Software Carpentry Bootcamp: An organiser’s story

Categories: resource, Workshops
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Published on: November 27, 2014

Lisa and I have been involved in two Software Carpentry Bootcamps this year: firstly the hosts of a Bootcamp in April at the University of Warwick, and the second, just last week, at a Bootcamp co-organised with the Centre for Genomic Research at the University of Liverpool. A few people at the Liverpool event expressed interest in organising their own workshops, so we thought we would talk you through the stages of hosting a bootcamp and share our experiences to help you decide whether you want to run one of your own.


1. Early planning: Decide where the event will be, who will pay, who your audience is and what topics you want to be covered.

It is (now) not free to host a Software Carpentry event. When we organised the Warwick Bootcamp, Software Carpentry was subsidised by the Mozilla Foundation, but since the recent move to its own Software Carpentry Foundation, events now command a fee (TBC) – it’s still a non-profit organisation though.

Software Carpentry trainers are volunteers but you will need to be able to reimburse their travel, food and accommodation expenses. They can come from anywhere in the world, so budget for transatlantic flights!

Other costs you will need to think about include venue hire, and travel, food and accommodation for the workshop participants. It is also up to you whether you want to charge people to attend the workshop to recoup some or all of your costs. For our first bootcamp at Warwick we had sufficient funding to make the event free for attendees, and we paid for one nights’ accommodation too. Because it was free, we did get some last-minute drop-outs, but we had a long waiting list to fill the empty spaces. At the Liverpool event, trainees paid a small registration fee, and paid for their accommodation themselves. Both events booked up quickly and were oversubscribed, so either model works.

We provided lunch and refreshments during both workshops (caffeine breaks are definitely recommended!), and also organised a dinner on the first night of the workshop.

Both of our bootcamps were for complete beginners, but if there are specific topics you need to cover, Software Carpentry can tailor a programme to your needs.


2. First contact with Software Carpentry: If you’re in the UK, the Software Sustainability Institute (SSI) in Edinburgh is your point of contact for organising Software Carpentry events. There is information and an email address on the Software Carpentry website.

Discuss your ideas for the bootcamp with Software Carpentry. We worked with Aleksandra Pawlik and Giacamo Peru from SSI over Skype and via email. Software Carpentry requires core topics to be covered, so there may be some negotiating as you work it out. As our bootcamps were for absolute beginners, unlike most Software Carpentry events, this took some time but was not at all difficult to sort out.

Decide on a date, making sure to consider other events that might limit both trainees and instructors.

The Software Carpentry website suggests being flexible with the dates to make finding instructors easier. I think this would mean pulling a bootcamp together very quickly, which might be ok for an institutional event but was impossible for us.


Arabidopsis Research Round-up

Categories: Arabidopsis, Global, Round-up
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Published on: November 26, 2014

There are some really interesting new papers for you this week. We have two different protein interaction studies, one on microtubules involving scientists from Durham, and one on meiotic chromosome movement from Oxford Brookes and Birmingham. There’s also a report on ‘FANS’, a new technique used to study Arabidopsis embryos from Nottingham researchers, a US–UK collaborative project to develop Araport – a new online resource for plant scientists, and an exciting new rapid report from theJohn Innes Centre. Enjoy!


  • Galva C, Kirik V, Lindeboom JJ, Kaloriti D, Rancour DM, Hussey PJ, Bednarek SY, Ehrhardt DW and Sedbrook JC. The microtubule plus-end tracking proteins SPR1 and EB1b interact to maintain polar cell elongation and directional organ growth in Arabidopsis. The Plant Cell, 18 November 2014.DOI: 10.1105/tpc.114.131482.

Researchers from the University of Durham were collaborators on this paper, which describes efforts to understand the interactions between the microtubule plus-end tracking proteins (+TIPS) EB1b and SPR1. Data suggest that SPR1 and EB1b have complex interactions as they load onto microtubule plus ends and direct polar cell expansion and organ growth in response to directional cues.


  • Slane D, Kong J, Berendzen KW, et al. Cell type-specific transcriptome analysis in the early Arabidopsis thaliana embryo. Development, 19 November 2014. DOI: 10.1242/dev.116459.

Ive De Smet from the University of Nottingham worked with a German–Belgian team to put together this ‘Techniques and Resources’ paper in Development journal. Here, the team describes the use of fluorescence-activated nuclear sorting (FANS) to conduct cell type-specific transcriptome analysis in the early Arabidopsis embryo.


  • Krishnakumar V, Hanlon MR, Contrino S, et al. Araport: the Arabidopsis Information Portal. Nucleic Acids Research, 20 November 2014. DOI: 10.1093/nar/gku1200.

This paper, involving scientists from the University of Cambridge, describes the Arabidopsis Information Portal (AIP, or Araport), a new online resource for plant biologists. At its core, it is the home for the Arabidopsis thaliana genome sequence and associated annotation, but it does much more than this. Users can access data curated from a variety of sources – including TAIR, GO, BAR, EBI, UniProt, PubMed and EPIC CoGe – as well as make use of feature-rich web applications to search, download, data-mine and genome-browse to their hearts content.

Araport also posts news, jobs and information relevant to the global Arabidopsis community – in fact, GARNet regularly posts information, including this Round-Up!


  • Varas J, Graumann K, Osman K, Pradillo M, Evans DE, Santos JL and Armstrong SJ. Absence of SUN1 and SUN2 proteins in Arabidopsis thaliana leads to a delay in meiotic progression and defects in synapsis and recombination. The Plant Journal, 21 November 2014. DOI: 10.1111/tpj.12730.

In eukaryotes, Sad1/UNC-84 (SUN)-domain proteins are part of a complex responsible for forming attachments between the chromosome telomeres and the components of the cytoplasm, which help the chromosomes to move appropriately during meiosis. This paper, involving scientists from Oxford Brookes University and the University of Birmingham, describes the discovery of homologous proteins – AtSUN1 and AtSUN2 – in Arabidopsis thaliana.


  • Nützmann H-W and Osbourn A. Regulation of metabolic gene clusters in Arabidopsis thaliana. New Phytologist, 21 November 2014. DOI: 10.1111/nph.13189.

This rapid report comes from Hans-Wilhelm Nützmann and Anne Osbourn from the John Innes Centre. Comparing gene expression in chromatin mutants, they find that ARP6 and H2A.Z are involved in the regulatory process required for the normal expression of metabolic gene clusters in Arabidopsis. Specifically, these proteins are implicated in localized chromatin modifications that allow contiguous genes to be expressed in a coordinated way. This is a major finding that could open up new opportunities for the discovery and manipulation of specific metabolic pathways in plants!

Natural variation in Arabidopsis, the MAGIC way

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Published on: November 24, 2014

The research: Finding the causes of variation in seed size and number

In the Arabidopsis Research Round-up a few weeks ago, Lisa highlighted a paper from a team at the University of Bath about natural variation in Arabidopsis seeds. Lead author Paula Kover and her team investigated the genetic basis of variation in seed size and number.

All plants negotiate a trade-off between the number and size of their seeds, so it was a surprise to learn that of 9 QTL for seed number and 8 for seed size, there was only 1 overlapping QTL. The strong negative correlation seen in size and number is logically due to resource use efficiency, but these data suggest that this is not determined genetically.

There is enough of a positive correlation between seed number and fruit length that fruit length is sometimes used to estimate seed number – though the correlation is not strong. Here too there was only 1 QTL overlapping between the two traits, suggesting that any correlation is not inherent and may vary according to environmental or internal factors.

Based on QTL analysis, Kover et al. identify five potential genes that underlie quantitative variation in seed size and number: AAP1 (AT1G58360) and KLUH (AT1G13710) on chromosome 1; and JAGGED LATERAL ORGANS (AT4G00220), YABBY 3 (AT4G00180), and BEL1 (AT5G41410) on chromosomes 4 and 5.


The tool: MAGIC Arabidopsis lines

All the above work was carried out using Mulitparent Advanced Generation Inter-Cross (MAGIC) Arabidopsis lines. Kover and others developed these lines to improve methods of identifying natural allelic variation that underlies variable phenotypic traits. The lines are recombinant, inbred over 6 generations, that originate from an intermated hereogenous stock. This pedigree means they represent a large diversity of genes in mostly homozygous lines; ideal for accurate QTL mapping. The original MAGIC paper from 2009 paper states ‘MAGIC lines occupy an intermediate niche between naturally occurring accessions and existing synthetic populations.’

The MAGIC lines are an incredible open resource for studying natural variation in Arabidopsis: they enable a researcher to map a trait to within 300kb. All lines in the 2009 paper are available from NASC. A set of digital tools, hosted at the Wellcome Trust Centre for Human Genetics, contains the (open source) software needed to run the QTL analysis and the data files associated with the lines.


Highlighted paper: Gnan, Priest and Kover. The genetic basis of natural variation in seed size and seed number and their trade-off using Arabidopsis thaliana MAGIC lines. Genetics, 2014. 10.1534/genetics.114.170746

Also cited: Kover et al. A multiparent advanced generation inter-cross to fine-map quantitative traits in Arabidopsis thaliana. PLOS Genetics, 2009. DOI: 10.1371/journal.pgen.1000551

For a comparison of resources for studying natural variation, see Weigel, Plant Phys, 2012 158:2-22

Arabidopsis Research Round-Up

Categories: Arabidopsis, Global, Round-up
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Published on: November 20, 2014

Here’s your weekly round-up of the latest Arabidopsis research from the UK, this week including a mixed bag of studies from the Universities of Edinburgh, Oxford,Worcester, Warwick and Nottingham.


  • Shi YZ, Zhu XF, Miller JG, Gregson T, Zheng SJ and Fry SC. Distinct catalytic capacities of two aluminium-repressed Arabidopsis thaliana xyloglucan endotransglucosylase/hydrolases, XTH15 and XTH31, heterologously produced in Pichia. Phytochemistry, 27 October 2014. DOI: 10.1016/j.phytochem.2014.09.020.

Janice Miller and Stephen Fry from the University of Edinburgh (with former lab member Tim Gregson now at the Lancaster Environment Centre) worked with Chinese collaborators on this study to further understand the roles of the xyloglucan endotransglucosylase/hydrolases (XTHs). They looked at two very different XTHs – XTH15 and XTH31 – to analyse their modes of action compared to the rest of this enzyme family.


  • Berns MC, Nordström K, Cremer F, Tóth R, Hartke M, Simon S, Klasen JR, Bürstel I and Coupland G. Evening expression of Arabidopsis GIGANTEA is controlled by combinatorial interactions among evolutionarily conserved regulatory motifs. The Plant Cell, 27 October 2014. DOI: 10.1105/tpc.114.129437.

Though a former member of the Coupland lab at the Max Planck Institute for Plant Breeding Research, which led this study, Réka Tóth is now on staff at the University of Oxford. This paper explores the role of Arabidopsis GIGANTEA in its contributions to photoperiodic flowering, circadian clock control and photoreceptor signaling; in particular its transcription, which is regulated by light and the circadian clock. Three evolutionarily contrained motifs (CRMs) are identified within the GIGANTEA promoter which, combined with EVENING ELEMENTs and ABA RESPONSE ELEMENT LIKE motifs, contribute to diurnal transcription patterns.


  • Andersson MX, Nilsson AK, Johansson ON, et al. Involvement of the electrophilic isothiocyanate sulforaphane in Arabidopsis local defense responses.Plant Physiology, 3 November 2014. DOI: 10.1104/pp.114.251892.

Working with Swedish and American partners, Gülin Boztas and Mahmut Tör from the University of Worcester were also collaborators on this paper. While the hypersenstive response of plants to pathogen effector molecules has long been documented, this research provides new detail on the nature of that response; specifically that sulforaphane – a compound triggering programmed cell death – is released by Arabidopsis thaliana when infected by Hyaloperonospora arabidopsidis.


  • Piquerez SJ, Harvey SE, Beynon JL and Ntoukakis V. Improving crop disease resistance: lessons from research on Arabidopsis and tomato. Frontiers in Plant Science, 10 November 2014. DOI: 10.3389/fpls.2014.00671. [Open Access]

GARNet PI Jim Beynon is co-corresponding author for this helpful review. In it, Jim and colleagues from the University of Warwick describes how the use of Arabidopsis and tomato as model organisms for plant research have contributed knowledge and understanding of plant defense mechanisms, and how these have been and will continue to be applied to modern crop improvement programmes.


  • Mellor N, Péret B, Porco S, Sairanen I, Ljung K, Bennett M and King J. Modelling of Arabidopsis LAX3 expression suggests auxin homeostasis. Journal of Theoretical Biology, 13 November 2014. DOI: 10.1016/j.jtbi.2014.11.003.

Former GARNet committee member Malcolm Bennett, together with colleagues from Nottingham, France and Sweden, present this paper in Journal of Theoretical Biology. They describe their development of a single-cell model of the auxin influx carrier LAX3 (which is mediated by the ARF7/19 IAA14 signalling module) to demonstrate that hysteresis and bistability may explain the experimentally observed ‘all-or-nothing’ LAX3 spatial expression pattern in cortical Arabidopsis root cells containing a gradient of auxin concentrations.

Arts and crafts with Arabidopsis

Categories: something fun
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Published on: November 14, 2014

These past couple of weeks, we at GARNet have noticed a number of amazing Arabidopsis artistic creations cropping up on our Arabidopsis twitter search tool (yes, we monitor Arabidopsis tweets – we’re cool like that). I thought I’d round them up for you – happy Friday!


Arabidopsis cake
Arabidopsis cake, made by Liam Walker and Mairi Walker.

I can personally confirm that this pot of flowering Arabidopsis plants is all edible (the tiny exception being the stems, which are made of wire). It was incredibly life-like, down to green sugar-dust algae clinging to the icing pot and oreo-crumb soil. The plants even had roots! It was created for a Gifford group lab meeting by Warwick undergraduate Liam Walker and his sister Mairi, who posted this photo on Twitter and kindly let me share it here.



Jackie Hunter, BBSRC: “Breakthroughs will happen where disciplines coalesce”

Categories: funding, synthetic biology
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Published on: November 12, 2014

Jackie Hunter, Chief Executive of BBSRC, delivered a lunchtime presentation at the University of Warwick’s School of Life Sciences on Monday this week. She gave an overview of BBSRC investments and strategy, and spent the final twenty minutes in discussion with the gathered researchers, who posed questions from the floor.

Supporting bioscience in the UK

BBSRC is the biggest source of plant science funding in the UK. Its charter is to fund research and training in world-class bioscience, deliver social and economic impact, and to promote public dialogue.

Hunter explained that BBSRC responsive mode funding (around £150m per year) aims “to ensure excellence in science, wherever it comes from.” It must be functioning well as the UK is top of citation impact index, and the UKPSF found that UK plant science, mainly funded by BBSRC, is second only to the US in terms of publication impact. Strategic funding, capital and campus capital funding to institutes (£6m, £73m and £30m respectively) is used to maintain skills and output in economically important areas of research at the institutes; though Hunter made it clear that ‘blue sky’ research, funded via responsive mode, is important for impact as it generates both top REF scores and top impact metrics. BBSRC also invests £29M per year in specific initiatives.

When asked for advice about increasing BBSRC funding to the department, Hunter emphasised that funding allocation is based on excellence, so departments should provide an environment where excellence can flourish. She also said, “Interdisciplinarity is important: breakthroughs will happen where disciplines coalesce.”

Training and skills

There are around 2000 PhD students at any one time in the Doctoral Training Partnerships that make up part of the £71M BBSRC investment in Knowledge Exchange, Training and Skills. During the discussion session, someone asked about support later in a researcher’s career and Hunter pointed out that investment in early career fellowships must come at the expense of something else. She suggested that BBSRC may consider the value of studentships versus early career fellowships carefully, and in consultation with the community, over the next few years.

Plant science and Agriculture

Jackie Hunter is on the Agri-tech Leadership Council, which aims to increase UK agricultural exports and the value of the UK agri-tech industry by aligning public and industry funding and building skills and research output in agriculture and agri-technology. She also spoke about future directions in BBSRC’s Agriculture and Food theme: improving the nutritional qualities of plants and biopesticides regulation are both likely to become priority areas of research.

Hunter trailed two documents intended to help make two arguments, both of value to the UK plant research community. The first is an upcoming review on animal and plant health, lead by Defra and with input from BBSRC. To be launched later this month, it will be a starting point for BBSRC and Defra to develop joint strategies in tackling current animal and plant health issues, and to work together to call for more funding in this area. The second is a discussion document about synthetic biology and other new ways of working; Hunter hopes this will help make the case for trait-based, rather than methods-based, regulation of new crops.

On-going activities

Hunter also highlighted a few current initiatives our readers might be interested in.

BBSRC has invested £18m in 13 Networks in Industrial Biotechnology and Bioenergy (NIBBs). Here at GARNet, we’re in touch with the High Value Chemicals from Plants Network about a synthetic biology event next year and I recommend you join (it’s free) if you’re interested in high-value plant products or synthetic biology. The other plant science network is the Lignocellulosic Biorefinery Network.

One of Hunter’s objectives as CEO is to promote dialogue between scientists and a broad audience, and the first step towards engaging with the general public is the Great British Bioscience Festival. It is taking place this Friday, Saturday and Sunday in Bethnal Green, London, and there will be some amazing plant science among the exhibits. Lisa will be visiting the Festival to cover it for the next issue of the GARNish newsletter so stay tuned for her report!

Arabidopsis Research Round-up

Just one new paper to share with you this week!


  • Binkert M, Kozma-Bognar L, Terecskei K, de Veylder L, Nagy F and Ulm R. UV-B-responsive association of the Arabidopsis bZIP transcription factor ELONGATED HYPOCOTYL5 with target genes, including its own promoter. The Plant Cell, 28 October 2014. DOI: 10.1105/tpc.114.130716. [Open Access]

Though he has a joint appointment at the Hungarian Academy of Sciences, Ferenc Nagy is also SULSA Chair of Cell Biology at the University of Edinburgh. Working with Swiss, Hungarian and Belgian colleagues, this paper describes research to understand the transcription factors regulating plants’ protective responses to UV-B. It is shown that, in Arabidopsis, binding of the bZIP transcription factor ELONGATED HYPOCOTYL5 (HY5) to the promoters of UV-B-responsive genes is enhanced by UV-B independently of the UV-B photoreceptor UV RESISTANCE LOCUS8 (UVR8).

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