Empowering biologists with SeDEx

Data and computations play an increasingly important role in many research fields. From chemistry and physics to economics, a lot of data is being generated these days, and increasingly sophisticated algorithms are being developed to make better use of that data.

Erik Schultes, scientific project lead on FAIR data at the Dutch TechCenter for Life Sciences (DTL), saw the same developments within the field of biology. On the one hand, a lot of data on protein sequence data is already available. On the other hand, over many decades numerous algorithms have been developed that use these data to predict the complex folded structures of proteins. Unfortunately, these two developments, data versus algorithm, remain largely isolated from each other, because biologists are not trained in the necessary computer science skills to put them into practice.

Digital image of a protein

SeDEx, a data platform for biologists without IT training

Large-scale protein structure prediction is still very difficult for the biologist without a lot of IT training. To fill in the knowledge gap between the known protein sequences and the unknown protein structures, Erik came up with the idea for the Sequenomics Data Exchange (SeDEx); a platform to make it easier for biologists to combine all this available data with state-of-the-art algorithms for structure prediction.

With the SeDEx, we need to do a lot of computations. It’s very parallelized but it is a lot. Nerdalize solves this problem for the SeDEx. It makes scalable compute resources easily available to biologists without IT training.

Erik Schultes

Converting protein sequence to structure
SeDEx fills in the knowledge gap between protein sequences and structures

The goal of SeDEx is to help biologists obtain predicted structures by making sequence data, structure prediction software, and compute resources easy to use through a simple graphical user interface. Nerdalize provides the computing power behind the SeDEx, making automatic structure prediction easy and affordable. The SeDEx is also a FAIR publication platform, allowing biologists to easily share their findings with the community. Applications of the SeDEx are found throughout basic research, biomedicine, nanotechnology, and industrial enzyme engineering.

The SeDEx opens a whole new window for the biologist, to the enormous universe of possible protein sequences and structures, even those yet to be discovered by life. A great use for our compute capacity! At Nerdalize we are very enthusiastic to be working together with DTL on making the SeDEx a reality.

Now that our compute jobs are so big, we needed to find a solution. Working together with Nerdalize has been a real breakthrough for us.

Erik Schultes