Methodologies for Digital Life - Focus on Metabolic Systems
Welcome to the first competence sharing network meeting “Methodologies for Digital Life”, 6. October in the centre of Bergen. Transdisciplinarity is an underlying approach of the centre and the meeting is intended for researchers from different disciplines to meet and discuss novel methodological approaches in the field of digital biotechnology. The meeting is free to attend and open for all interested participants.
The focus of this meeting is on metabolic systems – from single enzymes to global scale metabolism. How can approaches and concepts from mathematics, physics, computer science or engineering be utilized to assess or alter the activity and regulation of complex enzymes and enzyme systems? This approach aims to reveal new possibilities to understand and utilize biological systems, such as, for understanding human health, for utilizing organisms for production of biomaterials and for understanding ecosystems important for our existence.
If you are interested in metabolism or enzymatic systems from a multi-disciplinary perspective, this is a great opportunity to meet up with fellow scientists.
The program is available for download:
Volterra lecture by Bernhard Palsson
Palsson is professor of bioengineering and pediatrics and PI of the Systems Biology Group at UCSD. He is also CEO at the Novo Nordisk Foundation Center for Biosustainability at DTU (Technical University of Denmark). Palsson’s group has been leading the development of full-scale models of metabolism and methodologies for integrating global scale or high throughput data with such models.
AN EMERGING ERA OF GENOME-SCALE SCIENCE
After the first genomes were sequenced in the mid 1990s, the first genome-scale metabolic reactomes were assembled around 2000 through a workflow called metabolic network reconstruction. Subsequently, a field focused on the bottom-up approach to systems biology emerged where biochemical, genetic, and genomic mechanisms were explicitly described in mathematical terms leading to genome-scale models (GEMs). GEMs are now available for metabolism, protein expression, proteostasis, and ROS tolerance. GEMs can be customized based on condition-specific data to form whole cell models parameterized under the condition of interest to describe proximal causation. GEMs can also describe distal causation (i.e., biological function over many generations). Laboratory evolution can now be used to experimentally address distal causation. Automated Adaptive Laboratory Evolution (ALE) machines have been constructed leading to hundreds of evolved endpoint strains that have resulted in the identification of about 20,000 mutations whose causal effects form the basis for a systematic description of distal caution. The work presented will focus on E. coli and will illustrate many methods that Chemical Engineers have mastered.
Peter Ruoff, Centre for Organelle Research, UiS
The Kinetics of Biological Control
Ruoff´s research is focused on understanding the dynamics of biological systems - in particular the underlying mechanisms of homeostasis, adaptation and decision in metabolic pathways/reaction networks and circadian clocks.
Digital Life project session
Eivind Almaas, NTNU
RAMP – a method for handling uncertain data in genome-scale modeling
Jon Olav Vik, NMBU
Foundations of the Digital Salmon: constraint-based reconstruction and analysis
Nello Blaser, UiB
Model reduction under parameter uncertainty
The Volterra lecture series is organized by DLN in honor of the mathematician and physicist Vito Volterra, known for his pioneering contributions to mathematical biology.