Data Mining with iPlant

Categories: GARNet, Workshops
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Published on: September 20, 2013
Group photo taken on the last day (the survivors!)

All this week, the GARNet team have been busy with our Data Mining with iPlant workshop – though the iPlant team Dan Stanzione, Matt Vaughn, Naim Matasci and Jason Williams have certainly been even busier, training and coding new training materials by turns throughout the week.

You can see what we’ve been up to and even use the tutorials on the Data Mining with iPlant wiki page, set up by the iPlant guys for the workshop. Delegates have gone through real-time training in CHIP-seq and genomic interval analysis, examining differential expression in within an RNA-seq dataset, and been introduced to using iPlant for GWAS.

As I type, delegates are huddled in small groups while the iPlant team give advice about their particular challenges – as you can see on the wiki, most of the delegates have RNA-Seq data to analyse but others are looking at genome data or CHIP-seq.

The workshop was held in the Interactive Computational Learning Suite at the University of Warwick’s School of Life Sciences. (more…)

Plant Methods reviews NGS for Plant Science

Categories: GARNet, Workshops
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Published on: September 12, 2013

Were you at our Tools and Technologies to Advance Plant Research event at Liverpool last year? Well if you were, you can now hear more from three of the speakers in a mini-series of reviews in Plant Methods. And if you weren’t and you’re wondering if next generation sequencing can be applied to your plant research, here’s your chance to find out.

First, Tom Hardcastle wrote a review on using NGS sequence the methylome – it was published in June this year (Plant Methods 9:16). He gives an introduction to the role of cytosine methylation in the regulation of gene expression, and then takes readers through the stages of mapping genome methylation.

Arther Korte’s review on genome wide association studies (GWAS) was published in July (Plant Methods 9:29). He and Ashley Farlow, who are both working on the 1001 Genomes Project, discuss the advantages and disadvantages of GWAS and how to build a good project.

Most recently, a review on NGS for complex crop genomes by Klaus Mayer and colleagues was published (Plant Methods 9:35). They overview various approaches to managing extremely large, complex genomes like the recently sequenced wheat genome. They focus specifically on the Genome Zipper, which Mayer presented at the workshop.

Other workshop talks covered genome-wide association studies, mutant identification, genome mapping, transcriptomics using both ‘traditional’ RNA-seq and new method of direct RNA sequencing, and chromatin mapping. If you want to find out more about using NGS for these applications (it’s not just about nucleotide sequencing any more!), a good place to start is the Tools and Technologies to Advance Plant Research abstract book and the Storify of the workshop, which contains links to a lot more papers and reviews. I also wrote a report for the workshop sponsor, the Genetics Society, which you can read in their July Newsletter (page 28).

Image credit: Envel Kerdaffrec


Two GARNet Events

Image by for GARNet

We have some GARNet news to share!

First of all, we are pleased to finally open registration for the hands-on iPlant training workshop ‘Data Mining with iPlant‘. Unfortunately we’ve had to change the planned location, and it will now be at the University of Warwick. The date is still 17-20 September 2013.

For those who don’t know, iPlant is an incredible free resource which allows its users to access high performance computing power, large scale data storage, and analytical software needed for a variety of data- or compute- intensive research applications.

You can either come for just one day for a free hands-on introduction to iPlant, or stay for four days and get in depth training on how to analyse real data in iPlant. For more information go to:

Our second announcement is more of a save-the-date than an invitation. The GARNet general conference will return next year, possibly for one time only. GARNet 2014: The Past, Present and Future of the Genetic Model Revolution will be held at the University of Bristol on 9-10 September 2014. It will be a celebration of exciting new plant science, and a look at the evolving nature of model systems as well as the brilliant achievements made with them in the past.

The Journal of Experimental Botany kindly recorded and uploaded talks from the last GARNet conference in 2011. Here is Katherine Denby of the University of Warwick talking about the PRESTA project, which since this talk has produced two Plant Cell papers (1,2). You can see the rest of the talks from GARNet 2011 on the JXB website.

Starting your interdisciplinary journey

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Published on: May 14, 2013

This is a guest post by Susie Lydon, Outreach Officer at the University of Nottingham

Plant science is becoming increasingly interdisciplinary, and for early career researchers, gaining experience in working across the traditional subject boundaries can be very useful. A common problem is that many of the training opportunities in relevant areas of maths and computer science assume a level of background knowledge which many biologists do not have (or do not feel confident about).

The Centre for Plant Integrative Biology at the University of Nottingham has been running ‘summer schools’ (which actually take place in early September!) for six years now which aim to bridge the gap for interdisciplinary ‘beginners’.

Mathematical Modelling for Biologists is a four-day residential course which provides an introduction to biological modelling. The course comprises integrated lectures and computer practical classes, and the background knowledge assumed is ‘rusty A-level maths’ or equivalent. Participants learn from examples taken from gene regulation, biochemical reactions, population dynamics, and epidemiology.

Image Analysis for Biologists is a three-day residential course running for the second time in September 2013. The aims of this course are to allow participants gain an understanding of image analysis approaches commonly used in the biological sciences, and confidence in applying them. Like the modelling course, it comprises integrated lectures and practicals using relevant software. Many of the examples are drawn from CPIB’s work in plant image analysis, but the course is open to biologists from any discipline.

For more information about these courses, and to apply to attend in September 2013, visit the CPIB events page, or contact CPIB’s Outreach Officer, Dr Susie Lydon.

Image credits: Centre for Plant Integrative Biology

Mathematics in the Plant Sciences

Categories: bioinformatics, Workshops
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Published on: April 17, 2013

After the ELIXIR/GOBLET workshop before Easter, I headed to Nottingham for another workshop, this time as an onlooker. In a brilliantly eccentric set-up there were actually two parallel workshops, and the participants hopped between the two and had lunch, dinner, and tea breaks in the same rooms. The event I was officially attending was the final meeting of the ‘Systems approaches to study hormone regulated root growth’ US Partnering Award (USPA). The Sixth Mathematics in the Plant Sciences Study Group was in its final two days during the USPA workshop, and some of its attendees presented their research at the USPA meeting or sat in on a session they were particularly interested in.

The Study Groups are hackathon-style workshops at which mathematicians and computer scientists take on problems set by plant scientists. This year’s problems included analysing 300 standing-electron microscopy images of cell walls, and modelling nitrogen release from the symbiosome. As someone with a traditional science background, of course the solutions the teams came up with were a bit beyond me – which is, after all, the whole point of the Study Group. I was impressed by the solutions that had appeared after just four days of work, which ranged from programmes to quantify subtle differences in images, to a model which predicted the optimum light input for photosynthesis and explained plant acclimatisation to variable light sources.

There will be another Study Group and when it is announced, we’ll keep you informed. If you know any mathematicians or computer scientists with a liking for academic science problems and who likes hackathon events, let them know about Study Groups and encourage them to send their details to Susie Lydon, who organises the events. Similarly if your plant research has thrown up a thorny problem which needs specialist expertise, think about submitting it for the next Study Group.

Bioinformatics and Data Analysis Training for Plant Scientists

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Published on: April 11, 2013

Large datasets are now the norm in modern biology. Modelling is progressing from the protein and molecular interaction level to tissue, organ, and whole-plant scales; while everything from genomics through to phenomics and, increasingly, field-level and multi-scale biology involves high throughput experiments. All of these necessitate ever greater computing power and use of complex analysis tools and software. We need you to tell us (click for extremely short survey) which areas of bioinformatics and data analysis you would benefit from training in, ahead of an upcoming GARNet workshop (in association with iPlant and the Hartree Centre).

The iPlant Collaborative is a community of researchers, educators, and students working to deliver a useful and usable cyberinfrastructure for plant science. Users are able to store and analyse their data online, and use iPlant tools for genome assembly, comparative genomics, CHiP and RNA Seq analysis, and much more. A working group is developing modelling tools at the moment, which will take advantage of the high performance computing power iPlant provides, and will support the construction, parameter estimation, sensitivity analysis, and utilization of models. All the resources are free for users worldwide and all are web based, requiring no specialist hardware at the user’s location. (more…)

Bioinformatics: Training the Trainers

Categories: bioinformatics, Workshops
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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.


Conference Season

Categories: Workshops
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Published on: March 14, 2013

We are delighted that the Gatsby Charitable Foundation are kindly funding £500 travel bursaries to help four UK-based PhD students attend the annual International Conference on Arabidopsis Research (ICAR) conference, which this year will be in Sydney, Australia, on 24-28 June 2013.

If you would like to apply for this bursary please fill out the GARNet travel bursary GARNet travel bursary form and return it to me ( by the 14th April. To be eligible, you must be a current PhD student Ph.D at the time of the conference, and have submitted a poster abstract to present at the meeting. You must have permission from your supervisor to attend the conference.

If you want to go to a conference but can’t spare the funds or the time to travel to Australia, there are great meetings going on in the UK too. I made a list of travel grants you can use to go to conferences here.

UK PlantSci 2013: 16–17 April, Dundee, Scotland

UK Brassica Research Community: 9 May, Rothamsted.

An Introduction to Opportunities in Plant Synthetic Biology: 21-22 May, Nottingham, England

International Symposium on Plant Photobiology: 3-6 June, Edinburgh, Scotland.


Other major international plant science conferences this year are:

Plant Immunity Pathways and Translation: 7-12 April 2013, Montana, USA.

31st New Phytologist Symposium (Orchid symbioses: models for evolutionary ecology): 14-16 May, Calabria, Italy.

SEB Annual Main Meeting 2013: 3–6 July, Valencia, Spain

ASPB Plant Biology 2013: 20–24 July, Providence RI, USA

7th EPSO Conference: 1–4 September, Peloponnese, Greece

Plant Genome Evolution: 8-10 September, Amsterdam, The Netherlands.

32nd New Phytologist Symposium (Plant interactions with other organisms): 20-23 November, Buenos Aires, Argentina.

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