About Sara Ogston

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So far Sara Ogston has created 10 blog entries.

Analysis and Training Tutorials available

The RDS Omics team is thrilled to announce that all 20 analysis and visualisation tools, along with their tutorials, identified in 2016 are available and ready for use! This ends a 12 month effort by teams at Melbourne Bioinformatics (formerly VLSCI) and QCIF. Training workshops will be taking place throughout the remainder of 2017 and [...]

By |June 7th, 2017|Uncategorized|0 Comments

The Galaxy Australasia Meeting 2017 Wrap up

The Galaxy Australasia Meeting 2017 (GAMe 2017) took place at VLSCI, the EMBL-ABR Hub. Galaxy users and administrators came together from interstate and around the world, to learn and talk all things Galaxy. Important members of the international Galaxy team came to the University of Melbourne as part of their goal to make data-intensive biology accessible to [...]

By |February 14th, 2017|Uncategorized|0 Comments

Bioinformatics Workshop held in Perth

VLSCI and UWA ran a 2 day Bioinformatics Workshop  on The Genomics Virtual Laboratory and An Introduction to Microbial Genomics on the 22nd and 23rd of November. This is the second workshop held in Australia using newly generated tutorials for the Omics Platform. Participants learned about: Introduction to Galaxy - tutorial NGS Data - Omics [...]

By |November 29th, 2016|Uncategorized|0 Comments

Bacterial Genome Assembly and Annotation Workshop held in Brisbane

QCIF, QFAB nd RCC ran the first Australian workshop using RDS Omics training tutorials on Monday 22 November. The Bacterial Genome Assembly and Annotation workshop was held at  Griffith University, Southbank campus and attended by 20 life sciences researchers. Participants carried out practical exercises in the following topics Access and use the Galaxy bioinformatics analysis [...]

By |November 23rd, 2016|Uncategorized|0 Comments

Announcing the demonstration release of the RDS Omics Data Platform

We are extremely happy to announce the first Demonstration release v0.1 of the Omics Data Platform. This release represents significant development and integration work over the last 7 months by the project team across VicNode, VLSCI, EMBL-ABR, Intersect and QCIF, in partnership with the BPA Antibiotic Resistant Pathogens project. This release includes a connected platform [...]

By |October 10th, 2016|Uncategorized|0 Comments

Omics Platform architecture summary

The Omics platform that is being built through the RDS Omics project  is made up of 3 interconnecting components. These three components are: 1. The microbial-GVL which is a tailored version of the GVL (i.e. the "Genomics Virtual Laboratory", a cloud based suite of pre-configured genomics analysis tools and workflow platforms running on a scalable Slurm cluster), [...]

By |September 7th, 2016|Uncategorized|0 Comments

RDS Omics training materials successfully presented at international Galaxy conference

Preparation of training materials for microbial data are in progress for the BPA AMR/RDS Omics projects. A "Workshop for Microbial Genomics" has been developed to introduce key tools. This covers the basics of using the Galaxy analysis platform, genome assembly with Spades and Velvet, genome annotation with Prokka, and Variant calling with Snippy. Analysis results [...]

By |August 8th, 2016|Uncategorized|0 Comments

Combining, analysing and interpreting Genomic, Metabolomic, Proteomic and Transcriptomic data

To enable biologists to fully explore and integrate data, the omics.data.edu.au website provides a suite of tools for analysis, processing, and visualisation of multi-omic information. These tools will be available through the microbial Genomics Virtual Laboratory (mGVL). The mGVL includes a range of applications such as Galaxy, RStudio, Jupyter Notebook and even provides a Lubuntu [...]

By |August 2nd, 2016|Uncategorized|0 Comments

Omics Data Discoverability Phase

The RDS Omics Discoverability phase took place from December 2015 through to May 2016. During this time, project members met with various BPA data generators in each of the omics areas - Genomics, Metabolomics, Proteomics, and Transcriptomics - from Melbourne, Sydney and Brisbane. The object of these meetings were to discuss, understand and document: Types [...]

By |July 25th, 2016|Uncategorized|0 Comments

RDS Omics using Mediaflux for data management platform

One of the major deliverables of the RDS Omics project is to build a data management platform. This platform will be utilised for all streams of data generated through the BPA Sepsis project. The primary activities of this data management platform are: Securely hold primary and processed (from analysis applications) data and metadata Manage (organize, [...]

By |June 29th, 2016|Uncategorized|0 Comments