GARNet/Egenis meeting on 'Integrating Large Data into Plant Science: From Big Data to Discovery'
21st Apr 2016
GARNet and the Exeter Centre for the Study of the Life Sciences (Egenis) are excited to host a two-day workshop on ‘Integrating Large Data into Plant Science: From Big Data to Discovery’ to be held in the picturesque Dartington Hall in Devon on April 21st-22nd 2016.
The aims of this workshop are to:
1. Introduce examples of how researchers have re-used datasets in innovative ways.
2. Examine the intrastructure that exists to support the re-use of large datasets
3. Discuss the mechanisms by which the community deals with big data.
Please download the abstract book and look out for a meeting report coming in the near future.
GARNet/OpenPlant CRISPR Workshop
24th Sep 2015
GARNet and OpenPlant were delighted to invite over 140 attendees to the CRISPR-Cas workshop held at the John Innes Centre at the start of September 2015, sponsored by Plant Methods. This workshop was designed to introduce CRISPR technology and highlight what might be possible with his transformative technology. A report from the meeting can be found on the GARNet blog.
On Day Two of the workshop we hosted ~20 researchers to learn more detail about the basic principles for use of CRISPR-Cas technology. The workshop was split into the following parts: 1. Designing guide RNAs. 2. Making constructs using the MoCLo system. 3. Screening trangenic plants.
This workshop was run by Dr Nicola Patron and she is happy to share her notes from that session, which can be downloaded below. This will hopefully give some guidance to anyone embarking on use of CRISPR-Cas for the first time.
Data Mining with iPlant
20th Oct 2014
In September 2013, GARNet hosted a training workshop at the University of Warwick. The four-day 'Data Mining with iPlant' workshop gave delegates comprehensive training in how to use the iPlant Collaborative's cyberinfrastructure for storing, sharing and analysing 'Big Data' in plant science.
You can read more about this workshop by visiting our blog post about it. We also featured it in the December 2013 issue of GARNish (click download link below) and the Wiki-style materials used during the workshop can be found here: https://pods.iplantcollaborative.org/wiki/display/Events/Data+Mining+with+iPlant.
Following this workshop, we wrote and submitted a workshop report to the Journal of Experimental Botany, which I am pleased to say has now been published.
Martin L, Cook C, Matasci N, Williams J and Bastow R (2014). Data Mining with iPlant: A meeting report from the 2013 GARNet workshop 'Data Mining with iPlant', Journal of Experimental Botany, DOI: 10.1093/jxb/eru402 can be accessed via this toll-free link.
High-throughput sequencing technologies have rapidly moved from large international sequencing centres to individual laboratory benchtops. These changes have driven the ‘data deluge’ of modern biology. Submissions of nucleotide sequences to GenBank, for example, have doubled in size every year since 1982, and individual data sets now frequently reach terabytes in size. While ‘big data’ present exciting opportunities for scientific discovery, data analysis skills are not part of the typical wet bench biologist’s experience. Knowing what to do with data, how to visualize and analyse them, make predictions, and test hypotheses are important barriers to success. Many researchers also lack adequate capacity to store and share these data, creating further bottlenecks to effective collaboration between groups and institutes. The US National Science Foundation-funded iPlant Collaborative was established in 2008 to form part of the data collection and analysis pipeline and help alleviate the bottlenecks associated with the big data challenge in plant science. Leveraging the power of high-performance computing facilities, iPlant provides free-to-use cyberinfrastructure to enable terabytes of data storage, improve analysis, and facilitate collaborations. To help train UK plant science researchers to use the iPlant platform and understand how it can be exploited to further research, GARNet organized a four-day Data mining with iPlant workshop at Warwick University in September 2013. This report provides an overview of the workshop, and highlights the power of the iPlant environment for lowering barriers to using complex bioinformatics resources, furthering discoveries in plant science research and providing a platform for education and outreach programmes.
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.
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
- 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?
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.
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.
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.
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.
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.
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.