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An Introduction to Synthetic Biology for Plant Researchers

Categories: GARNet, synthetic biology, systems biology, Workshops

Tags: GARNet, GARNet workshop, synthetic biology

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Published on: February 20, 2013

Synthetic biology is a fast-growing research area both in the UK and further afield and UK policy makers and funders are taking it very seriously. In November last year, George Osborne announced a £20 million investment for Synthetic Biology and as a result Synthetic Biology is one of the few research areas in the BBSRC portfolio to receive an increase in funding. This is in addition to the numerous schemes that are already supporting Synthetic Biology (including BBSRC, EPSRC and TSB).

To make sure that UK plant researchers can make the most of these funding opportunities, GARNet is hosting a meeting to introduce the concept of Synthetic Biology and the many and varied applications of Synthetic Biology at the molecular, cell and whole plant level.

Like Systems Biology before it, Synthetic Biology can be viewed as both a tool and a scientific approach for understanding and furthering basic science and as a means of developing commercially important plant products. Synthetic Biology in plants is under-researched, but has enormous potential and it is time for UK scientists of all disciplines to explore it.

So to make sure you understand what Synthetic Biology is and how you might apply to your research area, make sure you register for An Introduction to Opportunities in Plant Synthetic Biology. For more information go to: http://www2.warwick.ac.uk/fac/sci/lifesci/news/synbio. Please note that registration fee covers the cost of accommodation and meals during the meeting

To help us promote the meeting, please print out this poster and put it up in your department. Please also forward this email to anyone from other departments you think will be interested.

GARNet Workshop: Plant Synthetic Biology

by Charis Cook

Categories: GARNet, synthetic biology, Workshops

Tags: GARNet workshop, synthetic biology

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Published on: January 22, 2013

It is important for UK plant scientists to consider synthetic biology, both as a tool for understanding and furthering basic science and as a means of producing commercially important plant products – the BBSRC has even chosen synthetic biology as an important emerging scientific sphere. To demonstrate the potential of synthetic biology in plant science and introduce synbio methods, tools, and resources to researchers new to the field, GARNet is having a workshop on Plant Synthetic Biology. Go to http://www2.warwick.ac.uk/fac/sci/lifesci/news/synbio for more information.

2013 dates for your diary

by Charis Cook

Categories: funding, GARNet, UKPSF, Workshops

Tags: BBSRC, funding, GARNet, UKPSF

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Published on: December 11, 2012

Yes, it’s nearly Christmas and before you know it, we’ll be into the new year. Here’s some dates for your diary so you can at least start 2013 on top of things.

Major Funding deadlines

ERA-CAPS First Joint Call: 15 Febuary

BBSRC: 9 January; 21-22 May; June (TBC).

EPSRC: Outline proposal batch meetings 11 February; 15 April; 16 June.

FP7 KBBE theme: 5 Febuary

Marie Curie Actions: Researchers’ Night, Industry-Academia Partnerships and Pathways, International Research Staff Exchange Scheme, all in January; Career Integration Grants, 18 September.

ERC Consolidator Grants: 21 February

NERC Standard Research and New Investigator Grants: 1 July, 1 December. NERC Doctoral Training Partnerships: 1 May (more…)

GARNet workshop in Tweets

by Charis Cook

Categories: GARNet, something fun, Workshops

Tags: GARNet, GARNet workshop, next generation sequencing

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Published on: November 29, 2012

The GARNet Tools and Technologies to Advance Plant Research workshop took place on Monday this week. It was my first attempt at live-tweeting, so I failed to take any meaningful notes for a proper blog post about it. However, you can see the abstract book here and the speakers’ slides will be online soon. In the meantime, I made a Storify of tweets from the workshop – who needs notes when you have Twitter? Thanks to @plantscience, @LiverpoolPlants, and @NeilHall_uk who all tweeted on the day and whose tweets are in the Storify.

A very planty November

by Charis Cook

Categories: funding, GARNet, resource, UKPSF, Workshops

Tags: BBSRC, GARNet workshop, NIAB, Society of Biology, UKPSF

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Published on: November 23, 2012

November is turning out to be a busy month for the plant science community, and here is a round-up of what you might have missed and what is still to come.

Coming up

NIAB has been granted over £600 000 to provide a community wheat transformation service. This is an excellent opportunity for Arabidopsis researchers to test the application of their research in a commercial crop – around 25 transformations will be granted to model crop researchers. For more information, go to the NIAB website and see this poster. Applications will open shortly.

This year’s meeting of the Genetics Society Arabidopsis special interest group is organized by GARNet and will take place on Monday in Liverpool, focusing on next generation sequencing applications in plant science research. It’s too late to register, but you can see the abstracts here, and the presentation slides will be online soon after the day. We will be live tweeting from the workshop on #ngsplant.

The European Research Area Network for molecular plant science (ERA-CAPS) launched its first joint call on 19 November. Up to £6M of BBSRC funding is available to support UK researchers in ERA-CAPS consortia. The deadline for application is 15 February 2013.

London-dwelling people with an interest in policy will be interested in a new series of events run by the Society of Biology, Policy Lates. On Thursday there will be a debate at Charles Darwin House on Do we need more scientists in Parliament. It is a free event and is now full, but there is a waiting list. I expect there will be live tweeting under #policylates – so keep your Twitter tuned if you want to be there virtually, if not in person.

Recent goings on

The UK Plant Science Federation had its second annual general meeting on 5^th November. I wrote a blog post on it for the UKPSF blog, and news from the meeting was also highlighted on this blog by Alan Jones.

I went to the Society of Biology Autumn Members Meeting, where I found out more about the Degree Accreditation Programme. If you feel that original research in UK undergraduate biology courses is poor, get involved by accrediting courses at your own institution, or signing up as an assessor.

The Higher Education team at the Society of Biology launched an Open Educational Resources website last Friday. All the resources on it are peer reviewed by experts, so they are top quality. You can download resources to use yourself, or submit your own resources so they can be used by other lecturers.

SpotOn London 2012 in brief

by Charis Cook

Categories: funding, Open Access, resource, Workshops

Tags: conference, funding, resource, SpotOn

Comments: 1 Comment

Published on: November 15, 2012

This weekend, Ruth and I were in London for SpotOn London 2012 at the Wellcome Trust. There were too many incredible sessions to attend, let alone to cover on this little blog – but all the talks were recorded and you can see them on the SpotOn youtube channel. There will be Storifies aplenty before the end of the week, which I will tweet if they cross my path.

I plan to write at least one ‘proper’ post about the sessions I attended, but for now here are some brief summaries of the topics most discussed in the sessions I attended at SpotOn 2012.

Open data: All the speakers and delegates assumed that everyone else understood and supported open access publishing. What was more interesting was the discussions of other issues in open science – digital licensing, openness in peer review, accessibility of raw data. A longer blog post on this is forthcoming, but I recommend Ross Mounce’s blog, in particular this post on price and ‘openness’ in open access journals, for more information about open science.

Crowd-funding: Around the fringes of publically funded science are small projects supported by funds raised by the researchers. Crowd-funded science is very much in the minority, but in the UK the University of Buckingham has survived for over thirty years without government support, including research programmes. For crowd-funding, excellent marketing and PR are crucial. If you have a public-good, sexy, relatively low-cost research project in your to-do list, and you have a flair for public relations and promotion, it is worth considering. You also need to be able to reward donations in some small way. Check out crowd-funded projects by Matthew Partridge (Cranfield University) and Ethan Perstein (Princeton) to find out more, or donate to their projects. Kickstarter is the best platform to raise your funds.

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Making Data Accessible to All

by Charis Cook

Categories: Workshops

Tags: data sharing, GARNet, GARNet workshop

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Published on: October 18, 2012

In July 2012, GARNet held a workshop entitled ‘Making Data Accessible to All’. Speakers included Mark Hahnel, founder of Figshare, TGAC Genome Analysis team leader David Swarbreck, senior editors and publishers from publishing groups, and a number of academics with experience in data dissemination. Together, workshop speakers and delegates discussed the current challenges in data storage, which data are ‘valuable’ and which may reasonably be left behind, and who should have the responsibility of sharing, storing, and curating data.

The report containing the summary of this workshop concludes that incentive, policing measures, and shifts in culture are needed in order for data sharing to take hold and bear fruit within biology as a whole. Funding bodies, universities, and publishers and journals can provide important ‘sticks and carrots’ by shifting priorities and attitudes to support the practice of data sharing, with all its demands. At the same time, researchers need to seriously commit to data sharing by making it part of their principal aims and outputs. In most cases, community involvement matters much more than the availability of technology. Recent initiatives to encourage data publication, such as data only journals, and data sharing, principally Dryad and Figshare, are acknowledged as important drivers of the shift toward an ethos of data sharing.

To see the resources and repositories GARNet recommends for sharing different types of data, including plant-specific ones, see this post.

Full list of speakers at the workshop: Sabina Leonelli, Andrew Millar, Nick Smirnoff, Jay Moore, Jacob Newman, Mary Traynor, Giles Jonker, Ruth Wilson, Mark Hahnel, Claire Bird, Sean May, David Swarbreck, Alan Pottage, and Paul Burlinson. Their affiliations and their presentation slides can be found on the UKPSF website.

Crop Plant Trait Ontology Workshop, Oregon State University

by Charis Cook

Categories: guest blogger, Workshops

Tags: crop science, GARNet workshop, ontology

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Published on: October 9, 2012

For the last few months, Ruth has been involved in organising a Crop Plant Trait Ontology Workshop which happened at Oregon State University on 13-15 September. Laura Cooper and the Crop Ontology Workshop Planning Committee put together a news piece about the event.

Plant breeders, biologists and bioinformatics specialists from ten countries and two plant agribusinesses gathered in Corvallis, Oregon for the Crop Plant Trait Ontology Workshop. The workshop was hosted by the Plant Ontology and the Trait Ontology consortiums, and co-organised by TransPlant, European Bioinformatics Institute, GARNet, Generation Challenge Program, Sol Genomics Network, and SoyBase.

The goal of the workshop was to engage researchers associated with major cultivated crops worldwide, in order to widen their awareness about ontologies and showcase the latest developments in ontologies for plants. In addition to hearing presentations, participants learned to use the ontology editor OBO-Edit and worked in small groups to classify plant trait terms which had been submitted in advance.

The main conclusion of the workshop was that there is a need for a broad, co-ordinated effort to create a semantic framework for meaningful cross-species queries using a Common Reference Ontology for Plants. This Reference Ontology will encompass all green plants and will facilitate queries for related gene expression and phenotype data from plant genomics, genetics experiments from the various species- and clade-specific databases, and describe accessions in the various international crop germplasm collections.

The hope is that in creating a Common Reference Trait Ontology for Plants, we will facilitate plant genetic and phenotypic data discovery and exchange.

For further information including a list of participants and sponsors, and links to presentations, visit the workshop wiki page at http://tinyurl.com/Trait-Ontology.

Other links:

Plant Ontology http://www.plantontology.org

Trait Ontology: http://www.gramene.org/plant_ontology/ontology_browse.html#to

TransPlant: http://transplantdb.eu/

European Bioinformatics Institute: http://www.ebi.ac.uk

GARNet: http://www.garnetcommunity.org.uk

Generation Challenge Program: http://www.generationcp.org

Sol Genomics Network: http://solgenomics.net/

SoyBase: http://soybase.org/

OBO-Edit; http://oboedit.org/