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.

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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100 Most Important Questions Facing Plant Science

8th Sep 2011

Plant scientist' should take its rightful place beside 'doctor', 'lawyer' and 'vet' in the list of top professions to which our most capable young people aspire, according to a hard-hitting letter by an international group of botanists and crop scientists published in New Phytologist on the 8th September 2011.

For further information visit http://www.100plantsciencequestions.org.uk/

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An International Model for the Future of Plant Science

16th Sep 2010

A variety of documents have been developed outlining visions for plant science with differing geographic and scientific foci. This report is unique in the scope and scale of its recommendations; it provides an international vision for the next decade to inform scientists, funders, and decision makers globally. Although the focus here is specifically on plant science, agronomy, soil science, the legal framework protecting plant varieties, ecology, and other areas not covered in this vision will also be crucial in translating fundamental understanding of plants into effective actions. This vision is a direct outcome of a meeting of plant science researchers from 10 different nations who were invited to the Banbury Center at Cold Spring Harbor Laboratory in the United States in 2009 to discuss their perspectives on the current and future challenges in plant science. Funding for the meeting was provided by three national funding agencies and coordinated through the International Steering Committee for Plant Genomics.

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EU 2020 European Vision for Plant Science

2nd Jun 2008

This report was generated from a workshop help in Bonn in 2008, which aimed to map a way forward for plant science in the next decade, by looking at the current major challenges facing biology and investigating how plants, particularly Arabidopsis, could provide solutions to these challenges.

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2020 Vision for Biology: The Role of Plants in Addressing Grand Challenges in Biology

3rd Jan 2008

Report from an NSF-sponsored workshop held January 3-5, 2008 that focused on the future directions for plant research, with special emphasis on the role of the reference species Arabidopsis in uncovering fundamental biological principles that will enable us to face future challenges to our well-being and that of the global environment.

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