Establishing a distributed national research infrastructure providing bioinformatics support to life science researchers in Australia

Schneider MV, Griffin PC, Tyagi S, Flannery M, Dayalan S, Gladman S, Watson-Haigh N, Bayer PE, Charleston M, Cooke I, Cook R, Edwards RJ, Edwards D, Gorse D, McConville M, Powell D, Wilkins MR & Lonie A (2017): Establishing a distributed national research infrastructure providing bioinformatics support to life science researchers in Australia. Briefings in Bioinformatics 20(2):384-389.

Abstract

EMBL Australia Bioinformatics Resource (EMBL-ABR) is a developing national research infrastructure, providing bioinformatics resources and support to life science and biomedical researchers in Australia. EMBL-ABR comprises 10 geographically distributed national nodes with one coordinating hub, with current funding provided through Bioplatforms Australia and the University of Melbourne for its initial 2-year development phase. The EMBL-ABR mission is to: (1) increase Australia’s capacity in bioinformatics and data sciences; (2) contribute to the development of training in bioinformatics skills; (3) showcase Australian data sets at an international level and (4) enable engagement in international programs. The activities of EMBL-ABR are focussed in six key areas, aligning with comparable international initiatives such as ELIXIR, CyVerse and NIH Commons. These key areas-Tools, Data, Standards, Platforms, Compute and Training-are described in this article.

UNSW Genome Annotation workshop, Tuesday 21st November 2017

I am pleased to announce that we will be running a replacement for July’s cancelled Genome Annotation workshop at UNSW on Tuesday 21st November 2017, 1100-1400.

Places are limited but it’s free and you can sign up here through Eventbrite.

DESCRIPTION

This workshop will include a short background lecture on the fundamentals of gene prediction and genome annotation followed by a hands-on component where we will conduct manual curation exercises using Apollo.

The workshop has been organised by EMBL-ABR and will be led by Dr Monica Munoz-Torres from Phoenix Bioinformatics who is an expert in genome annotation, current chair of the International Society for Biocuration Executive Committee, and former Project Manager of the Apollo Project.

Monica will be joining us direct from the San Francisco Bay Area, and we will have locally trained trainers on hand to help and facilitate the workshop locally.

TOPICS TO BE COVERED

• Genome Annotation - why is it important?
• Gene prediction
  • what is a gene
  • computation
  • annotation
• Genome curation
  • knowledge
  • curation - why is this necessary?
• Structural Annotation using Apollo
• Biological principles for curation with Apollo
• Apollo functionality: step by step
• Curation example

Requirements

Participants must bring their own eduroam-enabled laptop with either Chrome or Firefox installed.

Further information

https://www.embl-abr.org.au/genome-annotation-using-apollo-monica-munoz-torres/ or contact Richard Edwards.

UNSW Genome Annotation Workshop cancelled

Regrettably, due to unforeseen circumstances, EMBL-ABR’s Monica Munoz-Torres Australian tour has been cancelled. As a result, the planned UNSW Genome Annotation Workshop will no longer be going ahead. We hope to organise something similar in future, so will leave the registration page up for a bit longer to get a list of interested parties.

UNSW Genome Annotation Workshop

NOTE: Regrettably, this event has now been cancelled. We hope to organise something similar in future and will be in touch with registered individuals to gauge interest.

We are pleased to announce that we are hosting Monica Munoz-Torres from the Berkeley Bioinformatics Open-Source Projects group (BBOP) at Lawrence Berkeley National Laboratory as part of her EMBL-ABR Australian tour, sponsored by the School of Biotechnology and Biomolecular Sciences (BABS) and NSW Systems Biology Initiative (SBI).

In addition to a BABS seminar (details to follow), Monica will be giving a one-day Primer on Genome Annotation workshop at UNSW, with a particular emphasis on collaborative genome annotation using WebApollo.

• When: 0900-1700, July 7th, 2017
• Where: Red Centre, UNSW, Sydney, Australia
• Contact: richard.edwards@unsw.edu.au

You can pre-register for the workshop here or fill in the form below. Places are limited to 30 participants. We will be in touch to let you know if you have a place. Formal registration will require a $20 registration fee.

EMBL-ABR network: an interview with Richard Edwards

From the EMBL-ABR February newsletter:

On 3 February we released an interview with Richard Edwards, the developer of SLiMSuite, an open source bioinformatics tool for the prediction of short linear motifs (SLiMs) and related sequence analysis. In this interview Richard reflects on bioinformatics in Australia as well as the realities of building a sustainable model for the development and maintenance of useful bioinformatics tools such as his.

You can read the full interview: here.