Integration of thermodynamic data into the metabolic pathways represented by the Boehringer wall chart

Robert Giessmann / Bayer AG, Berlin, Germany

March 4, 2021, 3 - 4 pm CET

Online live talk

Introduction

The Boehringer/Roche "Biochemical Pathways" wall chart is a carefully arranged map of metabolism. It is larger than DIN A0 format: an enormous 1.4 x 1 m; but despite its unhandy size it's hanging in many laboratories around the world. Digital databases of metabolism like KEGG and MetaCyc can feel overwhelming to navigate on a small computer screen. Maybe it's indeed the comforting feeling of paper that makes researchers put up this wall chart with joy?

Unfortunately, though, coming from an analogue pen-and-paper world, the "Biochemical Pathways" poster is not that easily accessible for automated computer analyses. I wanted to know how many of the reactions on this poster are characterized in terms of their apparent equilibrium constants. I ended up colouring them with pencil myself, a process I don't want anyone to need to repeat.

This webinar is going to celebrate the "Biochemical Pathways" wall chart. It will look into how to bring this poster into a digitally tractable form. Similarly, this webinar will celebrate the "Goldberg reviews" for the enormous effort in bringing together data about apparent equilibrium constants from primary literature. Finally, it will look into what happens when you make computers let do the work for you in marrying thermodynamics and metabolism, and what to learn from this effort.

Robert Giessmann

Robert T. Giessmann (https://orcid.org/0000-0002-0254-1500) received his Ph.D. in Bioprocess Engineering for work on the kinetics and thermodynamics of nucleoside phosphorylase-catalyzed reactions. He studied Chemistry in Germany. In 2019, he started a job as Computational Life Scientist with a focus on FAIR Research Data Stewardship at Bayer, and works part-time since.

Robert is a strong proponent of Open Science, and wants to empower good Research Data Management. He believes that Linked Data has the potential to enable this at scale technologically, but that it will need years of alignment within and between the communities to agree on the corresponding standards. Not being dependant on optimizing his traditional academic metrics anymore, he can share all of his research ideas freely and is happy for anyone to take them up and collaborate on them.

Contact

The Beilstein Talks are organized by the Beilstein-Institut.
If you have any questions, please contact:

Dr. Carsten Kettner
Beilstein-Institut
Trakehner Str. 7–9
60487 Frankfurt am Main
Germany

T +49 69 71673-221
F +49 69 71673-219
ckettner@beilstein-institut.de