Work for GARNet!

Categories: GARNet
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Published on: March 5, 2015

As we have mentioned on our main website, we are searching for a new GARNet Coordinator. Until now, the job has been advertised for internal Cardiff University applications only, but as of today, anyone is eligible to apply. Would you like to work for GARNet? You can find the job advertisement here: Research Associate, GARNet Coordinator.

What does a GARNet Coordinator do?

Lots of things! The GARNet Coordinator is responsible for managing the day-to-day running of the network – you can find a full job specification on the Cardiff website, but practically, the job includes things like:

  • Maintaining the GARNet website, mailing list, Twitter account and blog;
  • Organising regular meetings with our Committee, including meeting room bookings, catering and logistics, taking minutes and ensuring actions from the last meeting are completed;
  • Identifying opportunities for workshops and events that will benefit the plant science community, and then organising those events – recent past examples include the GARNet Conference, Software Carpentry workshops at Liverpool and Warwick, and an iPlant workshop. You’ll need to find sponsorship, book event space and hotel rooms, organise transport and catering, prepare delegate information packs, and so on;
  • Staying abreast of what’s currently happening in Arabidopsis and basic plant science research, and networking and liaising with members of the plant science community by attending national and international conferences such as ICAR, SEB or UKPSF;
  • Writing – we have written a number of papers published in peer reviewed journals, as well as meeting reports, contributions to consultations, guest blog posts and articles, our Arabidopsis Research Round-up, and the twice-yearly GARNish newsletter;
  • Planning and developing grant applications for resources or projects identified by the plant science community as being of value – we recently secured renewed funding for GARNet itself, and we were heavily involved with putting together the application for iPlant UK.
The GARNet Coordinator needs to be a plant scientist who is well organised, a good writer, communicator and networker. You will, on occasion, need to travel nationally and internationally, and good computer skills are a must – experience with website management, blog platforms and creative publishing software such as Adobe InDesign and Photoshop are ideal.
If you’d like any more information about the GARNet Coordinator vacancy, please feel free to submit informal enquiries to Ruth Bastow.
The closing date for applications is 19 March 2015.

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!

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