Bioinformatics

Closing date: 31 May 2018

Get the skills to stay ahead of your colleagues and keep up with the data tsunami.

The application of high-throughput technologies and genome-wide analysis has transformed basic science and clinical approaches. Neuroscience in particular benefits from these approaches to gain insight into normal development, disease and injury. This has resulted in a rich landscape of publically available data which can be used by anyone to do original, publishable research.

However, this can be a daunting prospect for bench researchers who have limitless questions but lack programming skills.

This course is designed to overcome this hurdle by teaching you how to use selected online tools to rapidly test and develop your hypotheses or even make novel findings using freely available high-quality data ….. and no coding is required!

Each week, during a 2-hour hands-on workshop, a different tool or dataset will be demonstrated and explored. Tools included in the course cover genomics, transcriptomics and proteomics and include: UCSC genome browser, Integrated Genomics Viewer (IGV), GeneNetwork, GTEX, Gene Expression Omnibus dbSNP, OMIM, NHGRI GWAS Catalog, DisGeNET, SMART, PFAM , Intact, Genemania, Gemma, Stemformatics, Cytoscape.

Using worked examples, you will also be shown how different tools and datasets can be linked together to build an analysis pipeline to generate evidence supporting a hypothesis.

OUTCOME: In addition to building your knowledge and skill base, every student completes an individual research project to complement your PhD studies during this course.

Presenters:

Dr Victoria Perreau, A/Prof Justin Rubio (genomics), Dr Noel Faux (IBM Research-Australia)

Proposed timeframe:

Every Thursday 10.00am - 12.00pm commencing Thursday 19 July (introduction) through Thursday 20 September (final student presentations).

Please note there will be no formal workshop on Thursday 13 September as students will dedicate this time to prepare their final presentation.

Venue:

Each week, the workshop will be held in the Boardroom (Level 5) of the Kenneth Myer Building (KMB), Melbourne Brain Centre - Parkville, except for the final day (Thurs day 20 September), where student presentations shall be given in the Level 5 seminar room of the KMB.

Time Commitment:

Approximately 40 hours total including:

  • 18 hours contact time. This includes 8 x 2-hour hands-on workshops plus attendance at a 2-hour symposium where you will give a 10 minute presentation of your own project.

An additional 20 hours minimum commitment of your own time working on your individual research project is expected. Individual projects are supported by weekly drop-in hours on Mondays for personalised consultation. All software used in the workshop is freely available and instructions for downloading and installing will be provided where necessary.

Prerequisites:

A good understanding of molecular biology, including gene structure, transcription and translation is essential. Students must bring their own lap top computer to workshops. You do not need to know any coding and this course does not teach any coding, but coders are very welcome to apply.

Other relevant details:

All applicants must submit a brief project description (150 words maximum ) summarising the  research aim they propose to approach as an essential part of this workshop.

Preferred applicants will be those who articulate a research question in their application that may be approached using bioinformatics tools and connects in some way to their PhD studies. This is because you will work on your project throughout the workshop and present to the group at the conclusion of the workshop.

Vicky Perreau is happy to discuss your project ideas with you before applying, or to provide further information about the workshop syllabus and expectations.  This is the 4th year that this course has been offered and every project is unique.

Example of what you will learn:

The image below illustrates the power of bioinformatics applications to freely available data and is an example of what you learn to do in the workshop.

This Sashimi plot above illustrates use of the Integrative Genomics Viewer (IGV) from the Broad Institute to examine transcript variant expression of TrkB receptor (NTRK2) using RNAseq data from different cell types in the mouse brain. Astrocytes (red), neurons (blue) and oligodendrocyte precursor cells (green).

Viewing the data in this way shows how neurons typically express the long form of TrkB whereas astrocytes and some oligodendrocyte cells express the truncated receptor. Aligned RNAseq data used to generate this image is from the Allen Brain Atlas Cellular taxonomy of the mouse visual cortex. Aligned SAM files of the single-cell RNAseq gene expression data were downloaded from the NCBI SRA data repository.