“Coding is going to become the new English”: researcher on hacking the data deluge

Molecular biologist Tim Treis at Heidelberg University talks about using technology to manage information and organize his research

Tim at work
Tim Treis at work at Heidelberg University. (Photo by Chiara Di Ponzio)

Tim Treis, who is studying for the Molecular Biotechnology MSc at Heidelberg University, knows the importance of managing information.

Whether it’s analyzing the vast amount of data generated by a research project or coming to grips with the huge amount of research already available, researchers need strategies for handling information, as well as tools like Mendeley. As Tim points out, that can mean making use of what’s already available – or creating your own solutions.

Tim Treis“I think in many ways coding is going to become the new English in research, in the sense that everyone is going to have to have some level of fluency in it,” he said. “As researchers we’re producing more and more data, and if you don’t have an idea as to how to analyze that data, you’re going to miss out on a lot of insights.

“Of course, there are solutions out there but you tend to find they need a lot of adapting to each research case. Knowing coding can really accelerate your research if you know how to transform the data you have.”

As Tim points out, not every researcher will be coding every day, but an understanding of the basics, or even just what is possible, is becoming increasingly necessary:

Even if you never intend to write code yourself, you still need a basic knowledge of it so that you can discuss with other researchers on your team what you need.

By way of example, Tim points to his own work. Tim and his supervisor are currently building a fully automated incubator microscope from scratch. These devices typically have a price tag starting at $25,000, and high-end versions can cost upwards of $100,000, putting them out of reach of most research groups. However, they can be an extremely useful piece of lab equipment for conducting high quality experiments. An incubator microscope lets researchers automatically image cells inside an incubator, where they grow in optimal conditions; the alternative is to remove them from that optimum environment and image them manually. This can be a lot of work, even with modern equipment, and usually disturbs the cells under observation.

Cells viewed through the low-cost incubator microscope Tim Treis is building.“Who wants to do that?” Tim said. “It’s a lot of work, it means being in the lab at specific intervals – including in the middle of the night – and you’re taking your cells out of the optimum environment, affecting the quality of your experiment.”

By producing a low-cost incubator microscope built out of easily available parts, the team hopes to ensure that all researchers can conduct research without compromises.

Once a researcher has that kind of automated imaging, they can expect to generate a lot of data – in the region of 1,000 images an hour, each with more than 1,000 cells.

“How do you analyze all that?” asked Tim. “You can hire a bunch of students to look at the images, but that’s not going to be a rewarding experience for them. Creating an algorithm to analyze them means you can analyze much more data and that gives you better results than you would get from low data point numbers.”

With more people creating or fine tuning their own software, the more important an open platform becomes for the research information system envisioned by Elsevier.

“That’s something that would be really great for researchers,” said Tim. “An open platform will be very valuable. For example, a lot of databases have open APIs. If a research group with a combined presence in Mendeley has all their papers organized together and can then pull together all the related data behind those papers, that kind of thing would be very powerful for the research community.”

Tim uses Elsevier’s Mendeley tool as a way of organizing the information he needs to do his research:

That’s a good example of the value of an open system. I put everything into Mendeley, and because I work in Chrome, I can click once, with an add-on, and it’s in there. You can use it to structure the information you have, so by creating a folder system in Mendeley, wherever you find something related to your work, you save it in there. It saves you from having to continuously go to multiple places to look at different pieces of research.

Tim’s enthusiasm for Mendeley prompted him to become a Mendeley Advisor as a way of “giving back” to the free-to-use platform. “If I find something useful, I feel compelled to support it in some way – that was really why I wanted to share my experience with other researchers,” he explained.

Mendeley Advisors are a group of 5,000+ Mendeley lovers in 130 countries who help us to get the word out about the benefits of good reference and research workflow management. Learn more about the Mendeley Advisors here, including how to become one.

Ultimately, Tim sees organization as the key to success when dealing with huge amounts of information, whether its created by software or by technique. “I’d suggest that people look at project management techniques like Kanban. They help with research, they help with everyday life. And I’d definitely suggest that people write things down, so you don’t forget them, and they’re not rattling around in your head anymore.”

About Tim Treis

Tim Treis (@TreisTim) was born in Hamburg, in northern Germany. After school, he started studying Molecular biotechnology in Heidelberg to further pursue his interest in biology. During his BSc studies, Tim primarily worked on microbiology and then finally wrote his bachelor thesis on metabolic engineering in C. glutamicum in Bielefeld. Moreover, he very successfully participated in iGEM, a synthetic biology competition for students. While his formal training was wetlab-focused, he has always had a keen interest in informatics. Programming both in his free time as a web designer and in research projects, his field of interest slowly drifted towards bioinformatics/data science. In 2018 Tim started his MSc in Molecular Biotechnology at Heidelberg University and is currently working at the BioQuant, where his primary focus is systems biology. For his career, Tim plans to combine his lab and programming experience.

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