COPO 2015 Meeting

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Published on: June 25, 2015

COPO has big plans…. and if it is to be truly successful and benefit the plant community there needs to be a cultural change! That’s the simple if revolutionary message that came out of the recent COPO meeting held at TGAC on June 23rd-24th.

So the uninitiated will be asking: ‘What is COPO?‘ The answer is the Collaborative Open Plant Omics group which was funded by a BBSRC BBR grant in 2014. This is a >£1m collaboration between The Genome Analysis Centre (TGAC), University of Oxford, the European Bioinformatics Institute (EMBL) and the University of Warwick.

This workshop was to introduce the aims of COPO to a range of stakeholders, from curators of available data repositories to experimentalists who are generating large datasets. By the end of the 2-day session it was hoped that everyone would gain an understanding of what COPO can offer the community with regard facilitating the sharing of large datasets.

White Board Discussions

The workshop was led by Rob Davey (TGAC) and Ruth Bastow (GPC, GARNet, Warwick). Rob kicked off the meeting by describing the aims of COPO which included asking ‘What are the barriers for you and your data and how can COPO facilitate access to the workflows used to analyse data’.

Subsequently a range of stakeholders introduced the fantastic tools that are out there for repositing data of many different types. These included David Salt (University of Aberdeen, Ionomics), Elizabeth Arnaud (Montpellier, CropOntology), David Marshall (James Hutton Institute, Germinate: Plant Genetic Resources), Esther Kabore (INRA, Wheat Data Repository) Reza Salek (EMBL, Metabolights), and finally Tomasz Zielinski (Edinburgh, BioDare) who made the telling observation that ‘data Management is a user interface/user experience problem NOT a software engineering/ data modelling problem’. Many researchers are often reluctant to take the time and effort required to submit their data to an appropriate repository in a reasonable manner, for any number of opaque reasons. However the take-home message from the early talks was very positive as there are a large number of data platforms available for people to use and benefit from. One of the challenges for COPO is to not only to help convince people to use these resources but encourage them to share data in a standardised manner.

Following a useful coffee break it was time for researchers to explain the data they are producing and the challenges for their analysis. Miriam Gifford (Warwick) discussed her generation of transcriptomic data, Christine Sambles (Exeter) talked about developing a workflow for metabolomics data and TGAC group leader Ksenia Krasileva introduced her work on wheat functional genomics. Ksenia also highlighted a new portal for communication between data generators and data users called Grassroot Genomics.

The final three talks of the day highlighted the amount of data that can be produced in different sets of biological experiments. Ji Zhou (TGAC) and Chris Rawlings (Rothamstead) introduced cutting-edge field phenotyping technologies that use large imagers to capture visible and spectral aspects of plant growth. Workshop attendee Professor Peter Murray-Rust summed it up with a tweet: ‘Blown away by the crop monitoring equipment at Rothamstead’. On an opposite end of the spectrum Jim Murray (Cardiff) showed a single fluorescent image of a zebrafish taken on a light-sheet microscope that weighed in at an impressive 23Tb of data. Overall these talks served to highlight the vast amounts of data that can be produced and provided the second take-home message of the day that ‘Getting data is NOT the issue, making any sense of it IS the challenge’……

 

The task of second day discussions was to make sense of what had been presented the previous day and identify the best opportunities for COPO to impact on the process of data sharing. A lively first hour of debate included Dr Philippe Rocca-Serra (COPO Co-PI from Oxford) presenting a somewhat sobering eight slides of ‘Pain Points’ that he had taken out of the previous days presentations! However it was refreshing to observe that the challenge of the task was not underestimated and being tackled with realistic planning.

Pain Points!

Later in the morning discussions turned more specific with a white-board brainstorming session that was divided into ‘Data Collection’.Data Storage’ and ‘Data Analysis’ sections. Most progress was made in the first two sections with a long list of storage repositories identified that bridged the breath of biological data and with which COPO could potentially interact.

It was felt that successful interactions would be predicated on some level of data standardisation so perhaps the most effective initial use of the COPO resources would be to develop a workflow for standard data collection. This would hopefully make experimentalists think about the format of their data submission as they are planning and generating the data. The consensus was that attaching these standards to legacy-data might be a difficult task but that for future data generation, COPO could influence data sharing at this level.

IMG_8241

Ultimately it is clear that plant science has the same generic problems as many other disciplines and the greatest challenge is to change the ‘culture’ of sharing data. The most obvious and direct way to promote this change will be via the funders and publishers. Some progress has been made in this arena with a recent shift towards open access publication in the REF process, and it would only take another small additional step to make it a requirement to share data in any REF-returnable publications. So I hope that those with greater power and influence than me, are reading the GARNet blog!

Regardless of the pace of cultural change, the feeling in the meeting was that the COPO mandate is to encourage data sharing whilst moving to a position to effectively interact with the data that is shared. There is plenty of work to do but at the end of this exploratory workshop the COPO organisers had plenty to think about regarding the direction of the project. Watch their space!

Storify of tweets from the meeting

Multi-scale Biology Meeting.

What is Multi-scale Biology?

That was the overriding question that occupied attendees of the inaugural meeting of the Multi-scale Biology Network, held at the University of Nottingham on June 1st 2015. This newly funded BBSRC network brought together biologists, physicists, engineers, and the funding bodies (amongst others) for this meeting that aimed to set the agenda for this area of future collaboration. Storify of the meeting.

Those who had also been involved in the genesis of synthetic biology policy might have felt a touch of deja-vu over the questions being asked at this meeting. However whereas the term ‘synthetic biology’ might have remained opaque after those early meetings, the feeling at the end of this day was that good progress had been made into an understanding of what this network might achieve.

Although there were <a href="http://www.multiscalebiology.org.uk/events/event/springboard/" onclick="_gaq.push(['_trackEvent', 'outbound-article', 'http://www cialis 20mg en france.multiscalebiology.org.uk/events/event/springboard/’, ‘speakers from a range of biological disciplines’]);” target=”_blank”>speakers from a range of biological disciplines there was no requirement for forced interactions between different research areas. Instead there was a sense of ‘wondering what can be learnt‘ when for example, plant scientists talked to neurobiologists…

The meeting was kicked off by Professor Markus Owen from the Nottingham Maths department and the agenda had been clearly designed to encourage significant amounts of discussion, be it during the lecture period or over an extended lunch in which attendees split into small groups to discuss challenges in MSB.

Many of the attendees were involved in some form of systems biology so the sense was that MSB comes as the natural extension of that area of research. Instead of looking at a single network, how should researchers extend their thinking to include how these networks interact at different scales…..without losing the quality of analytic data?

Professor Alfonso Martinez-Arias (Cambridge) led the first discussion and made the important point that even though we now have enormous amounts of data, what is it we actually want to learn?….and is focusing on that type of question compatible with current necessity for publication in high quality journals?

Immediately after lunch Professor Carole Goble introduced a new ERASysApp network (FAIRdom) in which she is involved that aims to ensure that systems biology projects make their data, operating procedures and models, Findable, Accessible, Interoperable and Reusable (FAIR). This was a timely reminder that it is very important to produce data that is reusable by the community so that people aren’t reinventing the wheel in each experiment. In 2016 GARNet will be hosting a meeting with the Exeter Centre for the Study of Life Sciences that will address issues surrounding data reuse. Details to follow later in 2015!

Toward the end of the day Professor Martin Howard from the John Innes Centre led the final discussion that attempted to coalesce the thoughts of attendees. One suggestion was for biologists to act ‘like engineers’ and to use ‘dirty tricks’ as to get tasks completed. Understanding the details can come later…. getting the job done is most important….. whatever the job is that needs to be done! It was also discussed that coming to any ‘effective theory’ of biology is almost impossible given the unpredictable nature of the field.

The results of group discussions!

The results of group discussions!

Overall it seems that making any decisions about how multi-scale biology projects can be implemented will depend on the funding environment. To that end Michael Ward from the EPSRC stressed that mathematical biology is important for mathematical science funding and urged attendees not to be put off from looking in their direction. Ceri Lyn-Adams from the BBSRC informed the group that although there wasn’t any money specifically ring-fenced for MSB, they welcome applications in this area under existing mechanisms.  What was clear is that MSB and systems biology remain in the forefront of BBSRC funding strategy!

By it’s very nature MSB will require large projects that might bring together a few responsive mode-size projects under a single umbrella. Hopefully new researchers will be able to be involved in this type of project and the money doesn’t all go to large established groups.

Plant Scientists were well represented at the meeting most notably by Martin Howard, Malcolm Bennett and Leah Band, who gave the final talk of the day. The multi-scale nature of plant biology was highlighted in this more than any other talk, as Leah discussed biology at the organismal, tissue, network, cellular and enzyme level. Her work builds the prior knowledge of GA transport and biosynthesis to make mathematical models to predict tissue expansion.
Multi-scale Plant Biology

Importantly for the GARNet community, the take home message from the meeting was that plant scientists will play a major role in the future of multi-scale biology so once the funding opportunities are revealed they should not be reticent in submitting bids.

To tweet or not to tweet?

Here at GARNet, we’re pretty big fans of social media, and Twitter in particular. You can find me, for example @GARNetweets, Charis is @weedinggems, and Ruth has the enviable Twitter handle @plantscience. We regularly post links to news, journal papers, job posts etc., tweet from conferences, and encourage live-tweeting at our own events too.

Left behind at GARNet Towers while my colleagues attended the Plant & Animal Genome conference in San Diego last week, I followed events virtually, via the Twitter hashtag #PAGXXIII – thanks to everyone who tweeted for keeping me up to speed!

Though once upon a time it would have been considered rude to sit tapping away at your phone during a plenary lecture, in today’s WiFi-enabled world, more and more people are using social media during conferences. As John Innes Centre (@JohnInnesCentre) student Amelia Frizell (@AmeliaFrizell) points out in this blog post, there are many advantages to live-tweeting: it’s a great way to make notes, stay engaged with the speaker, increase your Twitter follower numbers and network with peers.

But there’s an ongoing debate, known as “Twittergate”, about whether it’s appropriate to tweet during a conference, what should and should not be tweeted, and what, exactly, the “twetiquette” is when engaging with social media during live events.

A Twitter account I follow recently retweeted a link to quite an old blog post on The Guardian website, which reminds us that there is a certain level of responsibility involved in live-tweeting. At academic conferences in particular, there are unwritten rules that should be followed. I recommend reading the article as there are some very useful tips and things to bear in mind.

You see, although many of us are fully subscribed to the idea of Twitter as a way to quickly give and receive snippets of news and information, not everyone feels the same way. Not everyone is aware of what Twitter is, how it works, or just how public a channel it is. Many distrust it and are sceptical. Some academics, for example, are comfortable with presenting unpublished work to an audience of peers in the room, but less happy to have it instagrammed and summarised in 140 characters or less and whizzed around the Twitterverse for anyone to read.

Having been lucky enough to attend quite a few conferences last year, it was interesting to note the uptake, or not, of Twitter in different places. At UKPSF (@UKPSF) Plant Sci 2014 and ASPB’s (@ASPB) Plant Biology 2014, for example, tweeting was encouraged and I was among a handful or two of other delegates all using the official conference hashtags. At ICAR 2014 (@ICAR2014) however, Charis, Ruth and I were practically the only ones online.

At SEB (@SEBiology) 2014 in Manchester there were noticeably more ‘tweeps’ in the plant science sessions than there were in the animal or cell biology talks, while at SpotOn London (@SpotOnLondon), a science communication conference I attended at the end of 2013, there were so many people tweeting and using electronic devices that it was a scrum to find available plug sockets to recharge during the lunch break!

Like Amelia, I think – when used responsibly – Twitter is brilliant for conference and workshop communication, and as Anne Osterrieder (@anneosterrieder) and others testify, social media is a great science outreach tool, too. Like it or not, Twitter is a ‘thing’ now. And it’s not just a frivolous plaything for younger students or early career researchers, it’s a bona fide tool for communicating and sharing news and joining in online conversations.

Speakers: don’t be offended if people spend more time looking down at their iPads than up at your slides. If they’re tweeting or live-blogging about your work, they are helping you to communicate your science to far more people than just those in the room. If you’re presenting something you’d rather not have published on the internet, or don’t want your photo taken, just say so during your talk – the twitterati will respect your wishes.

Embrace Twitter. Why not set up your own Twitter account and start posting links to your papers or research websites? Follow people you’re interested in (like us?!) and retweet what they have to say. Tweet about what you get up to in your lab. Put your Twitter handle on your conference presentations so people can @mention you in their tweets, or even start your own catchy hashtag? Who knows, you could end up trending!

EBI resources at PAGXXIII

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Published on: January 15, 2015

I spent Sunday morning wandering in and out of the ‘Tools and Resources from EBI’ session here at PAG. Some EBI resources for plant science will be very familiar to some of our community, but the presenters gave accessible talks that included some news and advice, so I thought I’d round them up for you.

Maria Keays presented ArrayExpress and ExpressionAtlas. These are the functional genomics tools from EBI. Keays defined functional genomics as the study of gene expression, gene function and gene regulation – these tools certainly aren’t just for microarray data!

Users submit their data to ArrayExpress via the Annotare submission tool, which encourages inclusion of information about how the samples were grown all the way through to data generation. Keays acknowledged that a user may encounter an error message they can’t get around, and assured us that emails sent to the helpdesk (Arrayexpress@ebi.ac.uk) are responded to quickly. Once submitted, the dataset and associated metadata is checked by a human curator before the user can upload it. The data can stay private until publication because two logins are provided; one for the submitter and one for the reviewer of the paper they hope to publish.

We’ve been encouraging our community to share data on NCBI GEO because it is able to disseminate almost any data type. But for functional genomics data, ArrayExpress is just as acceptable to journals as GEO, and the Annotare submission tool requires more extensive metadata and more stringent standards than GEO. (more…)

CoGe at PAGXXIII

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Published on: January 11, 2015

Happy New Year! We at GARNet enjoyed a long Christmas break and some of us have returned to work via California! Ruth, Jim and I are in San Diego this week for the Plant and Animal Genome Conference (PAG).

PAG is an enormous conference – take a look at the Twitter stream (PAGXXIII) for an idea of how many sessions run at any one time. Yesterday I went to sessions on Ontologies, Brassica and Tritaceae, and I thought I’d quickly update our blog readers about a workshop about the CoGe online tool. I mentioned CoGe in this post about the EPIC conference and it’s also featured in the June 2013 edition of GARNish.

Eric Lyons, one of the creators of CoGe, began the session by explaining that CoGe is a platform for managing, visualising, analysing and comparing genomes. It can deal with unlimited numbers of genomes of unlimited size—though there is a limit for the number of annotations per genome—and while there are tools set up for ease of use, users can perform custom, on-the-fly analysis too.

Throughout the session, Lyons was clear that CoGe is ‘Powered by iPlant.’ It uses iPlant middleware to enable data storage, universal log-in and much more functionality that the user might not be aware of but which makes their experience smooth and relatively stress-free. (more…)

Plant synthetic biology takes centre stage

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Published on: October 27, 2014

On Monday and Tuesday last week I was at the Marriott Heathrow for the Global Engage Synthetic Biology Congress. Plant synthetic biology had a dedicated track, and while this meant I regretted missing some talks in the other sessions, it did enable me to be suitably impressed at the quality of plant synthetic biology research, mostly coming from the UK and Europe, and its exciting range of applications.

Plant synthetic biology at Global Engage

A highlight for me was Matias Zurbriggen’s excellent presentation on using plant signalling pathways to remotely control mammalian cells. His objective is to understand plant pathways by reconstructing them in other systems, and via research on phytochromes he has developed a tool to remotely control gene expression in mammalian cells (1) and a light-controlled switch for plant cells (2).

Birger Lindberg Møller gave an interesting and accessible talk about plant synthetic biology for high value product (HVP) synthesis. Whatever your level of expertise, if you’re interested in this area I recommend you watch this earlier version of his talk.

Continuing the HVP theme were Brian King, Vincent Martin and plenary speaker Jules Beekwilder. They all aim to make HVPs using simple chassis instead of relatively energy-intensive, and often inefficient, plants. (more…)

GARNet 2014 presentations available online

As you’ll already know, we held our GARNet 2014 conference, Arabidopsis: The Ongoing Green Revolution, at the University of Bristol on the 9th and 10th September. If you didn’t know, you can read Charis’ report on it by clicking here to go to the main GARNet website, or here to see some photos!

Some of the researchers who spoke at our conference have kindly agreed to share their GARNet 2014 presentations with you online – please click the links in the programme below to view or download a PDF copy of the speaker’s slides.

 

Programme

Session 1: Physiology & Productivity

Session 2: Genome Biology

Session 3: Natural Variation

Session 4: Systems and Synthetic Biology

GARNet 2014: In pictures

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Published on: September 16, 2014

GARNet 2014, Arabidopsis: The Ongoing Green Revolution, is over! We had a great two days of discussions, networking, speciality cupcakes, and of course excellent talks from researchers at all career stages, from ‘one of the fathers of Arabidopsis research’ to a few of the UK’s brightest young PhD students.

There is a report on the conference on our website, and also a Storify of Tweets. Thank you to everyone who attended and contributed to discussions in situ and on Twitter – we’re delighted to work with such a supportive, enthusiastic community!

Here are a some pictures from the event – they’re mostly of the speakers (Maarten Koorneef, Andrew Millar, Cyril Zipfel, Kerry Franklin, and Miriam Gifford) and panel sessions, with a few pictures of the networking sessions towards the end.
garnet2014 1

(more…)

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