Past Meetup

2nd DNAdigest guest talk from Amy Tang, EBI: data sharing & open science

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DNAdigest's second invited speaker for 2017 is Dr. Amy Tang from EMBL-EBI.

Amy will share her experience in curating ArrayExpress submissions, discussing the challenges we face at the crossroad of submissions, data sharing, publishing and open science.

Old and new members are all welcome to join us for Amy's talk. Feel free to bring along anybody who might be interested!

Repositive is sponsoring this event by providing pizzas :)

We look forward seeing you on Friday, the 7th of July at the Red Bull.

On behalf of DNAdigest,

Alessandro Riccombeni

Title: Data sharing and reproducibility --- musings of a data archive's gatekeeper

Abstract: Research reproducibility has been a buzz word in recent years. Some mainstream media (e.g. BBC (http://www.bbc.co.uk/news/science-environment-39054778), Forbes (https://www.forbes.com/sites/quora/2017/02/09/how-the-reproducibility-crisis-in-academia-is-affecting-scientific-research/#26fd5fcb3dad),Guardian (https://www.theguardian.com/science/head-quarters/2015/jun/25/the-first-imperative-science-that-isnt-transparent-isnt-science)) have introduced the issue to the public, which helps to raise its awareness, but most of the discussions outside of the Open Data community remain at the level of dissecting the problem, or offering solutions which mitigate but not tackle the root causes. In this talk, I will share my experience from interacting with depositors of ~4000 data sets at ArrayExpress (http://www.ebi.ac.uk/arrayexpress) as well as my discussions with several journal publishers, on what I perceive as the major challenges in tackling poor reproducibility of research. As I bid farewell to EMBL-EBI this summer, I will also reflect on the measures we've implemented in ArrayExpress to address some of the issues, and what more can be done as a community.

Bio: Originally trained as a mouse developmental geneticist, Amy is the curation and training lead for ArrayExpress (http://www.ebi.ac.uk/arrayexpress)and Expression Atlas (http://www.ebi.ac.uk/gxa) databases. She leads the ArrayExpress data submission service for functional genomics data (e.g. expression arrays, RNA-seq, ChIP-seq), drives the user-centric development of submission tool Annotare (http://www.ebi.ac.uk/fg/annotare), and delivers training on best practices of sharing biological data. Before joining EMBL-EBI, Amy was a senior bioinformatician in the Ensembl GeneBuild team, curating gene models for key model organisms such as mouse and rat. She holds a PhD in mouse epigenetics (2006) and a MSc in Bioinformatics and Systems Biology (2008), both from Imperial College London.