EMBL-ABR: an interview with Jyoti Khadake

  • -

EMBL-ABR: an interview with Jyoti Khadake

Category : Uncategorised

Jyoti Khadake was in Melbourne recently as International Faculty on the Data Life Cycle workshop series, as our expert on microbial genomic data and data accessibility and challenges. As someone who works in biomedical research, she sees the social and ethical considerations vary greatly amongst bioinformaticians, depending on their area of study, but that they all need to adopt the agreed standards for data curation and management which are being implemented across this discipline.

Full interview.


  • -

EMBL-ABR: an interview with Jenny Martin

Category : Uncategorised

This week’s interview is with high-achieving Professor Jenny Martin, Director, Eskitis Institute, Griffith University in Australia. We are extremely pleased to announce that Jenny has agreed to join our International Science Advisory Group. 

Jenny’s comments on data and publishing models confirm some strong themes coming through from the research community in these interviews. We welcome what we know will be her robust contribution and guidance for our growing network.

Read more.


  • -

EMBL-ABR: an interview with Suzanna Lewis

Category : Uncategorised

This week’s interviewee Suzanna Lewis proposes nothing less than a revolution in research publishing orthodoxy where you get credit for the fact that someone can easily find and re-incorporate or integrate your information and where then the task of data curators moves from tidying up data to reviewing and synthesising it.

Read more.


  • -

2016 Interview Series: reflecting on bioinformatics

Category : Uncategorised

During 2016 we have contacted Australian and international expert bioinformaticans and asked them the same six questions. The variety of their responses reflects the diversity of our community and the challenges we face. Take some time to read them here:

Professor Mark Ragan, Queensland, Australia

Professor Marc Wilkins, News South Wales, Australia

Dr Jac Charlesworth, Tasmania, Australia

Mr Jason Williams, New York, USA

Dr John Hancock, Norwich, UK

Dr Nathan Watson-Haigh, Adelaide, South Australia

Mr Pedro Fernandes, Oeiras, Portugal

Mr Rafael Jimenez, Cambridge, UK

Dr Allegra Via, Bari, Italy

Dr Frederik Coppens, Ghent, Belgium

Dr Suzanna Lewis, California, USA

Prof Teresa Attwood, Manchester, UK

Prof Jenny L. Martin, Queensland, Australia

Ms Sandra Orchard, Hinxton, UK

Prof Rudi Appels, Perth, Western Australia

Dr Dieter Bulach, Melbourne, Australia

Ms Lavinia Gordon, Melbourne, Australia

Dr Kate LeMay, Canberra, Australia

Dr Jyoti Khadake, Cambridge, UK

We thank all the contributors of this series in 2016. Over summer we also interviewed

Dr Richard Edwards, Sydney, Australia, and he spoke about the difficulties of maintaining good bioinformatics software tools.

In 2017 we are focussing on Open Science & Bioinformatics – go to 2017 Series.


  • -

EMBL-ABR: an interview with Frederik Coppens

Category : Uncategorised

Philippa Griffin, our Open Data Coordinator, has been at Indiana University, Bloomington, Indiana, USA, as one of a team of instructors at the Galaxy Community Conference 2016. While there she had the opportunity to interview some leading practitioners from our global network of bioinformaticians. For this week’s interview she spoke with Frederik Coppens from Belgium.

Frederik’s comments echoed statements made at the first network meeting hosted at the EMBL-ABR Hub at VLSCI last week – that all roads lead to annotation. Answering a question about open data, he says, “I think open data is about making it easy for people to reuse your data for validation purposes or for completely different purposes that nobody ever thought of…. but you need to be able to tell what the data is, in a very structured way, through the metadata… It’s a very hard question to tackle because nobody’s used to spending time on actually making sure data is annotated well, annotated consistently, so that you don’t have to go through manually to make sure that all the definitions are accurate and useful.”

Read more.


  • -

EMBL-ABR network: an interview with Allegra Via

Category : Uncategorised

Trained as a theoretical physicist, Allegra Via was lured by the beauty of proteins into the life sciences, and using her unique skills, gravitated towards bioinformatics. She regularly teaches Bioinformatics and Python Programming Language to bioinformaticians and biologists and in 2010 she created the “Bioinformatics using Python for Biologists” course for the Gulbenkian Training Programme in Bioinformatics, Portugal. Besides her research activity, she takes part in initiatives devoted to bioinformatics learning, education, and training including as co-author of the 2014 book: Managing your biological data using Python. Allegra insists biologists must not only know how to do data science, but they also need to understand statistics, the limitations of bioinformatics approaches and resources and how to speak to specialist computational biologists and data scientists.

Read more.


  • -

EMBL-ABR network: an interview with Rafael Jimenez

Category : Uncategorised

This week we hear from Rafael Jimenez, who is working at the coalface of life science data infrastructure as Chief Technical Officer, ELIXIR Hub, based in the UK.

Rafael sees the need for faster adaptation to this big data era where we need to find new ways to fund, sustain and continue to develop the many useful outputs from research projects (knowledge, data and tools) beyond any grant funding period.  And of course training in how to do this needs to follow.

Read more.


  • -

EMBL-ABR network: an interview with Pedro Fernandes

Category : Uncategorised

In this week’s interview, we have a perspective from Portugal, but it could be from anywhere in the world. When asked what is missing in bioinformatics AND life sciences, Pedro Fernandes lists three things:
1. a better balance between formal and continuous non-formal education
2. lowering of barriers to access data and computational resources
3. greater standardisation of datasets and their annotation globally, to place them in coherent, discoverable repositories.

Read more.


  • -

EMBL-ABR network: an interview with Nathan Watson-Haigh

Category : Uncategorised

In a multi-disciplinary field such as bioinformatics, it is not possible to be an expert in everything. We bioinformaticians cannot expect life scientists to leave the lab behind completely to gain expertise in bioinformatics. Similarly, bioinformaticians cannot be expert biologists, computer scientists, software developers etc. It takes a team of bioinformatics, each with expertise in at least one of these domains to adequately address many of today’s scientific endeavours.

Read more.


  • -

EMBL-ABR network: an interview with John Hancock

Category : Uncategorised

Asked recently for his views on the current state of bioinformatics, the Head of the ELIXIR UK Node based at The Genome Analysis Centre in Norwich, Dr John Hancock, highlighted open data as an essential pre-requisite for modern bioscience and that it is definitely not something to be afraid of.

Read more.