Simon Gladman, Research Scientist specialising in microbial genomics, May-June UK tour, Blog #1
As our Genomics Virtual Laboratory expert, Simon Gladman was invited by colleagues in the UK and EU to spend time over summer on some key bioinformatics problems and to share some Australian know-how. He has already covered a lot of territory. Here he gives the first of several updates to come:
Applied Bioinformatics and Public Health Microbiology (ABPHM)
Sanger Wellcome Trust Institute – Hinxton
ABPHM is a conference for bioinformaticians and biologists from the public health space to interact. It has sessions on outbreaks, pipelines, bioinformatics tools, antimicrobial resistance, pathogen surveillance and accreditation. This conference attracts public health experts from around the world, including 15 participants from Australia this year including Ben Howden (Director, Microbial Diagnostic Unit, Peter Doherty Institute), Torsten Seemann (also representing Melbourne Bioinformatics), Susan Ballard, Deborah Williamson, Jason Kwong and Sarah Baines from the same group.
Some of the highlights included:
- A talk by Nuno Faria about the epidemiology of the Zika virus and its transmission from French Polynesia to the USA via Brazil and the Amazon basin. This work was done by driving a combi van around Brazil collecting samples of mosquitoes and sequencing the virus in situ with Minion instruments.
- Stephen Gillespie from Oxford University gave a presentation on the challenges and benefits to society of the proliferation of semi “real time” sequencing in sepsis and antimicrobial resistance.
- Paolo di Tommaso gave a talk on a bioinformatics workflow system in an effort to remove hardware differences from workflow outputs.
- Caroline Colijn gave a very impressive talk on bayesian inference of transmission events and a more robust method for determining them.
- Eric Marinier, National Microbiology Laboratory, Public Health Agency of Canada introduced their new tool called Neptune.
- Annamaria Crisan, University of British Columbia, Canada gave an excellent talk about data visualisation.
A number of talks focussed on the proliferation of antimicrobial resistance including an excellent one on carbapenem-resistant organisms in a hospital in Virginia and how they were living in the drains and spreading to various wards etc.
Australia was well-represented. Torsten and I gave e-poster demonstrations of our software (Nullarbor and the GVL respectively), Sarah, Susan and Deborah all gave excellent talks, Jason presented a poster and Ben was a member of the discussion panel on Day 3.
Overall, it was an excellent conference yet again. This was the 4th time I’ve attended this conference with Torsten and others from Australia. Jonathan Green – the conference convener – publicly thanked the international visitors and locals for getting the conference to be more like a movement than a collection of talks. It certainly does feel that way.
Microbial Bioinformatics Tools Hackathon
University of Bath – Somerset
Twenty of the conference attendees, from Australia, Portugal, the UK, Sweden and elsewhere, met up at Bath University for a hackathon based around everything discussed at the conference.
I enjoyed teaching a few of the participants how to get their tools into BioConda and as a consequence of this, there are now quite a few microbial-specific tools in BioConda and also BioContainers (automatic from BioConda.) We achieved a lot just in the two days I was there. We also workshopped around the gaps in our tool ecosystem and plans for other tools were drawn up. The hackathon continued for another three days but I had to come back to Cambridge for another one.
Galaxy Training Material Hackathon
Cambridge University Bioinformatics Training Room
This was a joint Elixir/Galaxy Training Network/GOBLET event to expand, compile and collect a lot of the existing Galaxy bioinformatics training material and make it generally available for use and modification.
Participants were from all over the world including Maria Doyle from Melbourne’s Peter MacCallum Cancer Institute. Other attendees included Dave Clements, Mallory Freeburg, Mo Heydrian and Dannon Bakker from the Galaxy project, Björn Grüning, Bérénice Batut, Saskia Hiltemann, Frederick Coppens, Gabriella Rustici, Ralf Weber, Victoria Bohler, Nicola Soranzo and many others from various ELIXIR Nodes and the wider Galaxy community.
The main outcome of the hackathon was a build system and structure for the Galaxy Training Network site and materials. I contributed a number of materials to the site including our Assembly tutorial. We also worked out a way to alter the structure to make it easier for external contributions in future.
The GVL project and Melbourne Bioinformatics has since been invited to assist the ELIXIR Node: France with their 4-day bioinformatics course in early July. The course will be run using the GVL and associated tools.
EMBL-ABR/ELIXIR-UK Virtual Training Environment Workshop
Cambridge University Genetics Department – Downing Site
This was a workshop led by EMBL-ABR and ELIXIR: UK Node, on the GVL and its implementation in Europe. The participants were Björn Grüning (ELIXIR: German Node), Frederick Coppens (ELIXIR: Belgian Node), Dave Clements and Dannon Bakker (Galaxy project), Yasset Perez-Riverol (EBI and the Biocontainers project), Vicky Schneider (EMBL-ABR and the University of Melbourne), Gabriella Rustici (Cambridge University) and me. I presented the GVL as a cloud bioinformatics platform and solution. We discussed how we could use the GVL along with Galaxy’s CVM-FS and Biocontainers to make bioinformatics tools universally available to biologists and bioinformaticians throughout Europe. We developed a schematic of how we think it will work. EMBL-ABR, Melbourne Bioinformatics and the GVL project now have the opportunity to be a link between parts of the Galaxy project and ELIXIR to help make this a reality.
Several ELIXIR Nodes have expressed interest in getting the GVL working on their clouds so we look forward to closer collaboration with them to help achieve this.