What is the Digital Research Environment?
The Digital Research Environment (DRE) is a cloud based, globally available research environment where data is stored and organized securely and researchers can quickly generate workspaces to collaborate in and use the applications they love. Globally available and accessible 24/7.read more
What is the Digital Research Environment?The Digital Research Environment (DRE) is a cloud based, globally available research environment where data is stored and organized securely and where researchers can quickly generate workspaces to collaborate in. Within these workspaces, researchers have preinstalled applications at their disposal, as well as the ability to bring own tooling. Globally available and accesible 24/7.
The DRE facilitates users to collaborate on research projects in a safe, yet flexible compute and storage environment. The architecture of the DRE allows researchers to use a solution within the boundaries of data management rules and regulations. Although General Data Protection Regulation (GDPR) and Good (Clinical) Research Practice still rely on researchers, the DRE offers tools to more easily control and monitor which activities take place within your projects.
Full controlWithin the DRE platform each of the projects you are a member of consists of a separate, secure folder, called a 'workspace'. Each workspace is completely secure, so as a researcher you are in full control of your data. You can invite (external) colleagues into your workspace for collaboration, and with the same ease revoke access at any time. Each workspace has its own list of users, which can be managed by its administrators.
ScalableEach workspace is fully scalable with regard to data quantity and computing power, thereby supporting anything from small to complex multicenter, multisource studies. Moreover, the workspace enables you to perform ‘worry free’ research, meaning that security, ICT infrastructure and compliance with laws and regulations are automatically taken care of when using the DRE.
Various sourcesYou can handle many data types from various sources within your workspace. Some examples: data collected with a survey tool or an electronic data capture tool like Castor or RedCap, data from measuring equipment, IKNL data, clinical data from Biobanks and omics data.
Install your own toolingThe DRE consists of a web-interface enabling access to virtual machines. Preinstalled tools consist of programs such as SPSS, R Studio, Matlab, and Office, but you are free to install your own tools. Because of the security boundary around workspaces, it is possible to offer users the ability to install their own tooling without harming others.
Thanks to the flexibility of the Azure cloud platform, on which the DRE has been built, we can offer a variety of virtualized hardware, including, but not limited, to:
- Standalone virtual Windows / Linux machines (e.g. 72 cores, 144 Gb RAM);
- Compute Clusters (HPC);
- Several storage options (tables/files/SQL/etc.).
DRE consists of a web portal, where, for each workspace separately, you can up- and download data, do member management and connect to virtual machines (launched by a simple click on the icon on your own desktop, like a computer in a computer).
What challenges does DRE solve?DRE solves many of the current problems researchers face, such as: time, right tools, cost, scalability, effectiveness, security & control.
What's the current problem?
It is time consuming to:
- Extract data
- Set up environment
- Store and manage data
It is difficult and expensive to get the fit-for-purpose tools in place.
- Difficult to assign cost and control cost
- Data to 'lost' after every research
- Difficult to get enough compute power
- Difficult to combine and re-use data for larger datasets
- Difficult, near impossible, to combine data sets
- Difficult to collaborate effectively and share data
- Difficult to get insight into progress
- Sharing data over unsecure channels
- Difficult to comply to laws and regulations
- Difficult to monitor if your institution is complying to laws
Does the DRE solve all of these challenges?In fact, yes. You will get cost control (pay for compute capacity by the second), control over security of you data, compliancy, who you collaborate with, and you can monitor progress, output and the data itself.
But way more important: DRE will make your life as a researcher as easy as possible. You will be able to get more research done in less time, need less time to completion and effectively produce more output and recognition.
Preinstalled and own toolsThe DRE consists of a web-interface enabling access to virtual machines. Preinstalled tools consist of programs such as SPSS, R Studio, Matlab, and Office, but you are free to install your own tools.
Because of the security boundary around workspaces, it is possible to offer users the ability to install their own tooling without harming others.
Thanks to the flexibility of the Azure cloud platform, on which the DRE has been built, we can offer a variety of virtualized hardware, including (but not limited) to:
- Standalone virtual Windows / Linux machines (e.g. 72 cores, 144 Gb RAM);
- Compute Clusters (HPC);
- Several storage options (tables/files/SQL/etc.).
Key features of DRE
- Import data sources, organize data, store data securely
- Use, manage, combine and re-use data
- Handle multiple types of data: clinical, images, omics, etc.
- Generate virtual workspaces for researchers
- Use the research tools and applications you want
- Invite fellow researchers into your workspace to collaborate on data and analysis
- Access it anywhere, any time, on any device
- With top security
- All data is compliant, by design
- Pseudonymization software
- High-performance computing
- For single and multi center studies
- A catalogue with data for re-use
- Self-service for researchers
Research Data LifecycleResearch data typically undergo several stages. Moreover, the current view is that the life span of research data is not restricted to the research project for which the data were created initially. Potentially, the data will be supplemented, edited, analyzed again and reused by other researchers. read more (Intranet, log-in needed)
Self service No long-term commitmentDRE allows researchers to pay for compute capacity by the second, with no long-term commitment or upfront payments. You can increase or decrease compute capacity via self service, always in charge of your costs.
Jack Fransen Accessible, low‐cost super computing power
As a specialist in light and electron microscopy, Jack Fransen, uses the computing power of DRE, Radboudumc’s digital platform, to analyze the images he produces with his equipment.read more
Jack Fransen Accessible, low‐cost super computing power
As a specialist in light and electron microscopy, Jack Fransen, uses the computing power of DRE, Radboudumc’s digital platform, to analyze the images he produces with his equipment. Due to the large format of the microscopic images, this is, in and of itself, a huge stride forward: making it simple to analyze data while cutting costs.Celluar biologist Jack Fransen is a manager at Radboudumc’s Microscopy technology center. He started working with the Digital Research Environment (DRE) when it was first launched in 2017, but at the start, it could not serve his needs. “The images are huge files. I had to physically send data on a hard drive to collaborating researchers. To give you an idea of how large: I remember traveling with a hard drive that contained three images – a terabyte each – from the United States.”
“You’re talking about computing power to be able to process some 100,000 images. The data in these images need to be averaged and fitted using special algorithms on a pixelby‐pixel basis to calculate one final image that we can work with. On a high‐end PC, this can take up hours to days.”
New possibilities"The first version of DRE did not have the computing power to process these microscopic images. I'm enthusiastic about the new possibilities of DRE 2.0. For the past five months or so, we have been using DRE to analyze data on different virtual machines in parallel, and the results are very promising."The virtual machine, on the other hand, has none of these disadvantages.
Jack Fransen explains that everyone in his field is looking for faster and cheaper ways to process the huge amount of data they collect. “Some universities are looking for answers in creating a large cluster of local computers that could deliver the necessary computing power. This has a few disadvantages. Firstly, the data is only accessible in one physical place. Secondly, when researchers use the machines for analysis, it cannot be used for research. Thirdly, these machines are very costly in both purchase and maintenance.”
“The virtual machine, on the other hand, has none of these disadvantages. The data can be accessed at any time and in any place. Researchers needing to analyze their data are not holding up our equipment and thus hindering new research. And the difference in costs is substantial. Within DRE, you only pay for computing power when you're using it. In other words, you can temporarily up the computing capacity. At € 1,50 an hour, it's easy to calculate that you are better off using a virtual platform than expensive machines that could cost anything up to € 11,000 a piece.”
Storing and sharing“Of course, the DRE environment is not yet perfect,” says Jack. “At the moment, it does take some time to upload the data to the cloud. The speed will need to improve, but I’m confident that this is where the future is, rather than physical computers.”
It is also good to note that, unlike the data derived in other fields of research, Jack Fransen and his colleagues don’t use DRE as a permanent storage database. The cost of keeping the files of a microscopic image in the cloud is too much. For now, images will still need to be stored on a physical computer.
“There are national projects in the field that are trying to find cheap alternatives to store and share data in a cloud‐based environment,” says Jack. That’s not to say that DRE will be obsolete when a possible other sharing environment is created. According to Jack, DRE offers a great workspace to help researchers with their analysis: “Users can customize the DRE workspace with any available open‐source software that suits our needs. We can also add analysis protocols to ensure that researchers are working the same way. It’s also a user‐friendly environment, meaning that even researchers that are less computer savvy can use it instinctively. A real plus for researchers who want to focus on research rather than digital tools.”
Jesse Oomen Accessing patient data is time‐efficient
Jesse Oomen uses DRE for collecting data from the medical center’s patient files. He uses these data sets to make reports for doctors from his department as well as for managers and financial controllers.read more
Jesse Oomen Accessing patient data is time‐efficientJesse Oomen is a data manager for the Department of Hematology. He was one of the first users of Radboudumc’s Digital Research Environment – known as DRE. He only uses it for one specific purpose: collecting data from the medical center’s patient files. He uses these data sets to make reports for doctors from his department as well as for managers and financial controllers. It has saved him hours of manual work.
“One of my tasks is to send my department’s management team monthly reports regarding our patients that receive hematopoietic stem cell transplantation and cellular therapy. I also register all these patients in the database of the European Society for Blood and Marrow Transplantation (EBMT). This entails collecting the same data every month and plotting the data in tables and graphs. Before the DRE, I had to collect the information manually.”
Collecting data from doctors"One of the first things I did when I began working for Radboudumc about five years ago was to develop a form the doctors could use to fill in the necessary patient information. Before this, every doctor registered different information in different ways. The form includes clinical information such as the status of the illness, what kind of donor they would receive – i.e., a family or non‐related donor – a score for their physical wellbeing before treatment, and such. This form helped get the data into EPIC – Radboudumc’s electronic patient files – in an orderly fashion.”
“At around the same time, the DRE project began to take shape, and it was a logical step that I joined the team as super‐user; to tell my needs and test the digital portal as new services were added. At this stage, they developed a tool called Cliniquest. This tool makes it possible for users to make a query to obtain EPIC data and generate a data set.”
Customizing a workspaceThanks to DRE, much of this work is now largely automated.“DRE further has a customizable workspace. I can add open‐source software to this workspace that will allow me to analyze the data the way I need to. It also gives me full control of the data: I can invite other users to my workspace. From here, these users can view the data and use it for analysis, but they may not download it without my express permission.”
“The data stewards recommended I should use the open‐source KNIME data analytics, reporting, and integration platform. This is a user‐friendly tool that helps me visualize the data with graphs, charts, and tables.”
Automated process“Thanks to DRE, much of this work is now largely automated. I still need to go to Cliniquest every month and change to the parameters of the query to include the last month, but that’s about it. I can then open KNIME in my workspace and request it make the same graphs and tables with the newly generated data set. I then download the report and email it to both the doctors of my department and management team.”
"Theoretically, I could give the doctors access to my workspace in DRE through their DRE accounts. They could study the information there. In practice, though, the doctors don't want another environment they have to log in to. They want to open their mail and see what they need to know. For now, that's fine. It's not a lot of extra work for me to email them.”
Recommending DRE“I recommend DRE to the researchers. I certainly see the benefits of it for their research. Privacy issues regarding patient sensitive information are tackled without them having to overthink about it. They can access their data anywhere – even when on research trips to other universities. They can also easily share data and thus collaborate with researchers anywhere in the world.”
“I only point out the possibility and advantages of DRE to them. They then contact the data stewards for further information and access to DRE. Although I haven’t talked extensively to them about the experience with DRE, I’ve certainly never heard any complaints. At the start, DRE wasn’t all too user‐friendly. It’s improved a lot since then and is very easy to work with. If you’re wondering whether to begin using DRE, this is a good time to give it a try."
Marieke van Rijn Benefits for doctors as well as researchers
Marieke van Rijn has several reasons why she started using DRE. As a researcher, she knows what the benefits of the digital workspaces are for researchers and discovered that it can even benefit doctors.read more
Marieke van Rijn Benefits for doctors as well as researchersUp‐to‐date analytical software, high amounts of computing power, and secure access to other people’s data are the main reasons why researcher Marieke van Rijn started using DRE. She knows firsthand what the benefits of the digital workspaces are for researchers and has discovered that it can even benefit doctors.
PhD candidate Marieke van Rijn was one of the first researchers to use the Digital Research Environment: a secure, cloud‐based workspace environment known as DRE. For the past three years, she has been working at Radboudumc's Nephrology department on research regarding prediction modeling. Her research includes processing large datasets.
How to deal with large data sets?I would always be using the latest version without any effort on my part.She quickly stumbled upon two big problems when working on the medical center’s internal workspace. The first was that the software program she needed to analyze her data had not been updated in years. Due to extensive security checks by the IT department, it could take several months before she could get the updated version she needed. The second problem was that the internal hard drive did not have the computing power she needed to process the vast quantities of data.
Marieke was glad to discover the recently launched research environment that had been created by Radboudumc’s Data Stewardship technology center. “It offered me a great solution for both my problems. Whereas the programs on the internal server are updated every few years, DRE updates all its programs every month. Not only was I able to use the latest version I needed, it meant I would always be using the latest version without any effort on my part.”
“Then there’s the advantage of the computing power. As a Radboudumc researcher, you get to use the standard applications and capacity free of charge. But whenever I need more, I can temporarily up the compute capacity. I only pay the exact time I use it – so, pay per minute. What’s more, before upscaling, I can get an estimation of the costs. The dashboard also allows me to see how much I have already spent. That way, I can keep the costs in check. And an extra benefit for researchers applying for grants is that they also get an idea of the computing costs and can add these to the grant application.”
Using patient data securelyBeing new when Marieke started using it, DRE still had bugs and issues that needed to be worked out. "The great thing is that the program administrators react quickly whenever I report something. In my experience, they solve bugs within days, and they seriously consider any suggestions I offer.”
Together with fellow researchers at her department and data stewards, Marieke van Rijn has also developed a very different use of the DRE: a practical one for the medical staff. DRE can securely and quickly help analyze current patient data, giving clinicians a much better idea of their patient body as a whole.
"Thanks to DRE, we as researchers can access EPIC data, Radboudumc’s electronic patient files. Data that you upload to DRE is automatically pseudonymized. That means that researchers at Radboudumc are now allowed to analyze it: something that was not possible before – or at least not in such a quick and easy way.
“I wrote an algorithm that analyzes the raw data of in‐house patients of the Nephrology department that had a complication. Every week, doctors can get an update. Now they can quickly get an idea of, for example, how many of their patients got an infection or compare it to the same period last year.”
Creating a user‐friendly dashboard and re‐usable script"It's a great spin‐off of the use of DRE. The doctors in our department are very enthusiastic about this application. Not all of them are very digital savvy, but they all find the dashboard user‐friendly. The many data they are obligated to register about patients now have a much more direct purpose for them. Without analyzing it, recording data can feel to have little meaning. Before, analyzing this data took manual labor and was time‐consuming. It did not happen regularly. This new tool helps them reflect on their care quicker.
“A real plus is that if needed, doctors are permitted to go back and track which patients stand out in the data. In other words, DRE can take the pseudonymized data and trace it back to an EPIC id, and the doctor uses that to track down the patient. Important: DRE only permits doctors to do this – not researchers – meaning it complies with GDPR.”
Marieke has written the script is such a way that different departments could re‐use it for various purposes. For anyone interested ‐ the DRE team is open to any requests. She can see that DRE has much more potential than its initial purpose: namely, helping researchers store, analyze, and share their data in a secure, user‐friendly environment.
Wynand Alkema An open source but secure environment
Radboudumc’s digital workspace DRE offers data analyst Wynand Alkema a secure environment to store and analyze data. Using DRE, he can access sensitive data without harming privacy. Among other things, it's ideal when writing a grant proposal for an international consortium.read more
Wynand Alkema An open source but secure environmentRadboudumc’s digital workspace DRE offers data analyst Wynand Alkema a secure environment to store and analyze data. In patient‐oriented medical research, he has to deal with stricter privacy issues than the commercial research on food projects he also does. He has, therefore, used DRE as a perk when writing a grant proposal for an international consortium.
Wynand Alkema works part‐time as a data analyst for Radboudumc’s Center for Molecular Biomolecular Informatics (CMBI). This center focuses on bioinformatics, comparative genomics, bacterial genomics, computational discovery and design, and protein structure bioinformatics. One day in the week, Wynand does fundamental research for the CMBI.
Getting acquainted with DREFor his CMBI‐related projects, he uses data from EPIC, Radboudumc’s electronic patient files. Thanks to the Digital Research Environment – known as DRE – he can access this privacy‐sensitive data without harming the patients privacy. The portal allows researchers to analyze pseudonymized patient information. Without DRE, only medical staff would be permitted to access this data.
“I’m responsible for setting up and managing a bioinformatics service facility at the CMBI. You could say I’m the middleman between the lab technicians and data stewards. Lab technicians and clinicians are experimentalists and not always familiar with data streams and virtual applications. Many researchers use Excel sheets to store data and know little about how to use statistic applications.”
No more manual analysesOnce researchers use DRE more often, it will get easier and quicker.“I help facilitate the use of DRE. I write applications to make it easier for the researchers at the center to use DRE.” As an example, Wynand mentions that his colleagues need to sift through 20,000 documents filled with patient‐related information. "Manually examining this data is no longer an option. I wrote an algorithm that does this for them and presents the results clearly and concisely within DRE.”
Although most researchers see the benefit, many also still need to get used to using DRE. “They have to log in, download a program; for some researchers, this is daunting. But this is also due to the strict privacy regulations. You have to jump through hoops to comply with them. I’m sure once they use DRE more often, it will get easier and quicker.”
Open but secureWynand Alkema also works as a contract researcher for, among others, NIZO. Here he is responsible for the acquisition and execution of big data‐driven projects for clients in the food and health sector. The data used in this research is not so much connected to patients; meaning the data is a lot less privacy‐sensitive. They have less need for all the precautions that DRE offers. However one of the advantages, scaling up computer power, could be usefull for them as well.
“Another difference with commercial use is the philosophy of data,” explains Wynand. He continues: “Data can be stored and analyzed in a cloud‐based environment that is only accessible for internal users. In commercial research, data has value that needs to be protected. The philosophy in academic research is to share data for reuse: the FAIR data principle. Your data needs to be open to external researchers but more secure. And DRE offers that. Thanks to pseudonymization, authorization of access, and an audit trail of users, data is protected but still available to researchers. And that anytime and anywhere in the world."
A great extraThese are just some of the reasons why Wynand Alkema decided to include access to DRE when applying for a grant for an international consortium. “In such a grant application, we can let the grantors know that at Radboudumc, we have a virtual portal with which to store, share and analyze data with all researchers that will participate in such a large project. And we don’t just have the facility, but also an entire department to support and maintain it. It’s a great extra to offer during a grant proposal.”
Mirjam Brullemans Designed by researchers for researchers
According to Mirjam Brullemans, getting researchers to understand the importance of efficient data management is not easy. She sees how the portal can unburden researchers so they can concentrate fully on their research.read more
Mirjam Brullemans Designed by researchers for researchersGetting researchers to understand the importance of efficient data management is not easy. Mirjam Brullemans realizes it may make some researchers cringe, but, as a data steward, she knows what can happen if researchers start thinking about it too late. As a member of the initial DRE project, she sees how the portal can unburden researchers so they can concentrate fully on their research.
Mirjam Brullemans is a data steward at Radboudumc and was involved in the creation of the Digital Research Environment, known as DRE. DRE is a globally available, cloud based portal where researchers can store and share their data as well as customize a workspace with the tools they need to analyze that data.
One of Mirjam’s primary functions is to advise researchers on how they can best manage and organize their research data. Mirjam acknowledges that there are still many researchers who know far too little about data management. “They don’t realize its importance or the impact of it on their research. This means they are often not storing their data in a way that complies with the European privacy regulations. Or they realize too late that they have to make their data available for reuse. They’ve recorded their data in a way that makes sharing near impossible without extensive manual reorganization.”
Focusing on what researchers wantThe system is a digital environment that is not just for researchers but was made with them.Due to these experiences with researchers, Mirjam was enthusiastic about becoming a consultant on the project that set up DRE. “We wanted to create an environment that would unburden researchers when it comes to handling data. I was asked to think about usability. Important was to get researchers involved from the start. What did they need, and what did they want? The system is a digital environment that is not just for researchers but was made with them.”
Data is safe in DRE for several reasons, explains Mirjam. “Firstly, data from Epic, our Electronic Health Record (EHR), can be consulted in a DRE workspace by using an application that pseudonyms the data. This safeguards patients’ privacy. Secondly, the researcher who uploaded the data regains control of it; they determine who gets permission to use it, and no one can download it without additional authorization. Thirdly, the portal registers activity. The owner can trace who uses what data when. Although the audit trail is not user‐friendly at the moment – we're working on that – it is recorded and retraceable."
The lifespan of research dataDRE can help in all phases of the ‘Research Data Lifecycle.' This cycle starts with planning and design and afterward collecting and creating data. Data is then stored and analyzed and finally archived and shared. Other researchers can then find your data during their planning and design phase, and perhaps decide to use it in their research and the research data lifecycle starts again.
“Data management should be part of a research plan. Not something organized separately as an afterthought. You should know how you’re going to store and work with data before you collect it. DRE is a great tool to help you store and analyze your data after you’ve collected it. You can ask collaborating researchers elsewhere in the world to also use DRE to store their data which will allow you to also use it securely. But, if you start too late, it will seem like more work than beneficial.”
The current view in academia is that the lifespan of research data is not restricted to the research project for which the data were initially created. DRE can also provide a solution. “Your research details can be added to the DRE catalog, which will enable other researchers to find it and request access. The DRE catalog is an addendum to the system and can also be used by researchers not using the DRE. If they fill the data details and where to find the data – from a personal hard drive or other cloud‐based storages – it
can be re‐used. It also helps institutions to better manage their data.”
UnfamiliaritySo why aren’t more researchers using DRE? One of DRE’s most significant problems at the moment is that not enough researchers know about it. Or think it’s more of a hassle than a help.
The Data Stewardship technology center realizes that researchers need to become more familiar with DRE. It is, therefore, trying to make data management part of Radboudumc’s educational curriculum in both the Master’s and the PhD programs. And of course, also by asking researchers who work with DRE to help their colleagues get acquainted with it. “It’s really not just the digital savvy that can use DRE. The idea is that you can research as you were used to, but in a safe and compliant manner.”
Jan van den Brand Focusing on research instead of red‐tape
To store, share, and analyze research data, Jan van den Brand uses DRE. It also allows him to generate a customized workspace with which he can share data he collects without losing ownership over it or compromising patients’ privacy.read more
Data Stewardship team
The Data Stewardship technology center provides services in the area of research ICT. We currently provide support and training for the Digital Research Environment (DRE), Castor, Epic for research , Labguru and general research data management.