Work for GARNet!

Categories: GARNet
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Published on: March 5, 2015

As we have mentioned on our main website, we are searching for a new GARNet Coordinator. Until now, the job has been advertised for internal Cardiff University applications only, but as of today, anyone is eligible to apply. Would you like to work for GARNet? You can find the job advertisement here: Research Associate, GARNet Coordinator.

What does a GARNet Coordinator do?

Lots of things! The GARNet Coordinator is responsible for managing the day-to-day running of the network – you can find a full job specification on the Cardiff website, but practically, the job includes things like:

  • Maintaining the GARNet website, mailing list, Twitter account and blog;
  • Organising regular meetings with our Committee, including meeting room bookings, catering and logistics, taking minutes and ensuring actions from the last meeting are completed;
  • Identifying opportunities for workshops and events that will benefit the plant science community, and then organising those events – recent past examples include the GARNet Conference, Software Carpentry workshops at Liverpool and Warwick, and an iPlant workshop. You’ll need to find sponsorship, book event space and hotel rooms, organise transport and catering, prepare delegate information packs, and so on;
  • Staying abreast of what’s currently happening in Arabidopsis and basic plant science research, and networking and liaising with members of the plant science community by attending national and international conferences such as ICAR, SEB or UKPSF;
  • Writing – we have written a number of papers published in peer reviewed journals, as well as meeting reports, contributions to consultations, guest blog posts and articles, our Arabidopsis Research Round-up, and the twice-yearly GARNish newsletter;
  • Planning and developing grant applications for resources or projects identified by the plant science community as being of value – we recently secured renewed funding for GARNet itself, and we were heavily involved with putting together the application for iPlant UK.
The GARNet Coordinator needs to be a plant scientist who is well organised, a good writer, communicator and networker. You will, on occasion, need to travel nationally and internationally, and good computer skills are a must – experience with website management, blog platforms and creative publishing software such as Adobe InDesign and Photoshop are ideal.
If you’d like any more information about the GARNet Coordinator vacancy, please feel free to submit informal enquiries to Ruth Bastow.
The closing date for applications is 19 March 2015.

iPlant is coming to the UK

Back in 2013, the GARNet team brought the iPlant Collaborative over to the UK to run a four-day workshop. Now, we’ve secured funding to bring iPlant to the UK again – but this time, it’s here to stay!

During 2014, the GARNet team and committee – together with iPlant collaborators in the US – were busy preparing a grant application for an invited BBSRC capital funding call. Our proposal was to work with iPlant to develop a ‘node’ of iPlant here in the UK. Our application was sucessful and the award was announced at the end of January at the AAAS 2015 meeting.

What is iPlant?

Funded by the US National Science Foundation (NSF) the iPlant Collaborative provides free and open access to ‘cyberinfrastructure’, originally just for plant scientists, but now for all the life sciences. Here’s a short video clip to explain more:

Harnessing the power of some of the world’s most powerful supercomputers, iPlant users can access the cloud-based Data Store, which provides very large amounts of space for researchers to store, and quickly transfer and share ‘big data’ files.

iPlant users also have access to the Discovery Environment – a web-based, graphical interface that provides access to an ever-expanding suite of modular, integrated ‘apps’ for data analysis. Apps can be built either by the iPlant team or by more experienced users, and cover a wide range of analysis needs. They are user-friendly and very intuitive, meaning that even researchers with little or no knowledge of command line computer programming can easily run an app, or create a pipeline of apps, to analyse large and complex data files.

Why do we need iPlant UK?

iPlant, which is free for anyone around the world to use, is currently distributed across three locations in the US – the Texas Advanced Computing Center, the University of Arizona and Cold Spring Harbor Laboratory. Though the high performance computing power it utilises is currently sufficient, iPlant was designed to be extendable to spread resources between even greater numbers of ‘nodes’. iPlant UK will be the first – hopefully of many – international iPlant hubs to ensure the future sustainability of the resource on a global scale.

As we noted in our recent Journal of Experimental Botany paper, one of the drawbacks of having iPlant located solely in the US, is that technical user support is only currently available during US office hours. When we hosted our workshop at the University of Warwick in September 2013, iPlant’s US-based support engineers kindly agreed to be woken up if we needed them – and we did! Clearly that’s not an ideal solution going forwards, especially as the number of worldwide users grows and grows.

As well as having access to technical support on the GMT timezone, the project’s collaborators at the Universities of Warwick, Liverpool, Nottingham and at The Genome Analysis Centre (TGAC), aim to convert existing BBSRC-funded software tools for the iPlant environment. This will increase community access to these useful resources, and their uptake, giving the plant science community even greater opportunities for efficient, effective, collaborative research.

How will it work?

iPlant UK will run as an independent, UK-hosted iPlant node that will centralise compute power and data storage to a single site at TGAC.

The team at TGAC, managed by Dr Tim Stitt and Dr Rob Davey, will work together to install and maintain new and existing hardware infrastructure at TGAC, and once that phase is complete, they will start work to establish and launch the iPlant UK node.

Meanwhile, teams at the Universities of Warwick, Nottingham and Liverpool will convert software tools they have created from their existing formats to the iPlant environment.

  1. University of Liverpool: Next generation sequencing workflows (led by Professor Anthony Hall). Working with the wheat community, the team at Liverpool will optimise a wheat genetic tool bench for next generation sequencing, and a pipeline for mapping-by-sequencing.
  2. University of Warwick: Gene expression, networks and promoter motif tools and pipelines (led by Professor Jim Beynon). The Warwick team will port tools from the PRESTA project into the iPlant environment. These tools include those for identifying differential gene expressions, clustering and network inference, and promoter analysis.
  3. University of Nottingham: Image-based phenotyping (led by Professor Tony Pridmore, Centre for Plant Integrative Biology). The team at Nottingham will convert a range of popular tools for visualising root phenotypes, so that they can be accessed and used from the iPlant environment.

If you are interested in getting involved with this project, two posts at TGAC are currently being advertised (but hurry, the closing date is tomorrow, 3rd March!)

Opportunities at Warwick and Nottingham will be announced soon so stay tuned for updates!

Arabidopsis Research Round-up

Categories: Arabidopsis, Global, Round-up
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Published on: February 23, 2015

Some interesting and diverse papers in the Arabidopsis Research Round-up this week – check out these offerings from the University of Warwick, University College London, John Innes Centre, University of Cambridge and University of Leicester.

 

  • Szakonyi D, Van Landeghem S, Baerenfaller K, Baeyens L, Blomme J, Casanova-Saez R, De Bodt S, Esteve-Bruna D, Fiorani F, Gonzalez N, et al. The KnownLeaf literature curation system captures knowledge about Arabidopsis leaf growth and development and facilitates integrated data mining.Current Plant Biology, 7 February 2015. DOI: 10.1016/j.cpb.2014.12.002. [Open Access]

This Current Plant Biology paper was authored by a multi-national collaboration including Vicky Buchanan-Wollaston from the University of Warwick. It describes the development of KnownLeaf – a database connecting Arabidopsis leaf growth and development genotype to phenotype data mined from scientific literature. In addition, the network LeafNet has also been developed to graphically represent leaf phenotype relations in a molecular context.

 

  • Schwarte S, Wegner F, Havenstein K, Groth D, Steup M and Tiedemann R. Sequence variation, differential expression, and divergent evolution in starch-related genes among accessions of Arabidopsis thaliana. Plant Molecular Biology, 8 February 2015. DOI: 10.1007/s11103-015-0293-2.

This largely German team (though Fanny Wegner is also affiliated to University College London) is exploring genetic diversity in starch-related genes. Twenty-six different Arabidopsis accessions were sequenced, and sequence data on a further 80 accessions were accessed from public database, to determine differences in transcript levels of 25 genes. Diversity was found to vary greatly between accessions, with starch synthases and phosphorylases showing the highest levels of nucleotide diversity, and pyrophosphatases and branching enzymes being the most highly conserved.

 

  • Shimotohno A, Sotta N, Sato T, De Ruvo M, Maree AFM, Grieneisen VA and Fujiwara T. Mathematical modelling and experimental validation of spatial distribution of boron in the root of Arabidopsis thaliana identify high boron accumulation in the tip and predict a distinct root tip uptake function.Plant & Cell Physiology, 9 February 2015. DOI: 10.1093/pcp/pcv016.

Scientists from the John Innes Centre worked with Italian and Japanese colleagues to produce this offering from Plant & Cell Physiology, in which mathematical modelling is used to predict boron distribution in the Arabidopsis root tip. The model predicted that the concentration of soluble boron would be higher in a region around the quiescent centre; this was then validated experimentally by determining root boron distribution via laser ablation-inductivity-coupled plasma mass spectrometry.

 

  • Mateos JL, Madrigal P, Tsuda K, Rawat V, Richter R, Romera-Branchat M, Fornara F, Schneeberger K, Krajewski P and Coupland G. Combinatorial activities of SHORT VEGETATIVE PHASE and FLOWERING LOCUS C define distinct modes of flowering regulation in Arabidopsis. Genome Biology, 11 February 2015. DOI: 10.1186/s13059-015-0597-1. [Open Access]

 

Working with plant scientists from around the world, this study of the combined and individual effects of transcription factors related to the initiation of flowering in Arabidopsis also included Pedro Madrigal, who is affiliated to the Wellcome Trust Sanger Institute and the University of Cambridge. Looking at the MADS-box transcription factors FLC and SVP, which form a complex, it was found that there is substantial flexibility in the ways these proteins work together, accounting for variation and robustness in the regulation of plant flowering.

 

  • Huang Z, Ölçer-Footitt H, Footitt S and Finch-Savage WE. Seed dormancy is a dynamic state: variable responses to pre-and post-shedding environmental signals in seeds of contrasting Arabidopsis ecotypes. Seed Science Research, 12 February 2015. DOI: 10.1017/S096025851500001X.

Led by Bill Finch-Savage, this team from the University of Warwick looked at how environmental signals during seed development affected the mother plant in a winter and summer ecotype of Arabidopsis thaliana. Results presented show that environmental signals both pre- and post-shedding determine the depth of physiological dormancy and therefore the germination response to the ambient environment.

 

  • Schoft VK, Chumak N, Bindics J, Slusarz L, Twell D, Kohler C and Tamaru H. SYBR Green-activated sorting of Arabidopsis pollen nuclei based on different DNA/RNA content. Plant Reproduction, 13 February 2015. DOI: 10.1007/s00497-015-0258-2.

With colleagues from Austria, Switzerland and Sweden, David Twell from the University of Leicester was involved in the preparation of this manuscript, which describes a novel method to separate SYBR Green-stained plant sperm cells using fluorescence-activated cell sorting (FACS). This method will be of great help to anyone studying germ cell genetics and epigenetic reprogramming during sexual reproduction, and should be applicable to crop plants too.

Arabidopsis Research Round-up

Categories: Arabidopsis, Global, Round-up
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Published on: February 9, 2015

Here’s your Arabidopsis Research Round-up for this week! Today we have plenty of Scottish delights, including papers from the University of Aberdeen, Dundee,Glasgow, Edinburgh and the James Hutton Institute. There is also new work from researchers at the University of Durham, Nottingham, Leeds and Oxford.

 

  • Pokhilko A, Bou-Torrent J, Pulido P, Rodrígues-Concepción M and Ebenhöh O. Mathematical modelling of the diurnal regulation of the MEP pathway in Arabidopsis. New Phytologist, 16 January 2015. DOI: 10.1111/nph.13258.

Alexandra Pokhilko and Oliver Ebenhöh are two members of the University of Aberdeen’s Institute for Complex Systems and Mathematical Biology. Both contributed to this New Phytologist paper, in which they describe a mathematical model of the diurnal regulation of the 2-C-methyl-d-erythritol 4-phosphate (MEP) pathway. Data show that flux through the MEP pathway is accelerated in light conditions. It is also shown that pathway products regulate the abundance and activity of DXS (the first enzyme in the pathway, 1-deoxy-d-xylulose 5-phosphate synthase), which alters flux under varying conditions.

 

  • McCormick AJ and Kruger NJ. Lack of fructose 2,6-bisphosphate compromises photosynthesis and growth in Arabidopsis in fluctuating environments. The Plant Journal, 20 January 2015. DOI: 10.1111/tpj.12765.

Here, Alistair McCormick from SynthSys at the University of Edinburgh and Nick Kruger from the University of Oxford describe their research on understanding the physiological role of the signal metabolite fructose 2,6-bisphosphate (Fru-2,6-P2). Plants from three independent T-DNA mutant lines deficient in 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase (F2KP) grow normally in constant environments, but have reduced growth and seed yield in fluctuating light and/or temperatures. McCormick and Kruger suggest that Fru-2,6-P2 is involved in the modulation of photoassimilate partitioning, and that this is an important determinant of growth and fitness in natural environments.

 

  • Calixto CPG, Waugh R and Brown JWS. Evolutionary relationships among barley and Arabidopsis core circadian clock and clock-associated genes.Journal of Molecular Evolution, 22 January 2015. DOI: 10.1007/s00239-015-9665-0.

Presented by scientists from the James Hutton Institute and the University of Dundee, this paper provides a comprehensive analysis of circadian clock and clock-associated genes in Arabidopsis thaliana, barley, and eight other plant species. It is proposed that the common ancestor of Arabidopsis and barley had two-thirds of the key clock components identified in Arabidopsis prior to the divergence of monocot and dicot groups.

 

  • Verma V, Sivaraman J, Srivastava AK, Sadanandom A and Kumar PP. Destabilization of interaction between cytokinin signalling intermediates AHP1 and ARR4 modulates Arabidopsis development. New Phytologist, 30 January 2015. DOI: 10.1111/nph.13297.

Working with Singaporean colleagues, this New Phytologist paper involved the work of Ari Sadanandom from the University of Durham. The group describe their research on the previously poorly understood relationship between histidine phosphotransfer proteins (e.g. AHP1) and response regulator proteins (e.g. ARR4 ).

 

  • Wilson MH, Holman TJ, Sørensen I, et al. Multi-omics analysis identifies genes mediating the extension of cell walls in the Arabidopsis thaliana root elongation zone. Frontiers in Cell & Developmental Biology, 2 February 2015. DOI: 10.3389/fcell.2015.00010. [Open Access]

Scientists from the University of Leeds and the University of Nottingham (including former GARNet committee member Malcolm Bennett) here describe a multi-omics approach to understanding the regulation of cell wall extension in Arabidopsis roots.

 

  • Preuten T, Blackwood L, Christie JM and Fankhauser C. Lipid anchoring of Arabidopsis phototropin 1 to assess the functional significance of receptor internalization: should I stay or should I go? New Phytologist, 3 February 2015. DOI: 10.1111/nph.13299.

John Christie and student Lisa Blackwood from the University of Glasgow were involved in another New Phytologist paper, led by a Swiss team from Lausanne. The group is attempting to work out why, when irradiated, a fraction of the plasma membrane-associated phototropin 1 (phot1) blue light receptor is internalized into the cytoplasm. Transgenic plants expressing a lipidated version of phot1 permanently anchored to the plasma membrane were used to assess the effect of internalisation on receptor turnover, phototropism and other phot1-mediated effects, however, data suggest that internalisation is not linked to receptor turnover or desensitisation.

Arabidopsis Research Round-up

Categories: Arabidopsis, Global, Round-up
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Published on: January 21, 2015

Lots of new and interesting papers to catch up on from the New Year break this week. Fans of proteomics will be happy as we have three proteomics papers fromEdinburgh, Cambridge and Birmingham! The John Innes Centre and University of Warwick also have an update for us on how histone dynamics affect transcription;Norwich and Sainsbury Lab Cambridge-based researchers tell us more about ELF3; Rothamsted scientists reveal roles for CER2-LIKE proteins; and Donna Bond andProfessor Sir David Baulcombe reveal how virus-induced gene silencing can be used to study transposable elements.

 

  • Krahmer J, Hindle MM, Martin SF, Le Bihan T and Millar AJ. Sample preparation for phosphoproteomic analysis of circadian time series in Arabidopsis thaliana. Methods in Enzymology, 26 December 2014. DOI: 10.1016/bs.mie.2014.10.022.

This useful review from former GARNet PI Andrew Millar and team discusses methods used in phosphoproteomics – the study of post-translational protein phosphorylations.

 

  • Rosa S, Ntoukakis V, Ohmido N, Pendle A, Abranches R and Shaw P. Cell differentiation and development in Arabidopsis are associated with changes in histone dynamics at the single cell level. The Plant Cell, 30 December 2014. DOI: 10.1105/tpc.114.133793. [Open Access]

In this really interesting Plant Cell paper, researchers including those from the John Innes Centre and the University of Warwick, provide evidence to suggest that stem cells have relatively mobile histones, whereas as cells differentiate, the histones become acetylated and thus more and more ‘fixed’ to the chromatin. This helps to explain how stem cells have the propensity to generate cells with different gene expression profiles, and why differentiated cells of a given type all express genes in a coordinated manner.

 

  • Box MS, Huang E, Domijan M, et al. ELF3 controls thermoresponsive growth in Arabidopsis. Current Biology, 30 December 2014. DOI: 10.1016/j.cub.2014.10.076.

Published just a little too late for Christmas (!), this paper comes from a collaboration between mostly Norwich Research Park-based scientists and those at the The Sainsbury Lab in Cambridge. The paper explores the role and function of the transcriptional regulator ELF3 (EARLY FLOWERING3). This gene encodes a protein that rapidly and reversibly binds to transcriptional targets in a temperature-dependent mechanism, thus regulating cell elongation in response to changes in ambient temperature.

 

  • Marondedze C, Wong A, Groen A, Serrano N, Jankovic B, Lilley K, Gehring C and Thomas L. Exploring the Arabidopsis proteome: influence of protein solubilization buffers on proteome coverage. International Journal of Molecular Science, 31 December 2014. DOI: 10.3390/ijms16010857. [Open Access]

Led by a Saudi Arabian team but involving the work of Arnoud Groen and Kathryn Lilley from the University of Cambridge, here’s another paper on the subject of methods in proteomics. In this work, using Arabidopsis thaliana as a model, the group assesses how variations in techniques and detergents used as the solubilisation buffer can affect the results of a proteomic study.

 

  • Roitinger E, Hofer M, Köcher T, Pichler P, Novatchkova M, Yang J, Schlögelhofer and Mechtler K. Quantitative phosphoproteomics of the ATM and ATR dependent DNA damage response in Arabidopsis thaliana. Molecular & Cellular Proteomics, 5 January 2015. DOI: 10.1074/mcp.M114.040352. [Open Access]

More proteomics! Jianhua Yang from the University of Birmingham is an author on this Austrian-led paper, in which a novel mass spec-based phosphoproteomics approach to study DNA damage repair in Arabidopsis thaliana is described. The approach allowed identification of nearly 11,000 proteins and 15,500 unique phosphopeptides, of which 134 ATM/ATR-dependent phosphopeptides were up-regulated, and 38 were down-regulated. Both known and novel targets of ATM/ATR were found.

 

  • Bond DM and Baulcombe DC. Epigenetic transitions leading to heritable, RNA-mediated de novo silencing in Arabidopsis thaliana. Proceedings of the National Academy of Sciences of the USA, 5 January 2015. DOI: 10.1073/pnas.1413053112. [Open Access]

This PNAS offering is from Donna Bond and David Baulcombe from the University of Cambridge. Investigating the mechanisms by which RNA-directed DNA methylation (RdDM) is achieved to silence transposable elements, the authors wondered whether DNA methylation can be induced de novo at naïve sites, or whether it can only re-establish epigenetic silencing of active transposable elements. Using virus-induced epigenetic silencing (VIGS)-RdDM, it is demonstrated that epigenetic silencing can be achieved in a genetic mutant plant, mediated via virus-derived small RNAs. This has great potential for use as a tool in gene silencing studies.

 

  • Haslam T, Haslam RP, Thoraval D, et al. CER2-LIKE proteins have unique biochemical and physiological functions in very-long-chain fatty acid elongation. Plant Physiology, 14 January 2015. DOI: 10.1104/pp.114.253195. [Open Access]

This article, which involved the work of Richard Haslam, Frédéric Beaudoin and Johnathan Napier from Rothamsted Research, explores the functionality of the enzyme CER2 and its homologues; required for the elongation of fatty acids with chains longer than 28 carbons. Three CER2-LIKE proteins are shown to have unique effects on the substrate specificity of the same condensing enzyme (required to catalyse the first step of the fatty acid elongation process), and furthermore are important in cuticle formation and pollen coat function.

Arabidopsis Information Portal at PAGXXIII

Last Monday the Arabidopsis community gathered for the Arabidopsis Information Portal workshop at PAG XXIII. The Arabidopsis Informatics Portal (AIP) was funded by NSF and BBSRC to move beyond the Arabidopsis genome resource provided by TAIR toward linking the genome to the epigenome, proteome, transcriptome and interactome.

AraportThe first talk was a short update from Eva Huala, formerly of TAIR and now of Phoenix Bioinformatics, the nonprofit company she started in order to keep TAIR going. Huala explained that after TAIR’s NSF funding ended, the pay-to-access model was chosen over the alternative pay-to-submit (open access) approach. This means TAIR is focussed on ensuring the subscribers get the best possible value for money by providing the best possible database curation, manual annotation and user experience. Most TAIR subscription fees are paid by libraries, as if it was a journal, but researchers from institutions whose libraries do not pay the fee will be able to access TAIR’s manual annotation after a year’s embargo.

Next, Sean May (NASC, University of Nottingham) explained that NASC is a module of AIP and is currently integrating with the ABRC. He is consulting the community about the development of NASC, so make sure you have your say in the NASC Strategy Survey: http://bit.ly/1J24Hgk

Chia-yi Cheng (JCVI) gave an overview of Araport, the online home of the AIP. Araport federates diverse datasets from other places, for example TAIR, UniProt and BAR, and maintains the Col-0 ‘gold standard’ annotation. It uses JBrowse as the default genome browser and hosts datasets including the CoGe epigenomics resource, which I blogged about last week. (more…)

To tweet or not to tweet?

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Published on: January 19, 2015

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

Categories: conferences, resource
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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…)

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