Training

2018 Upcoming Events and Training Sessions

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

NB Course dates may change when registration links are posted.

Course Date Training Course Location Signup link
21 Feb 2018 Introduction to Matlab Camperdown Register
22 Feb 2018 Visualisation Masterclass Camperdown Register
26 Feb 2018 Introduction to GPU computing - CUDA, OpenACC Camperdown Register
27 Feb 2018 NVIDA Deep learning Camperdown Register
27 Feb 2018 Introduction to REDCap Westmead Register
27 Feb 2018 Research Data Management: eNotebook and more Westmead Register
28 Feb 2018 Introduction to R Camperdown Register
1 Mar 2018 Matlab and HPC Lidcombe
7 Mar 2018 Excel for Researchers Camperdown Register
8 Mar 2018 Advanced REDCap Camperdown Register
13 Mar 2018 Advanced REDCap Westmead Register
13 Mar 2018 Regular Expressions Camperdown Register
13 Mar 2018 Version Control with Git Camperdown Register
15 Mar 2018 DNA/RNA sequence analysis workshop Westmead Register
15 Mar 2018 Experiment and survey design workshop Westmead
15 Mar 2018 Sydney Hacky Hour Westmead Details
21 Mar 2018 Introduction to Unix Camperdown Register
20 Mar 2018 Introduction to REDCap Camperdown Register
20 Mar 2018 Research Data Management: eNotebook and more Camperdown Register
28 Mar 2018 Introduction to Artemis Camperdown Register
28 Mar 2018 Data transfer and RDS for HPC Camperdown Register
4 Apr 2018 Introduction to Python Camperdown Register
5 Apr 2018 Introduction to REDCap Camperdown Register
4-5 Apr 2018 Pawsey Supercomputer Training Camperdown Register
13 Apr 2018 Introduction to Matlab Camperdown Register
19 Apr 2018 Sydney Hacky Hour Camperdown Details
17 Apr 2018 Advanced REDCap Camperdown Register
20 Apr 2018 Introduction to R Camperdown Register
16 May 2018 Introduction to Artemis Camperdown Register
16 May 2018 Data transfer and RDS for HPC Camperdown Register
29 May 2018 Matlab and HPC Camperdown
29 May 2018 Intermediate HPC: Automating Jobs Camperdown
21 June 2018 Accelerated Computing for Innovation (Artemis Conference) Camperdown Details to come
26 June 2018 Introduction to Artemis Camperdown Register
26 June 2018 Data transfer and RDS for HPC Camperdown Register
17 July 2018 Matlab and HPC Camperdown
17 July 2018 Intermediate HPC: Automating Jobs Camperdown

Sessions are free for researchers and post graduate students of the University of Sydney.
*The Pathogen Genomics and Global Health course is run in collaboration with external partners and has a registration fee.

For more information about these courses please email sih.training@sydney.edu.au

Expressions of Interest (EOI) for 2018 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

A few course that we can host are offered by our training partners at Intersect: Intersect Training⬀

Also, the Library offers regular training in a wide range of services: Library Training⬀


The university also has a subscription to lynda.com, log on with your university credentials to gain access. This site provides training covering a huge range of domains. Some courses of interest may be:


Hacky Hour

A monthly meetup held in different locations around campus for any questions about data, coding, analyses, visualisation, modelling, experiment and survey design, and research problems. Details here



Description of Regular Courses

Check the calendar above for upcoming courses.

Research Computing

Hosted by SIH.

Slides for SIH computing courses can be viewed here.

Programming and Software

Hosted by Intersect⬀

Bioinformatics

Hosted by SIH

See detailed descriptions of bioinformatics courses offered by the SIH.

Research Data Management

Hosted by SIH

See detailed descriptions of reseasrch data management courses offered by the SIH.


Research Computing Courses

Slides for SIH computing courses can be viewed here.

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.

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.

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.

Artemis+MDCS: Running HPC Jobs from MATLAB

Synopsis:Learn how to use Matlab 2017a to run your fucntions and scripts in parallel on the Artemis High Performance Computer.

Target audience:Matlab users that need more power from their scripts.

Pre-requisites:Basic Matlab skills are assumed. OWN LAPTOP with Matlab 2017a installed required.

Bioinformatics courses

Introduction to RNASeq

Register Interest

Introduction to genomics

Register Interest

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

Pathogen genomics and global health

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).

Register EOI

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 introductory training learn how to build a simple data entry project and set up a survey.

Target audience: Students and staff who need to collect electronic data or responses from participants into a structured database.

Follow-on courses: Many additional features available in REDCap are not covered in this training. Please refer to the Advanced REDCap training.

Essential pre-requisites: 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 use of the following features: Branching and conditional logic, Repeatable Forms and Events, Survey flows and invitations, and 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.

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).

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.


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