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…)

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…)

CoGe at PAGXXIII

Comments: 1 Comment
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 in Europe

Categories: GARNet, synthetic biology
Comments: 1 Comment
Published on: May 20, 2014

Helsinki

On 8-9 May I attended a meeting hosted by PlantEngine to discuss the idea of a synthetic biology repository in Europe. The presentations were varied and interesting, and hopefully the other delegates enjoyed mine (PDF) too,

The meeting was at VTT in Espoo, a city very close to Helsinki. The local host Heiko Rischer gave a brief introduction to VTT, which is a Finnish institute but has bases all over the world. VTT is very separate from the university system, and although fundamental research gets done there it has a big commercial focus and strong links to Finnish industry. For example, VTT developed Arctic cloudberry stem cell technology for cosmetics with the R&D team from Finnish skincare company Lumene Oy.

PlantEngine itself was introduced by lead PI Heribert Warczecha. It is a European network focused on enhancing capacity in plant metabolic engineering by activities like defining target pathways, disseminate new technologies, and setting standards. There are currently over 70 labs in 23 EU countries in the network. They run training schools and workshops, and fund short-term scientific missions – check it out if you’re looking for funding for a short research trip to another lab.

One of PlantEngine’s aims is to explore synthetic biology for engineering plant products, which is the reason for the meeting I attended. (more…)

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