Open Science: quicker access and more transparency

Oncode Investigator Bas van Steensel (NKI), is one of the Open Science advocates within Oncode Institute. Not a topic that is high on everyone's priority list, but that makes Bas extra passionate to explain the importance of it, and – not in the least – why researchers can benefit from it.

Elize Brolsma

To Bas, the essence of Open Science is to share scientific results earlier and in a more transparent way. We need to make knowledge available faster and easier. Bas: “It can take years between doing an experiment and the moment people are able to read about the results. This lag slows down global scientific progress. One rate-limiting step is the process of getting manuscripts published in a journal; this easily takes half a year and often much longer. Posting manuscripts on pre-print servers such as BioRxiv offer a solution to this problem. This way everyone can read the results much earlier, and the scientific community can move forward more quickly.”

Oncode Investigator, Bas van Steensel

What does he see as a more transparent way of doing research? "

"There are several aspects to this. One is to inform the community of your ongoing research at an early stage, to avoid unnecessary double efforts and to foster exchange and collaborations. I encourage my lab members to share unpublished projects they are working on. We have a blog for this on our lab website."

"Another way is to share all of our data. In particular, I feel it is time that we start to release our lab notebooks documenting all of the experiments that we have done for a paper..."

It has already become common practice to put genomics and proteomics datasets into public repositories, so why not publish the records of the actual wet-lab experiments we have done?

Why does Bas think that this important? “I know it’s a sensitive topic, but how honest are we as scientists? We are under a lot of pressure to report our results as 'simple stories'. But in reality, science is rarely simple. We are frequently confronted with unexplained results, failed experiments or poor reproducibility. We have to make difficult choices: which data do we include, which do we leave out? These issues are often not reported in the final paper. If releasing the lab notebooks were common practice, then everyone could look up the real data behind the 'simple story'. This level of transparency would probably make us think twice before we report over-simplified results."

What does Bas actually do to implement Open Science in his lab? "We are working towards making our lab journals available online. This is not trivial, but it is becoming much easier now that professional software is available for Electronic Lab Notebooks. This is a great opportunity. The NKI has recently adopted such a system, so now we are investigating how we can use it to release our notebooks online together with our papers. As a first concrete step, we recently released a lab notebook extract together with one of our papers. So it is possible."

What does Bas see as the most important challenges? "One complication is that we often work on multiple projects at the same time which are all reported in the same notebook. And when you note things down, you don’t know yet what’s relevant and what’s not. Therefore, you need to think about how to combine the relevant pages at the end of your project. I know people are worried about the fact that this will take too much time. Software solutions may help. And of course, it takes time and effort, but it can save others immense amounts of time in their research. And the idea is, when other researchers do the same: you will profit from it in your own research as well.”

The core of doing science is that your research has impact. That your findings are being picked up by others, that something actually happens with it

Are all his team members pleased about his enthusiasm for Open Science? “Some really support it and see the advantages, others are a bit more reluctant. I understand this. Making your project and results available before it is formally published can be a bit scary, and even publishing your notebook may give a sense of vulnerability. These things need to be discussed. But the core of doing science is that your research has impact. That your findings are being picked up by others, that something actually happens with it. And that’s what Open Science is trying to facilitate. We need to spend our public money wisely, and sharing our research more openly is one way of doing that.”

Please feel free to contact Bas if you’d like to discuss this topic further or join him at his Open Science session during the Oncode Masterclass on June 6th.

Oncode & Open Science

Oncode supports widespread access to its cutting-edge research and knowledge in order to enable others to use and build on them. In Open Science, not only publicationsbecome open access, and data available as supplemental proof of the publication conclusions, but all data is opened for other researchers as early as reasonably possible. Good data stewardship is the key to make this possible. It is key to knowledge discovery and innovation. Apart from making sure research groups better understand and repurpose results from their own research, it allows to generate value for a research community beyond the initial researchers. Oncode also aspires to create an Open Access environment within and between Oncode institutes, enabling the sharing of biomaterials and data in a seamless way. Oncode is making tools, training and people available, so researchers can make the next step towards Open Science and FAIR Data. As a start, Oncode created an Open Access Publishing policy, which can be found here.

Contact the Open Science team if you’d like to receive more information about the Open Science and FAIR data programme.

Other Stories

Rene en Deborah site
‘De vleugels van de wetenschap' - een verhaal over fundamenteel onderzoek met levens veranderende impact
- Dutch translation of the English article - Wat hebben de Nederlandse onderzoeker en Oncode Investigator Rene Bernards (NKI) en de Britse columniste en podcaster Deborah James met elkaar gemeen? Ze zijn beiden op een missie om kanker te bestrijden. Bernards ultieme doel is om zijn onderzoeksresultaten naar de kliniek te vertalen en daarmee impact te hebben op het leven van mensen. James veranderde de diagnose stadium 4 darmkanker in een missie, niet alleen om de ziekte te bestrijden, maar ook om het gesprek erover te veranderen. De twee ontmoetten elkaar in 2018: toen James geen behandelingsopties meer had, was het Bernards innovatieve therapie die haar te hulp schoot.
Bianca-OliviaNita
Rene en Deborah site
‘The Wings of Science’ – a story of basic research with real life impact
What do Dutch researcher and Oncode Investigator Rene Bernards (NKI) and British columnist and podcaster Deborah James have in common? They are both on a mission to fight cancer. Bernards’ ultimate goal is to bring his research findings to the clinic and by that to impact people’s lives. James turned her own stage 4 bowel cancer diagnosis into a mission not only to fight the illness but also to change the conversation around it. The two met in 2018: as James was running out of treatment options, it was Bernards’ innovative therapy that came to her rescue.
Bianca-OliviaNita
494877 COVID 19 Beleggingshuizen reageren d9ef
Een crisis vraagt om samenwerking: hoe drie Oncode-onderzoekers helpen oplossingen voor COVID-19 te vinden
- Dutch translation of the English article - Al meer dan een half jaar is het vinden van oplossingen voor de huidige COVID-19-crisis een prioriteit, niet alleen in Nederland, maar in de hele wereld. Toen de laboratoria gesloten waren en het hele land in lockdown was, leverde dat een enorme druk op. Te midden van alle chaos besloten Oncode-onderzoekers Marvin Tanenbaum (samen met Wouter de Laat), Hans Clevers (werkzaam bij het Hubrecht Instituut) en Lude Franke (UMC Groningen) hun kennis en vaardigheden in te zetten.
ElizeBrolsma

<span>Elize</span><span>Brolsma</span>

Elize is part of Oncode’s communication team. She has over 10 years of experience in the com-munication industry, both for commercial and non-profit organisations. After obtaining her bache-lor and master degree in communication at Utrecht University, Elize worked as a communication professional at a research institute, PR agency, law firm and internet company. She has a strong focus on external communications and Public Relations. At Oncode - together with her colleagues - Elize produces the monthly newsletters for Oncode Investigators & Researchers and the Oncode digital magazine. She publishes content for the Oncode website and is responsible for all social media channels. She enjoys discussing science with researchers and support them in their outreach.