All systems go – a look at a 2018 systems biology course
Interested in systems biology? Meet the organizers and find out about the plans for a 2018 FEBS Practical Course providing hands-on systems biology training
The 8th International Practical Course in Systems Biology, supported by the FEBS Advanced Courses programme, will take place in Gothenburg, Sweden, June 4–15, 2018. The course offers unique hands-on experience in data collection, modelling, simulation, prediction and verification on the analysis of the dynamics of defined molecular systems. Here, an interview with the course organizers – Marija Cvijovic and Stefan Hohmann – introduces this research area and explains something of the event organization. Check out the course website for more details, and note the application deadline in March 2018!
Introducing the course organizers
Marija Cvijovic is an Associate Professor in systems biology at the University of Gothenburg. "My interdisciplinary research group comprises biologists, biotechnologists, physicists and mathematicians and we study the complexity of cellular ageing using experimental and computational methods. Developing, integrating and applying new methods allows us to gain a systems view of ageing using budding yeast as a model organism."
Stefan Hohmann is a Professor at the Department of Biology and Biological Engineering at Chalmers University of Technology, Gothenburg. "We are interested in understanding and using the dynamic behavior of signal transduction pathways. For this we integrate experimental studies with mathematical modelling and prediction. We use the yeast Saccharomyces cerevisiae as an experimental organism. Our research has focused on the HOG signaling pathway, which controls adaptation to osmotic stress, and the AMPK/SNF1 pathway, which controls cellular energy homeostasis. In recent years we have increasingly employed studies in single living cells to capture signaling dynamics."
Introducing the course: a Q&A with the course organizers
In your view how does the field of systems biology fit in with other approaches used in molecular life science research, and what have been some of its successes?
Systems biology complements and bridges standard approaches in molecular life science research. Systems biology investigates emergent systems’ properties that cannot be derived from the study of single genes or proteins. This is achieved, for instance, by elucidating the quantitative relationships, interactions and cellular distribution of molecules. Mathematical models and predictions made from simulations are a key element of the approach. Examples of major projects in systems biology include the Virtual Human Heart, the Virtual Liver Network, the Human Metabolic Atlas and projects in the frame of the international Virtual Physiological Human programme and Physiome Project. A system-level understanding of biological processes enables personal medicine, biotechnology as well as agro-science.
How did you get into systems biology?
Marija: I am a trained mathematician having a big interest in biology. After my bachelor studies in mathematics, I decided to combine my love for both and went for a master program in bioinformatics, which led further to a PhD in systems biology. Being a mathematician, it always fascinated me how we can describe nature using equations and get profound understanding of how cells function.
Stefan: In the 1990s I studied signal transduction mechanisms in yeast cells (and I still do that today). I realised that we could not understand the mechanisms that tune the activity of signalling pathways without a more global understanding of how the proteins involved cooperated in quantitative terms. I also felt we would need mathematical models and simulations to achieve that type of understanding. I wrote a grant proposal, which a close colleague read. He asked me: did you hear about systems biology?
What's exciting in the field right now?
Development of single-cell experimental techniques and single-cell data analysis. It holds great potential and could probably challenge our current views on biological systems.
What are some of the challenges that remain with the systems biology approach?
Building whole-cell dynamic in silico models requires integration of different time scales at which biological changes occur, as well as integration of different data types. Also understanding implications on systems behaviour is hindered by uncertainty in parameters, initial conditions and to some extent the network structure.
What led you to start this practical course?
Complexity of problems encountered in biology often requires a combination of different expertise. We believe that an interdisciplinary approach in systems biology is becoming increasingly important. We need to train students to phrase and communicate research questions in such a manner that they can be solved by the integration of experiments and modelling, as well as to communicate and collaborate productively across different experimental and theoretical disciplines in research and development.
How has the course evolved over the years?
The course was held for the first time in 2005 and was one of the first, if not the first, of its type. Still today, we do not know many courses that combine experiments and modelling. We tested different periods – the longest version of the course was three weeks. We always have been clear that we wish to involve students from both an experimental and mathematical background. By going through one systems biology cycle from data to model to prediction to verification, students experience systems biology and teach each other in an interactive and intense manner. In this way they learn about one of the most important aspects of systems biology: interdisciplinary collaboration.
How do you cater for participants with different backgrounds and interests?
We have instructors and tutors from both experimental and theoretical approaches and the first three days are dedicated to introduction lectures bringing everyone to more or less the same starting point. The most important thing is that the students are motivated to learn about a complementary discipline and achieve the understanding of how mathematics and biology can go hand in hand. Participants learn a lot from each other through the project they are involved in.
How do you select speakers and instructors for the course?
Some instructors have been with us from the early beginnings – their research is deeply rooted at the systems biology approaches where they have appreciation for interdisciplinarity.
The idea with invited speakers is to bring an additional dimension to the course. All speakers are within the systems biology field, but working on different model organisms, diseases and mathematical frameworks. Another benefit is the networking component, which is important for young scientists.
How important is the hands-on element of the course, and how is this organized?
The hands-on element is the key component and one of the main strengths of our course. Participants work on a project in smaller groups: four persons/group where each group has two theoreticians and two experimentalists. The project mimics the whole systems biology cycle and each group does the labwork together, collects the data and then develops mathematical model. At the end of the course each group presents their findings.
What's your view on social programs in scientific meetings, and what do you have planned?
We carefully prepare our social program as at these occasions team spirit is built. We kick off the course with bowling where we have an experimentalists vs theoreticians competition. We have our legendary midsummer party at Stefan’s place, with great food and a (voluntary) swim at the nearby lake. During the course, evenings are dedicated to the presentations by participants with supper and beer. There are often long days and there is no better way of team building than suffering together 😊. Participants are also located at the same hostel, so the bonding happens continuously and naturally.
Thanks to Marija Cvijovic and Stefan Hohmann for answering these questions. For more information on this FEBS Practical Course, visit the event website: http://icysb.se/