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 I encourage my lab members to share unpublished projects they are working on.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 publications become 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 Rita Azevedo if you’d like to receive more information about the Open Science and FAIR data programme.

Other Stories

Edwin Cuppen
Edwin Cuppen discusses tumour-agnostic drugs for cancer patients
Cancer medicine has traditionally focused on the site of a tumour, but in recent decades research has held out the promise of spotlighting its genetic background instead. The ultimate goal is to achieve more personalised treatment. Now that the first ‘tumour-agnostic drug’ has been authorised, that moment has finally arrived.
Vesnade Jong
Erica 1
Getting the patient’s voice into cancer research
Erica van Wuijtswinkel and Jacco van Rheenen on the importance of patient engagement
Marloesvan Amerom
“We have underestimated the complexity of cancer.”
Anton Berns doesn’t sound like someone who is about to stop working. The 74 years old professor in Molecular Genetics talks with great enthusiasm about new technologies which, according to him, will drive the progress in cancer research the coming years.
Hidde Boersma