REPORTSREPORTS

Over the years GARNet has either produced or provided information and evidence for a variety of reports and meeting transcripts. A number of which are available to download here. We hope you find them really useful.

GARNet 2014 - Arabidopsis: The Ongoing Green Revolution

15th Oct 2014

GARNet hosted its conference, Arabidopsis: The Ongoing Green Revolution, at the University of Bristol on 9th and 10th September 2014. You can read more about the conference by clicking here, find a Storify of tweets here, or view some photos from the event on our Weeding the Gems blog here

Below is the programme of speakers we enjoyed over the two days. To download presentations from some of these speakers, please visit our blog: http://blog.garnetcommunity.org.uk/garnet-2014-presentations/.

Clicking the Download link below will take you to the conference abstract book. 

Programme

Session 1: Physiology & Productivity

  • Alistair Hetherington, University of Bristol: The response of stomata to environmental signals
  • Miriam Gifford, University of Warwick: Understanding plant root developmental plasticity using cell-specific genomes
  • Steve Penfield, University of Exeter: A cryptic switch formed by external temperature coincidence generates a life history strategy for Arabidopsis
  • Beatriz Lagunas, University of Warwick: The AtSCL26 transcription factor controls cross-talk between GA- and Nitrogen- control of root architecture in Arabidopsis thaliana roots

Session 2: Genome Biology

  • Siobhan Brady, University of California, Davis, USA: Getting to the root of things: spatiotemporal gene regulatory networks in plant roots
  • Ian Henderson, University of Cambridge: Unravelling interactions between genetic diversity and recombination in Arabidopsis
  • Antony Dodd, University of Bristol: Circadian signalling between subcellular genomes
  • Emily Hawkes, John Innes Centre: Evolutionary conservation of an Arabidopsis long non-coding RNA, COOLAIR, supports a regulatory function

Session 3: Natural Variation

  • Maarten Kournneef, Max Planck Institute for Plant Breeding Research, Germany: Exploring Arabidopsis natural variation
  • Adrian Brennan, University of Durham: Population genetic strcuture and natural variation of the model plant Arabidopsis thaliana in its native southern range extremes
  • Javier Agusti, University of Oxford: Using natural variation to identify new cambium regulators
  • Monika Mierzwinska, University of Aberdeen: Natural variation in endodermal development and plant mineral nutrient homeostasis
Session 4: Systems and Synthetic Biology

  • Andrew Millar, University of Edinburgh: Systems for biological timing in the green cells
  • Siobhan Braybrook, The Sainsbury Laboratory, Cambridge: Understanding the physical basis of growth from the top down
  • Leah Band, University of Nottingham: Systems analysis of auxin transport in the Arabidopsis root tip
  • Matthew Hindle, University of Edinburgh: The reduced kinome of Ostreococcus tauri: core green lineage signalling components in a tractable model species

Session 5: Plant Interactions with their Environment

  • Paul Schulze-Lefert, Max Planck Institute for Plant Breeding Research, Germany: Functions of the Arabidopsis bacterial root microbiota in plant health
  • Cyril Zipfel, The Sainsbury Laboratory, Norwich: Regulation of early receptor kinase-mediated immune signalling
  • Kerry Franklin, University of Bristol: Sunlight, photoreceptors and plant development
  • Sophie Berckhan, University of Nottingham: Why do plants sense oxygen?

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Developing Plant Synthetic Biology in the UK: Opportunities and Recommendations

1st Apr 2014

The report summarises the results of discussions at GARNet’s 2013 workshop, An Introduction to Plant Synthetic Biology

The UK plant science community has excellent research output and trusted community structures, including GARNet and the UK Plant Sciences Federation, so it is well placed to develop a world leading plant synthetic biology base. GARNet will work with dedicated synthetic biology initiatives to action the report's recommendations.

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An Introduction to Opportunities in Plant Synthetic Biology

7th Feb 2014

In May 2013, GARNet ran a meeting introducing plant scientists to the potential and opportunities presented by synthetic biology. Speakers presented a range of synthetic biology applications, from synthetic molecules to whole plant engineering, and will introduce the wide range of available synthetic biology methods, tools, and resources. There was also a time for open discussion about what the plant science community needs to take synthetic biology in plants further. The meeting report has now been published in the Journal of Experimental Botany, who kindly sponsored the event. 

Cook C, Martin LA, Bastow R (2014) Opportunities in plant synthetic biology, Journal of Experimental Botany doi:10.1093/jxb/eru013 can be accessed via this toll-free link

Abstract: Synthetic biology is an emerging field uniting scientists from all disciplines with the aim of designing or re-designing biological processes. Initially, synthetic biology breakthroughs came from microbiology, chemistry, physics, computer science, materials science, mathematics, and engineering disciplines. A transition to multicellular systems is the next logical step for synthetic biologists and plants will provide an ideal platform for this new phase of research. This meeting report highlights some of the exciting plant synthetic biology projects, and tools and resources, presented and discussed at the 2013 GARNet workshop on plant synthetic biology. 

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Making open data work for plant scientists

27th Nov 2013

In July 2012, GARNet and Egenis hosted a ‘Making Data Accessible to All’ workshop at the Innovation Centre, University of Exeter. Participants discussed data donation and use, data dissemination, and means of tracking and evaluating data use, with the aim of making recommendations about data use in plant science. The themes at the workshop were picked up in a paper detailing the current status of data sharing in the plant sciences.

Leonelli S, Smirnoff N, Moore J, Cook C and Bastow R (2013) Making Open Data Work for Plant Scientists, Journal of Experimental Botany doi: 10.1093.jxb/ert273 was published under Open Access and is available here

Abstract: Despite the clear demand for open data sharing, its implementation within plant science is still limited. This is, at least in part, because open data-sharing raises several unanswered questions and challenges to current research practices. In this commentary, some of the challenges encountered by plant researchers at the bench when generating, interpreting, and attempting to disseminate their data have been highlighted. The difficulties involved in sharing sequencing, transcriptomics, proteomics, and metabolomics data are reviewed. The benefits and drawbacks of three data-sharing venues currently available to plant scientists are identified and assessed: (i) journal publication; (ii) university repositories; and (iii) community and project-specific databases. It is concluded that community and project-specific databases are the most useful to researchers interested in effective data sharing, since these databases are explicitly created to meet the researchers’ needs, support extensive curation, and embody a heightened awareness of what it takes to make data reuseable by others. Such bottom-up and community-driven approaches need to be valued by the research community, supported by publishers, and provided with long-term sustainable support by funding bodies and government. At the same time, these databases need to be linked to generic databases where possible, in order to be discoverable to the majority of researchers and thus promote effective and efficient data sharing. As we look forward to a future that embraces open access to data and publications, it is essential that data policies, data curation, data integration, data infrastructure, and data funding are linked together so as to foster data access and research productivity.

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The Model Plant: A Social Science Perspective

17th Oct 2013

In July 2013, GARNet Advisory Committee member Sabina Leonelli (University of Exeter), with Rachel Ankeny from the University of Adelaide, presented a perspective on model organisms at the 2013 meeting of the International Society for the History, Philosphy and Social Studies of Biology in Monpellier.

Her presentation, available to download by clicking the button on the right, features GARNet as a examplar organised model organism research community and is an interesting perspective on how the operates, which is usually considered from the biological sciences research viewpoint. Leonelli and Ankeny have published a written version of their presentation in the journal Endeavour (37:209; http://dx.doi.org/10.1016/j.endeavour.2013.06.001)

Abstract: This article explains the key role of model organisms within contemporary research, while at the same time acknowledging their limitations as biological models. We analyse the epistemic and social characteristics of model organism biology as a form of “big science”, which includes the development of large, centralised infrastructures, a shared ethos and a specific long-term vision about the “right way” to do research. In order to make wise use of existing resources, researchers now find themselves committed to carrying out this vision with its accompanying assumptions. By clarifying the specific characteristics of model organism work, we aim to provide a framework to assess how much funding should be allocated to such research. On the one hand, it is imperative to exploit the resources and knowledge accumulated using these models to study more diverse groups of organisms. On the other hand, this type of research may be inappropriate for research programmes where the processes of interest are much more delimited, can be usefully studied in isolation and/or are simply not captured by model organism biology.

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Plant Science in a Changing World

9th Aug 2013

UK PlantSci 2013, was held at the University of Dundee. GARNet staff Charis Cook and Ruth Bastow, with Mimi Tanimoto, wrote the meeting report, which was published in July 2013 in the journal New Phytologist.

Cook C, Tanimoto M and Bastow R (2013) Plant science in a changing world, New Phytologist, 199: 636–638, doi: 10.1111/nph.12389 was published under open access, and is accessible here.

Abstract: The UKPSF's second annual conference, UK PlantSci 2013, was held at the University of Dundee in April, with support from the Gatsby Charitable Foundation, the Society for Experimental Biology, the Genetics Society and numerous other commercial sponsors. UK PlantSci 2013 welcomed a broad spectrum of plant scientists, from molecular biologists and bioinformaticians to ecologists and breeders, to share news and discuss the future of UK plant science. The meeting carried the overriding theme of ‘Plant Science in a Changing World’. We present here some of the topics that ran throughout many of the discussions: the food security challenge, the excellence and impact of plant science research in the UK, the value of public outreach and education initiatives in promoting plant science and inspiring the next generation of scientists, and the need for evidence-based policy.

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Summary of GARNet activities

23rd May 2013

GARNet has been active for 13 years, and in that time has been instrumental in establishing a number of now commonplace activities and initiatives. These slides explain GARNet's structure and give an overview of GARNet's activities in recent years, as well as significant older achievements. 

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New Technologies to Advance Plant Research

24th Jan 2013

GARNet and The Genetics Society hosted a free workshop on the many and varied applications of next generation sequencing (NGS) at the University of Liverpool on 26 November. Speakers travelled from the UK and Europe to present their work to 90 delegates from all over the UK, including students, post-docs, and PIs. Many more people were able to follow the workshop online by following the Twitter hashtag #ngsplant. Two of the talks are now available online.

The day was packed full of demonstrations of the goldmine of information NGS provides, however as highlighted by one of the meeting organisers, Anthony Hall, there just wasn’t enough time to squeeze in a session on bioinformatics. Analysing data generated by NGS requires specialist skills and software, not to mention enormous computing power. The GARNet committee is looking into possible future workshops to help inform the plant science community about NGS bioinformatics analysis. Check the GARNet website for updates if you would be interested in a resource or event linked to bioinformatics for NGS.

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Making Data Accessible to All

27th Jul 2012

On Thursday 12 July, GARNet and Egenis hosted the ‘Making Data Accessible to All’ Workshop at the Innovation Centre, University of Exeter. Participants discussed data donation and use, data dissemination, and means of tracking and evaluating data use, with the aim of making recommendations about data use in plant science.

Programme: 

Making Data Accessible to All: Introduction – Sabina Leonelli (Egenis, University of Exeter)

Session 1: Data donation, analysis and use

Creating, leveraging and sustaining public data (and more) with uncertain funding ­– Andrew Millar (University of Edinburgh)

Accessing and using metabolomics data – Nick Smirnoff (University of Exeter)

From bench to web, via spreadsheets: practical data sharing in research groups – Jay Moore (University of Warwick)

Sharing Data with Omero – Jacob Newman (University of East Anglia)

Session 2: Curating and publishing data

Providing more actionable data associated with articles – Mary Traynor (editor of Journal of Experimental Botany)

Connecting Scientific Articles with Research Data – Giles Jonker (Executive Publisher for Agronomy at Elsevier)

Integrating Research Data and Publications – Ruth Wilson (publisher at Nature Publishing Group)

Getting credit for all of your research – Mark Hahnel (Founder of Figshare)

What role can publishers play in managing data? – Claire Bird (Senior Publisher, Life Sciences, Oxford Journals)

Session 3: Data curation and management

NASC: Reciprocal CTRL-ALTruism – Sean May (NASC)

Data Deluge - A bioinformatics centre's perspective – David Swarbreck (The Genome Analysis Centre)

Traces of a botanical economy; on the regulation of collecting – Alan Pottage (London School of Economics)

Data sharing: a perspective from the BBSRC – Paul Burlinson (BBSRC)

The workshop talks are now available at: http://www.plantsci.org.uk/news/workshop-talks-now-available-making-data-accessible-all

 

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Next Generation Sequencing in Arabidopsis Research Workshop

22nd May 2012

TGAC hosted a workshop at the JIC on 17th April 2012 to outline the Next Generation Sequencing platforms and pipelines at The Genome Analysis Centre (TGAC) and how they can further Arabidopsis research.

Programme

Welcome and introduction to TGAC - Mario Caccamo (Head of Bioinformatics)

Sequencing libraries and platforms - Melanie Febrer (Library Construction Team Leader)

Re-sequencing Arabidopsis accessions - Sarah Ayling (Computational Genomics Team Leader)

Introduction to GridGate (a bioinformatics as a service platform) - Greg Compton (i-Abra)

Hands on experience using the ShoreMap pipeline

Expression analysis (RNA-seq) - David Swarbreck (Genome Analysis Team Leader)

The Tuxedo pipeline in GridGate - Greg Compton

The workshop talks are available at http://www.plantsci.org.uk/events/next-generation-sequencing-arabidopsis-research-workshop

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