Data Mining with iPlant

Categories: GARNet, Workshops
Comments: 4 Comments
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
Comments: No Comments
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


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 to let her know.

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