - click the links to register your attendance

Date Training Course Location Signup
15 Nov Surveys in REDCap Camperdown Info Register
20 Nov Data Wrangling Drop-in Session Camperdown Info
21 Nov Github for beginners School of Geoscience 2-5pm Register
27 Nov Data Wrangling Drop-in Session Camperdown Info
28 Nov Intermediate-Advanced Python Camperdown Info Register
28 Nov Hacky Hour Brain and Mind Centre Info
29 Nov Advanced REDCap Camperdown Info Register
29 Nov Matlab on Artemis HPC Camperdown Info Register
29 Nov Intermediate HPC Camperdown Info Register
4 Dec Data Wrangling Drop-in Session Camperdown Info
5 Dec Advanced Github School of Geoscience details to come
10 - 11 Dec Data Carpentry Geospatial Data Analysis with R Camperdown Info Register
11 Dec Data Wrangling Drop-in Session Camperdown Info
18 Dec Data Wrangling Drop-in Session Camperdown Info
13 Feb Data visualisation for exploration and communication Camperdown Info/Register

NB Course dates may change when registration links are posted. For more information about any courses please email sih.training@sydney.edu.au

SIH training courses are free and available to all researchers at the University of Sydney.

For training notices and updates, subscribe to the computing training mailing list!

Expressions of Interest (EOI) for future training

We are calling for expressions of interest for future training programs. If you or your research group would like training in something that we do not currently offer, please take the time to complete this form: Future Training Programs

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Course Descriptions

The Sydney Informatics Hub run a range of courses to enable researchers to analyse their data using University Enterprise digital tools and on the University’s research computing infrastructure.

Course slides can be found here.

Research Computing

Bioinformatics

Research Data Management

Programming and Software

These courses are hosted by INTERSECT, Pawsey and NVIDIA.

Intersect

Pawsey supercomputing courses

Nvidia

  • Introduction to GPU programming - Cuda and OpenACC
  • Deep learning

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Research Computing Courses

Introduction to the Artemis HPC

Synopsis: Learn about the University of Sydney’s High Performance Computer (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.

Target audience: Students and staff who would like to learn how to run compute jobs on Artemis HPC. Participants must have a valid USyd unikey.

Essential pre-requisites: Competency on the Unix/Linux command line. If you are interested in learning HPC but have no Unix/Linux command-line skills, you MUST first take an ‘Introduction to Unix/Linux’ course. OWN LAPTOP REQUIRED.

Follow-on courses: This course is designed as a 2-part session, with ‘Introduction to the Artemis HPC’ in the morning and ‘Data transfer and RDS for HPC’ in the afternoon. It is recommended to register for both, however you may choose to take these courses on separate days as suits your needs. ‘Intermediate HPC (Automation)’ is another recommended course to follow up with.

Slides for SIH computing courses can be viewed here.

Data transfer and RDS for HPC

Synopsis: Learn how to transfer data between your local computer, an external source, the Research Data Store (RDS) and the Artemis HPC. Learn how to back up Artemis HPC output onto the RDS.

Target audience: Students and staff who would like to learn how to move data to and from the Artemis HPC and how to backup HPC output with RDS. Participants must have a valid USyd unikey.

Essential pre-requisites: Competency on the Unix/Linux command line. If you are interested in learning HPC but have no Unix/Linux command-line skills, you MUST first take an ‘Introduction to Unix/Linux’ course. OWN LAPTOP REQUIRED.

Follow-on courses: This course is designed as a 2-part session, with ‘Introduction to the Artemis HPC’ in the morning and ‘Data transfer and RDS for HPC’ in the afternoon. It is recommended to register for both, however you may choose to take these courses on separate days as suits your needs. ‘Intermediate HPC (Automation)’ is another recommended course to follow up with.

Slides for SIH computing courses can be viewed here.

Intermediate HPC: automating analysis with job arrays on Artemis

Synopsis: This course is aimed at researchers who currently use the University of Sydney’s High Performance Computing (HPC) cluster ‘Artemis’ and would like to learn how to automate multiple-run analyses with job arrays and do simple bash scripting on Artemis. The live training consists of four hours of instruction and practical exercises. Simple job arrays using a single-integer parameter as well as more complex analyses reading inputs from a configuration file will be demonstrated.

Target audience: Students and staff who are already using the Artemis HPC and who would like to learn how to use job arrays and bash scripting to automate the submission of multiple jobs simultaneously.

Essential pre-requisites: Competency on the Unix/Linux command line and prior use of the Artemis HPC. You must have your own Artemis HPC account. If you are interested in this workshop but do not meet the pre-requisites, you MUST first take the ‘Introduction to Unix/Linux’ and ‘Introduction to the Artemis HPC’ courses. OWN LAPTOP REQUIRED.

Slides for SIH computing courses can be viewed here.

Artemis+MDCS: Running HPC Jobs from MATLAB

You must have MATLAB R2017a installed if you wish to complete the training examples. No other version of MATLAB will work with the version of the MDCS currently installed on Artemis.

Version R2017a can be downloaded here.

Synopsis: The University of Sydney’s Artemis HPC hosts a Matlab Distributed Computing Server - this allows users to take advantage of the compute power of Artemis from directly within the Matlab client installed on their local machines. Come and learn how to make use of this service.

Target audience: Students and staff who use MATLAB, and wish to run their codes on Artemis.

Essential pre-requisites: A basic understanding of Matlab is assumed. It is also highly recommended that you have taken the ‘Introduction to the Artemis HPC’ course, unless you already have experience using Artemis. These are scheduled regularly on campus.

Slides for SIH computing courses can be viewed here.

Bioinformatics courses

Introduction to DNASeq and RNASeq

This course is designed to introduce you to basic concepts in DNA and RNA sequencing analysis pipelines on Galaxy, a user-friendly web-based research cloud. In the DNA sequencing course, we will use DNA sequencing reads and learn how to perform quality checks, de novo assembly, annotate and call variants. In the RNA sequencing course, we will use RNA sequencing data to align, visualise and perform differential expression analysis.

Slides for SIH computing courses can be viewed here.

Introduction to bacterial genomics using Galaxy

Synopsis: This event is a free, half day introductory workshop on Bacterial Genomics using Galaxy provided by SIH, Intersect, and Melbourne Bioinformatics.

The Galaxy Platform is an open, web-based analysis and workflow platform designed for biologists to analyse their own data and can be used to run a variety of bioinformatics tools. Specifically, the training course will include: - How to use the Galaxy bioinformatics platform - Bacterial genome assembly and annotation - Bacterial reference mapping and variant calling - Galaxy workflows

The RDS Omics project is an RDS-funded flagship project to provide cloud-based data services and tools for Australian Life Science Researchers to combine, analyse and interpret genomic (DNA), transcriptomic (RNA), proteomic (proteins) and metabolomic (small molecules) data. The project is building the first Australian platform to allow 4 distinct ‘omics’ data types to be: - co-analysed and stored in one system; - managed through a common data management system; - able to have bioinformatics analysis performed on these data via a common interface - made accessible to biology researchers in Australia and internationally; - published to international repositories

Click this link to access the course training material.

Galaxy Australia Training Series

The Sydney Informatics Hub is a node of EMBL-ABR. EMBL-ABR is working with the Biosciences Data Enhanced Virtual Lab (DeVL) Galaxy Australia project to undertake a national training program. Four workshops will introduce Galaxy Australia capabilities to researchers, with demonstrations based around different themes. The training will be led by a Galaxy expert who is available online throughout the hands-on sessions, and facilitated locally by trained staff at participating EMBL-ABR Nodes. All workshops are free, but places are limited.

Currently, the workshops include:

  • Genome Assembly
  • Variant Detection
  • RNA sequencing analysis
  • Metagenomics

Please see the Sydney Informatics Hub training schedule above or the EMBL-ABR training & events page to find out which workshop is running next.

Next Generation Sequencing Analysis on Artemis

Please note: OWN LAPTOP REQUIRED. If Windows operating system, please ensure your laptop has a terminal client installed.

Synopsis: This workshop is comprised of three courses and aims to teach essential concepts for analysing next generation sequencing data on the University’s Artemis High Performance Computer (HPC). Concepts learnt can be applied to analyzing either whole genome, exome or transcriptomic data. Attendees will also learn how to automate their jobs using job arrays and how to visualise data on Artemis, omitting the need for a local desktop.

  1. Next generation sequencing: Getting to know your data – raw reads and quality control using job arrays and interactive queue on Artemis (10am – 12pm)

  2. Next generation sequencing: All about reference mapping (1pm - 3pm)

  3. Next generation sequencing: Variant detection and variant annotation for mutation detection (3.30 - 4.30pm)

Target audience: Students and staff who would like to learn how to run ‘omic sequencing pipelines on Artemis HPC.

Essential pre-requisites: Competency on the Unix/Linux command line and basic familiarity with Artemis. You MUST first take an ‘Introduction to Unix/Linux’ and ‘Introduction to Artemis’ course. These are scheduled regularly on campus. Participants must have a valid USyd unikey.

Introduction to CLC Genomics on Artemis

Please note: OWN LAPTOP REQUIRED, with CLC Genomics installed (see below).

Synopsis: CLC Genomics on Artemis has recently launched. CLC Genomics on Artemis will provide users with even higher throughput and better data security than ever before. In this course, we will teach you how to use CLC on Artemis including data management, importing/exporting data and launching jobs on Artemis.

Target audience: Current users or anyone who is interested in using CLC Genomics. Participants must have a valid USyd unikey.

Essential pre-requisites: Please try to install CLC Genomics Workbench 10.1.1 prior to the course. Download it for Mac, Windows, or Linux.

Pathogen genomics and global health summer school

Synopsis: This Summer School aims at young graduates, researchers, clinicians and public health professionals that are interested in translational research the field of public health pathogen genomics and communicable disease control. The program includes a mix of inspiring keynotes and master classes, practical hands-on demonstrations and laboratory visits. We will teach the basics of genomics of bacteria, viruses, fungi and parasites with epidemic potential and critically examine the approaches to the analysis of genomes in global health context. Hands-on exercises will be organised to illustrate the power of genomics, functional genomics and metagenomics in answering important questions on the assessment of evolution, virulence, transmissibility and drug resistance as well as on detection of outbreaks and deciphering of transmission pathways. The School will also offer opportunities for exchange of ideas and discussions with presenters and fellow participants. The number of participants is limited so the organisers will select participants based on their information about motivation, prior knowledge and interests provided in the expression of interest.

Dates: 12 - 16 February, 2018

Venue: Sydney Nanoscience Hub (SNH), University of Sydney, Camperdown and Centre for Infectious Diseases and Microbiology – Public Health, Westmead Hospital, Westmead

Registration fee: $450 for international and Australian participants. Registration covers refreshments (morning tea and lunch) and course notes.

Program: The final program is available here

Accommodation: There is a choice of affordable hotels in the Sydney CBD around Camperdown (at own cost).

The summer school is organised by the Centre for Infectious Diseases and Microbiology - Public Health, the Marie Bashir Institute, and the Sydney Informatics Hub, with support from the University of Sydney Strategic Education Grant.

Research Data Management

Introduction to REDCap

Synopsis: 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 project
  • How to enable a longitudinal project
  • How to invite collaborators to a project

Target audience: Students and staff who need to collect electronic data or responses from participants into a structured database. This session is open to all University of Sydney Staff, Students and Affiliates.

Follow-on courses: Many additional features available in REDCap are not covered in this training. Please refer to the Survey (#surveyred) or Advanced REDCap training.

Essential pre-requisites: Bring your own device (laptop).

Surveys in REDCap

Synopsis: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 set up a survey
  • How to flow participants through surveys
  • How to distribute surveys

Target audience: Students and staff who who will be conducting data collection through surveys. This session is open to all University of Sydney Staff, Students and Affiliates.

Essential pre-requisites: Experience in building REDCap projects using the basic functions. Bring your own device (laptop).

Advanced REDCap

Synopsis: 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:

  • Customising formatting with HTML
  • Complex branching and conditional logic
  • Data Imports, exports and reports

Target audience: Students and staff who have been designing projects in REDCap and would like to utilise more advanced features. This session is open to all University of Sydney Staff, Students and Affiliates.

Essential pre-requisites: Experience in building REDCap projects using the basic functions. Bring your own device (laptop).

eNotebooks and other Research Data Management (RDM) tools

Synopsis: Management, curation, storage and sharing of data improves the value of your research. The University provides and supports research data management technologies to help researchers maintain their data with best practice principles. These include an electronic notebook (provided by Labarchives), Dropbox, Research Data Store, Github and Office365. This training will focus on how to best utilise the various features of the eNotebook for your research, with a brief overview of other tools.

Target audience: Any staff or student researcher.

Essential pre-requisites: Bring your own device (laptop).

Data Wrangling Drop-in Session

Synopsis: Do you want to boost your research from data collection to publishing? How about real-time interactions with your supervisors and collaborators to share your bright ideas? Do you want to effectively curate and communicate your fascinating research findings? Come along and meet Research Data Consulting (Sydney Informatics Hub) and Digital Curation (Library) teams and learn about support services available across the University as well as digital platforms and tools to enhance your research.

In this drop-in session, you can request consultations for:

  • DashR, REDCap, eNotebooks and other University-supported digital research tools
  • Research data management planning and best practices
  • Data archiving, publishing and visualisation

Time: Every Tuesday 12 - 4 pm

Location: ThinkSpace (above SciTech Library)

Target audience: Any staff or student researcher

Essential pre-requisites: Bring your own device (laptop)

Pawsey Supercomputing Centre

Pawsey Short Courses

Pawsey Supercomputing Centre will offer the following short courses on supercomputing, data and visualisation topics at the University of Sydney.

  • Introduction to Pawsey: 9:00 – 9:30am Wednesday 4 April
  • Introduction to Unix: 9:30 – 11:30am Wednesday 4 April
  • Introduction to pshell: 11:30 – 12:00pm Wednesday 4 April
  • Nimbus research and cloud training: 1:00pm – 4:00pm Wednesday 4 April
  • Introductory Supercomputing: 9:00am – 12:00pm Thursday 5 April
  • Intermediate Supercomputing: 1:00pm – 4:00pm Thursday 5 April
  • Courses are delivered in a face to face classroom style.

Attendees are expected to bring and work on their own laptops. Staff from the Supercomputing Team will be facilitating so you can meet and chat with them.

Venue: University of Sydney Abercrombie Business School ABS Learning Studio 3100 (H70.3100)

Additional Information

  • Attendees are encouraged to bring their laptops for the sessions.
  • Courses are free of charge and open to all, however places are limited.
  • Light refreshments will be provided on each day.
  • Lunch can be purchased at nearby cafeterias.

If you have any queries, please email help@pawsey.org.au. To register, please fill out the form on this page.

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For more information about SIH services please email sih.training@sydney.edu.au