EMBL-ABR: an interview with Malvika Sharan

Malvika Sharan, Computational Biologist at the European Molecular Biology Laboratory (EMBL) in Heidelberg, Germany

March 2017

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Open Science: what is it for you and why does it matter?

As I grew into my scientific career as a bioinformatician, I got in touch with people who actively engaged in Open Science and those communities. In that process, I learned and practised the principles more and more in my daily tasks, and now, I passionately believe that it is the only way to go. It matters to me because I see an important role of Open Science in engaging our communities to advance science in a collaborative manner regardless of geographic location, gender, ethnicity, social-background, etc.

Open Science and Bioinformatics: is there a link?

Open Science is the practice of making different elements of scientific research open, which in the case of bioinformatics are: source code, software, research plans, data sets, manuscripts etc. All these elements constitute the core of bioinformatics by serving as the tools to enhance efficiency, reproducibility, reusability and share-ability of biological data, its analysis and management. So, I’d say that there is indeed an inherent link between Open Science and bioinformatics.

What makes sense to resource as a national effort when it comes to Open Science versus local resourcing/support?

In my opinion, a local resourcing and support is extremely important and should be given required freedom when it comes to research. However, resourcing as a national effort has more influence on standardising the way we store, share and disseminate scientific data to different scientific communities in and across the nation.

How would you recommend a novice biologist to approach Open Science and where can they find guidance, resources, and tools for getting on board, especially if they are not in Germany or within EMBL?

For a novice biologist, it is critical to engage with the local and international scientific communities to seek guidance and exchange knowledge related to Open Science resources and tools. International conferences often include special interest groups to facilitate communication among the scientific communities, for example, the Bioinformatics Open Source Conference (BOSC) runs during ISMB conferences. Young scientists should also look out for opportunities to collaborate with fellow researchers in informal events like hackathons. Furthermore, one can connect to specific scientific communities by means of social media, such as twitter, slack, Stack Overflow, gitter channels and meet-up.

What are the top three actions/initiatives you would suggest biosciences’ domains to prioritise to enable Open Science, and what type of support would they need?

Bioscience domains should promote transparency by providing solutions to share different components of scientific research, encourage collaboration with other researchers, and subsidise publications in peer-reviewed Open Science journals. All these initiatives can be successfully realised when backed by both senior and early stage scientists, and are communicated well within the community.

EMBL-ABR is a distributed national research resource providing bioinformatics support to life science researchers in Australia. What role would you see for EMBL-ABR when it comes to Open Science for Australian Biosciences?

Bioinformatics service providers should develop various bioinformatics training programs and – I see, EMBL-ABR is already involved with such activities – in addition to providing infrastructure and related support. I believe that it will not only help scientists to learn about Open Science bioinformatic tools and resources but will also promote transparency and reproducibility in scientific research.

Is there Bioscience discipline-specific limitations that require tailored solutions when it comes to Open Science rather than enough common denominators to share resources/tools and solutions?

One such example is biorXiv, which allows pre-publication archiving and distribution of manuscripts and data related to biosciences. It was developed after preprint archiving service of arXiv, which has allowed communities from different scientific fields such as physics and informatics, to share their research findings and in turn protect their intellectual property.

The one thing you would like EMBL-ABR to do in the future when it comes to connections with existing international efforts is…

… organising periodic events that involve activities to encourage best practices to share and organise data, familiarise scientists with various Open Science resources, develop mentoring options for young scientists etc. This should ultimately aim to build a sustainable community to promote Open Science on an institute level.

What is the best example you can think of when it comes to Open Science in the biosciences and did bioinformatics play any role?

The Human Genome Project is certainly one of the best examples of how bioinformatics contributed to Open Science in biosciences in a large scale.

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Biosketch: Malvika Sharan is a computational biologist in the EMBL, Heidelberg, where she is mainly working in the Bio-IT project that aims to provide a platform for knowledge exchange and networking in bioinformatics community. She is involved in the development of training and outreach resources at the Heidelberg center for Human Bioinformatics, de.NBI.

Malvika carried out her PhD research in bioinformatics from the University of Würzburg, where she also co-founded Würzburg Unseminar in Bioinformatics (WUBSyB) to facilitate informal discussions among bioinformaticians.

Her other interests are in open science, community building, equal rights, knowledge transfer, and fair representation of women in science.