iPlant is coming to the UK

Back in 2013, the GARNet team brought the iPlant Collaborative over to the UK to run a four-day workshop. Now, we’ve secured funding to bring iPlant to the UK again – but this time, it’s here to stay!

During 2014, the GARNet team and committee – together with iPlant collaborators in the US – were busy preparing a grant application for an invited BBSRC capital funding call. Our proposal was to work with iPlant to develop a ‘node’ of iPlant here in the UK. Our application was sucessful and the award was announced at the end of January at the AAAS 2015 meeting.

What is iPlant?

Funded by the US National Science Foundation (NSF) the iPlant Collaborative provides free and open access to ‘cyberinfrastructure’, originally just for plant scientists, but now for all the life sciences. Here’s a short video clip to explain more:

Harnessing the power of some of the world’s most powerful supercomputers, iPlant users can access the cloud-based Data Store, which provides very large amounts of space for researchers to store, and quickly transfer and share ‘big data’ files.

iPlant users also have access to the Discovery Environment – a web-based, graphical interface that provides access to an ever-expanding suite of modular, integrated ‘apps’ for data analysis. Apps can be built either by the iPlant team or by more experienced users, and cover a wide range of analysis needs. They are user-friendly and very intuitive, meaning that even researchers with little or no knowledge of command line computer programming can easily run an app, or create a pipeline of apps, to analyse large and complex data files.

Why do we need iPlant UK?

iPlant, which is free for anyone around the world to use, is currently distributed across three locations in the US – the Texas Advanced Computing Center, the University of Arizona and Cold Spring Harbor Laboratory. Though the high performance computing power it utilises is currently sufficient, iPlant was designed to be extendable to spread resources between even greater numbers of ‘nodes’. iPlant UK will be the first – hopefully of many – international iPlant hubs to ensure the future sustainability of the resource on a global scale.

As we noted in our recent Journal of Experimental Botany paper, one of the drawbacks of having iPlant located solely in the US, is that technical user support is only currently available during US office hours. When we hosted our workshop at the University of Warwick in September 2013, iPlant’s US-based support engineers kindly agreed to be woken up if we needed them – and we did! Clearly that’s not an ideal solution going forwards, especially as the number of worldwide users grows and grows.

As well as having access to technical support on the GMT timezone, the project’s collaborators at the Universities of Warwick, Liverpool, Nottingham and at The Genome Analysis Centre (TGAC), aim to convert existing BBSRC-funded software tools for the iPlant environment. This will increase community access to these useful resources, and their uptake, giving the plant science community even greater opportunities for efficient, effective, collaborative research.

How will it work?

iPlant UK will run as an independent, UK-hosted iPlant node that will centralise compute power and data storage to a single site at TGAC.

The team at TGAC, managed by Dr Tim Stitt and Dr Rob Davey, will work together to install and maintain new and existing hardware infrastructure at TGAC, and once that phase is complete, they will start work to establish and launch the iPlant UK node.

Meanwhile, teams at the Universities of Warwick, Nottingham and Liverpool will convert software tools they have created from their existing formats to the iPlant environment.

  1. University of Liverpool: Next generation sequencing workflows (led by Professor Anthony Hall). Working with the wheat community, the team at Liverpool will optimise a wheat genetic tool bench for next generation sequencing, and a pipeline for mapping-by-sequencing.
  2. University of Warwick: Gene expression, networks and promoter motif tools and pipelines (led by Professor Jim Beynon). The Warwick team will port tools from the PRESTA project into the iPlant environment. These tools include those for identifying differential gene expressions, clustering and network inference, and promoter analysis.
  3. University of Nottingham: Image-based phenotyping (led by Professor Tony Pridmore, Centre for Plant Integrative Biology). The team at Nottingham will convert a range of popular tools for visualising root phenotypes, so that they can be accessed and used from the iPlant environment.

If you are interested in getting involved with this project, two posts at TGAC are currently being advertised (but hurry, the closing date is tomorrow, 3rd March!)

Opportunities at Warwick and Nottingham will be announced soon so stay tuned for updates!

Plant science – making an impact on scientific publishing

Categories: Arabidopsis, resource
Comments: No Comments
Published on: September 5, 2013

This year is proving to be a good year for plant science publications. So far there have been special plant science issues in Science and Genome Biology (and I have it on good authority that there will be plant synthetic biology special issue of another journal coming soon) as well as a landmark birthday for New Phytologist.

Special Issues for Plant Science

The open access journal Genome Biology published their Plant Science Special Issue in June 2013. It was guest edited by Mario Caccamo, acting director and Head of Bioinformatics at The Genome Analysis Centre. He discusses the issue and explains the importance of plant genomics, alongside Dale Sanders and other experts, in this podcast from Biome, BMC’s online magazine. The special issue itself features a whole host of UK researchers, including  Cristobal UauySebastian SchornackAnna Amtmann and Edgar Huitema.

The Science Special Issue, published just last month, unsurprisingly had a much broader focus – Smarter Pest Control. The featured reports take a global look at issues surrounding crop protection from pests, including RNAi-based pesticides, possible health problems caused by traditional pesticides, and tracking the effects of pesticides in wild animal populations.

New Phytologist Celebration

The Lancaster based journal New Phytologist, founded in 1902, is celebrating 200 volumes in October. By my reckoning, it’s the second oldest plant science journal in the world, after Annals of Botany which began life in 1887 as the Journal of Botanical Science (special mention for strictly botany journal, Flora). There is an incredible celebratory Virtual Special Issue of New Phytologist available here, featuring historic articles from throughout the journal’s lifetime including a 1904 critique of the then fashionable field of plant-based ecology from the great man himself, Sir Arthur Tansley.

Arabidopsis UK research roundup

On a related more local note, our new team member Lisa has been searching the literature each week for publications from UK Arabidopsis or other basic plant science researchers. She’s posting the Arabidopsis Research Round-up to the GARNet News pages, so check it out if you want to keep up with new research from your UK colleagues. If you’ve been published and want to make sure we spot your paper (we’re not perfect!), feel free to email Lisa at lisa@garnetcommunity.org.uk to let her know.

Bioinformatics: Training the Trainers

Categories: bioinformatics, Workshops
Comments: No Comments
Published on: April 9, 2013

My apologies for the GARNet radio silence over the last couple of weeks – we’ve been busy helping with PlantSci 2013 preparations as well as working on our own 2013 meetings (announcement of our September workshop coming soon!), going to a few external meetings, and enjoying that arctic Easter break too.

The week before Easter I went to an ELIXIR/GOBLET Training the Trainers workshop at TGAC (The Genome Analysis Centre). If you don’t know what ELIXIR or GOBLET are … don’t worry. They’re fairly new bodies and at the moment have quite a niche target market/audience, but they will be influencing bioinformatics and computational biology use and training over the next few years.

The ELIXIR project was FP7-funded in 2007 and aims to establish a sustainable European infrastructure for biological information. The infrastructure should eventually be a place for data storage, access, and analysis – for anyone who wants to use it in one of the member countries. Sixteen countries are participating, and each has a ‘node’ responsible for a different aspect of the project. ELIXIR-UK is based at the EBI in Cambridge, and is both the co-ordinating hub of the entire project and the training node.

GOBLET is the unusually straightforward acronym for Global Organisation for Bioinformatics Learning, Education and Training. Its mission is essentially to support trainers and educators in bioinformatics and computational biology. ‘Training’ can be either a full-time job, or incorporated into another job. Their aims include establishing guidelines and standards for training, gather funding, and forming a networking and support hub where resources can be shared internationally.

(more…)

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