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December workshops - presentations now available
Rafael Jimenez (Chief Technical Officer, ELIXIR Hub, UK) and Vicky Schneider (EMBL-ABR Deputy Director) were joined by Jason Williams (CyVerse) in delivering the following best practice in bioinformatics workshops in Melbourne this month. Link on each one to access full presentations and documentation:
Open Source and Software Development Best Practice
This workshop looked at CyVerse and ELIXIR Software Development Best Practices to explore how we might harmonise our efforts in this area in Australia.
Registries in Bioinformatics: tools, datasets, standards, events & training
An introduction to existing solutions and methods for selecting and accessing these registries.
Open & Scalable Training
This session considered the demands in Australia for bioinformatics training: are they being met, how do we compare with the rest of the world, and could we scale up and share training expertise, employing the principles of open software and open data as applied to training?
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Another very successful BioInfoSummer
28 Nov - 2 Dec
Each year Bioinfosummer, organised by the Australian Mathematical Sciences Institute (AMSI), attracts over 200 Australian students and researchers to a week-long symposium on the world of bioinformatics.
This year it was held in Adelaide, South Australia. Open Data Coordinator, Philippa Griffin, represented EMBL-ABR, delivering a comprehensive overview of the national and international research infrastructure for the life sciences and showing EMBL-ABR's activity across this landscape. She welcomed lots of insightful questions and comments.
Highlights of the program for Pip were Katherine Pillman's talk on differential splicing quantification in RNA-seq, Denis O'Meally's talk on the koala genome project, and Terry Speed's talk on the history of theoretical attempts to crack the genetic code. This story reminded us that even the most elegant mathematical theories about biology often don't survive encounters with biological data, said Pip.
Overall, it was great to talk to enthusiastic students, ECRs and other speakers throughout an action-packed week, Pip said.
Our thanks to AMSI organisers for this opportunity to engage with this important life science community.
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Paul Flicek presenting on current EBI activities to the All-Hands meeting.
Report from All-Hands meeting
7 December
This inaugural meeting, held in Melbourne at the EMBL-ABR Hub, attracted 62 participants from the bioinformatics communities across New South Wales, Queensland, Victoria, South Australia, Western Australia and Tasmania. They were joined by ISAG members who contributed to discussions about how this community might direct future bioinformatics network building activities in Australia.
Afterwards Vicky commented: It was great to see nine of the ten nodes represented and so many key experts from both dry and wet sciences present. Both Vivien's and Paul's talks highlighted several efforts taking place globally that are relevant to the EMBL-ABR community and I'm particularly looking forward to seeing how we can best access these to help expand our community, resources and activities through 2017.
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In Melbourne
3-9 February 2017
Follow
@GalaxyAustralia
#GAMe_2017
Keynote speakers are now confirmed:
Dr James Taylor is the Ralph S. O’Connor Assoc Prof of Biology and Computer Science at Johns Hopkins University. He is one of the original developers of the Galaxy platform for data analysis, and his group works on extending the Galaxy platform, and understanding genomic and epigenomic regulation of gene transcription through integrated analysis of functional genomic data. James received a PhD in computer science from Penn State University, where he was involved in several vertebrate genome projects and the ENCODE project.
Dr Björn Grüning is with the Bioinformatics Group at Albert-Ludwigs-Universität Freiburg, Germany, where he heads the Freiburg Galaxy Project. He is a prominent contributor to, and is a driving force in, the Galaxy community. In the past year alone, he helped organise the Bioconda Contribution Fest, Swiss-German Galaxy Days, the Galaxy Training Materials Contribution Fest, the Galaxy DevOps Workshop, and the Conda Dependencies Codefest, and presented and taught at GCC2016. His research interests include data visualisation, computational chemistry, and drug discovery.
Current sponsors include AGRF, Cray, EMBL-ABR, Galaxy, University of Melbourne, VLSCI
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Thank you to all the Heads of Nodes for working with us on some tight timelines to have the Node flyers ready in time for the ISAG and All Hands meetings. To order printed copies, contact Christina Hall. All pdfs are now online and available for download.
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ABACBS
The Australian Bioinformatics and Computational Biology Society (ABACBS) meeting ran in conjunction with the B3 symposium, the COMBINE symposium, and the GOBLET meeting, forming a 'Festival of Bioinformatics' in Brisbane in November. Pip Griffin, Open Data Coordinator and Sonika Tyagi, Training Coordinator both represented EMBL-ABR.
Pip reported that she very much enjoyed the opportunity to meet so many bioinformaticians from around Australia and to hear about their diverse research activities. She particularly enjoyed Nouri Ben Zakour's talk on tracking evolution of microbial pathogens, Jimmy Breen's talk on multi-omic analysis of old and young grapevine clones, and Terri Attwood's closing talk on biological data curation and linking the underlying research data in the scientific literature - (Terri was featured in an EMBL-ABR interview earlier this year).
Pip and Sonika also attended the GOBLET Best Practices in Bioinformatics Training meeting and commented on the excellent workshop on the mixOmics package for multi-omic data analysis.
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Global mapping of bioinformatics training in Australia
Combined surveys conducted by EMBL-ABR over 2016 have identified, among other things, specific demand for more training in data management and statistics. These results were presented at ABACBS.
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Interview series:
Jyoti Khadake was in Melbourne recently forming part of the International Faculty on the Data Life Cycle workshop series, as our expert on microbial genomic data and data accessibility and challenges. As someone who works in biomedical research, she sees the social and ethical considerations vary greatly amongst bioinformaticians, depending on their area of study, but that they all need to adopt the agreed standards for data curation and management which are being implemented across this discipline.
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