Tag Archives: Workshop

Bioplatforms Australia – CSIRO NGS Workshop (July 1-3, 2014)

Last July 1-3, 2014, the latest Bioplatforms Australia – CSIRO joint Next Generation Sequencing hands-on workshop was held at the University of New South Wales, Sydney. The workshop was delivered using the established Bioinformatics Training Platform running on the NeCTAR Research Cloud and provided bench biologists and PhD students with NGS training on the following topics:

Introduction to the command-line interface – Software Carpentry
Introduction to Next Generation Sequencing
Illumina Next Generation Sequencing Data Quality
Sequence Alignment Algorithms
ChIP-Seq Analysis
RNA-Seq Analysis
de novo Genome Assembly

Sequence data quality analysis and visualisation using FastQC and FASTX-Toolkit.

The R@CMon team helped the workshop organisers in updating the training environment with the latest tools, datasets and other materials as well as ensuring resource stability throughout the 3 day workshop. Future Bioplatforms Australia and CSIRO joint workshops will be announced on the Bioplatforms Australia Training page.

Alignment visualisation using IGV.

The trainees have the following to say about the workshop:

“The practical component made it 1000 times easier to get my head around the course and I feel like I can be confident in actually applying what I’ve learned (instead of just in lecture format).”

“The beginning with introduction to Unix environment and explanation of the de novo assembly was the best part of the course as the commands were described in more detail so I could understand what the different commands were executing. There was more practical work with the de novo assembly which was good.”

“Hands on experience is good, and the first part on command lines is good for the beginners.”

Deakin Bioinformatics Workshop (February 17-19, 2014)

Leave a Reply

Last February 17-19, 2014, a bioinformatics workshop was held at Deakin University – Geelong Waterfront Campus. The workshop covered Genotype By Sequences (GBS) methodologies using various well known bioinformatics tools. The two main tools used in the workshop were Trait Analysis by aSSociation, Evolution and Linkage (TASSEL) and Bowtie. TASSEL is used to investigate relationships between phenotypes and genotypes while Bowtie is a tool used to align DNA sequences to the human genome.

Trainees at the Deakin workshop, using the NeCTAR-provisioned training environment.

The workshop was delivered using the NeCTAR Research Cloud infrastructure and Bioplatforms Australia Training Platform. The R@CMon team supported the workshop organisers at Deakin University in creating a customised cloud image containing required tools and datasets as well as ensuring allocation of computational and storage resources in the cloud. The CloudBioLinux-based cloud image has been instantiated for each trainee, giving each one a dedicated virtual desktop environment for their analyses.

Workshop trainers demonstrating Genotype By Sequences (GBS) methodologies and tools using a custom NeCTAR cloud image.

Feedback collected from participants on the day was overwhelmingly positive. However, some user-experience issues were encountered with the remote desktops (NX), those can be attributed to the network between the cloud servers (hosted on the eRSA Node in South Australia) and the participants. Though such issues haven’t shown up for BPA workshops utilising the Monash Node up-and-down the east coast, this demonstrates the importance of being able to reserve local cloud capacity for certain use-cases like this which are latency and jitter sensitive. Fortunately those issues were isolated and according to instructors from Cornell University, the training platform used in the workshop was one of the best they’ve used and the trainees were keen to attend future GBS-related workshops delivered using the cloud.

Bioplatforms Australia – CSIRO Metagenomics Workshop (February 6-7, 10-11 2014)

Leave a Reply

Bioplatforms Australia and CSIRO conducted an “Introduction to Metagenomics” workshop last February 6-7, 2014 at University of New South Wales and February 10-11, 2014 at Monash University. The workshop was aimed for bench biologies with no or little experience in Bioinformatics using publicly available data resources and toolsets.

As per previous Bioplatforms Australia workshops, the Metagenomics workshop was delivered using the Monash node of the NeCTAR Research Cloud infrastructure – R@CMon. Cloud provisioning tools used in previous workshops have been reused to provide a seamless virtual desktop training platform.

The R@CMon team worked with Bioplatforms Australia, CSIRO and EMBL-EBI in producing an appropriate cloud image and toolset for the workshop. Some of the tools used in the workshop are QIIME, FastQC, and InterProScan.

Given the success and popularity of the training, R@CMon has begun work with Bioplatforms Australia and other nodes of the NeCTAR Research Cloud to scale the training environment with trainees as they progress from taking the course, to taking the training environment home with them, to preparing for production genomics facilities.

The trainees have the following to say about the 2-days workshop:

“Everyone is very helpful and the content was clear and concise. I thank everyone for getting this program up and running and I would definitely like to return for similar courses.”

“Definitely a fantastic & informative 2-days. I definitely feel that most of what I learned today can be directly applied to the molecular work I am currently engaged in.”

“Good amount of hands on to actually see what happens during the analysis of big data, most of what was taught was very clear and concise. good range of programs were used, only wish there was more time to go through more analyses.”

“I strongly recommend this as a complete course for students or beginners in NGS analyses. i think the first metagenomic workshop is a winner.”

“Definitely this course has provided me a great basis to look at future data sets.”

“Well ran, good materials, virtual machine made life easy.”

Bioinformatics Training on R@CMon

Leave a Reply

A multidisciplinary partnership between Monash eResearch Centre and Bioplatforms Australia has provided a broadly accessible solution to delivering hands-on bioinformatics workshops with seamless access to cloud computing using the new NeCTAR Research Cloud infrastructure.

Running hands-on bioinformatics workshops in Australia has previously been hampered by the lack of specialised bioinformatics training facilities and a paucity of skilled trainers to develop and deliver these courses.

To improve the bioinformatics skills of bench scientist now faced with handling gigabyte size datasets generated by next-generation sequencing technologies, Bioplatforms Australia and CSIRO have been collaborating to advance bioinformatics expertise among Australian ‘omics researchers. Through an international partnership with the EMBL European Bioinformatics Institute in the UK, a cutting-edge three-day Australian hands-on NGS workshop has been created. This course introduces bench scientists to quality control of NGS data, alignment, ChIPSeq, RNASeq and de novo assembly workflows and software.

Professor Paul Bonnington, Director of the Monash eResearch Centre and the R@CMon team contributed to this training initiative through the development of a cloud computing-based NGS bioinformatics training platform based on the open source bioinformatics software package CloudBioLinux. The platform allows sharing of data, tools and applications and enables trainers anywhere in the world to readily work together to develop and test new workshop material.

The Bioplatforms Australia Next Generation Sequencing workshop platform enables compute-intensive NGS training courses to be easily delivered and accessed widely around Australia and requires very little local IT expertise or need for high end computational hardware. The first hands-on workshops using the NGS workshop platforms were held in July 2012 at Monash University in Melbourne and at University of New South Wales in Sydney. To date 10 workshops have been delivered around Australia in Melbourne, Sydney, Brisbane, Adelaide, Perth and Canberra to 345 trainees.

The team of trainers from Bioplatforms Australia and CSIRO in collaboration with EBI-EMBL and Monash eResearch Centre are currently developing a metagenomics 2-day workshop using a bespoke metagenomics image built by R@CMon. This course will be run at University of New South Wales in Sydney on the 6-7 February 2014 and at Monash University on the 10-11th February 2014.

Monash University is one of the nodes of NeCTAR‚ a research cloud platform, a landmark investment that will extend the advantages of high-performance computing and high capacity networks to Australian researchers. This exciting initiative provides on-line access to scalable computational power and data storage allowing a new realm of data sharing and collaboration.

The Bioplatforms Australia Next Generation Sequencing workshop platform is now freely accessible on the NeCTAR research cloud and provides access to hundreds of bioinformatics software packages.

Further information on the Bioplatforms Australia Next Generation Sequencing workshop platform is available from Catherine Shang, Bioplatforms Australia at cshang@bioplatforms.com. Contact Prof. Paul Bonnington, MeRC Director for further details and assistance on e-research solutions.

Software Carpentry Bootcamp for Bioinformaticians (Adelaide/Melbourne) – UPDATE

Leave a Reply

Last September 24-26 and October 1-3, the latest Software Carpentry Bootcamps were held in University of Adelaide and Monash University.

These Software Carpentry Bootcamps were designed for Bioinformaticians to enhance their knowledge and skills in programming and software development practices.The bootcamps were delivered using the NeCTAR Research Cloud where each trainee has been given dedicated access to a specific virtual workstation.

With the use of an automatic provisioning system, each virtual workstations have been preconfigured with the required tools, training materials and computing resources to perform the hands-on exercises.

On the first day of the bootcamp, the Software Carpentry instructors including the R@CMon team introduced the trainees to Python. The second day was mostly about software testing and documentation. The last day was when the trainees applied their knowledge from the previous sessions into collaborative group exercises.

Photos taken by Nathan Watson-Haigh (ACPFG).

“Thanks a lot for this information and also your kind efforts in running such a useful and informative workshop” – Fariborz Sobhanmanesh (Research Engineer, Bioinformatician with CSIRO Animal, Food and Health Sciences Centre)

“I recently attended the SWC bootcamp in Adelaide and found it incredibly useful. Sure there was a lot of information in a short amount of time but the topics covered were practical and very relevant to my daily work. Thanks must go to the presenters and organisers who kept things moving along brilliantly.” – Terry Bertozzi (Research Scientist with the South Australian Museum)