what: a Static Analysis in Systems Biology (SASB) workshop
when: 28.8.2018
where: Katholische Akademie, Freiburg im Breisgau, Germany
why: presentation of Biochemical Space Language
SASB is a one-day workshop aimed to static analysis in systems and synthetic biology. Recently, we proposed a novel modelling language call Biochemical Space Language and developed several static methods for analysing models written in the language. Since the language is oriented (but not restricted) to biological systems, we decided to submit to this workshop a paper describing the language and the methods.
Monday 27.8.
My colleague Matej and I left Brno in the late afternoon. We went by train to Prague, where we took a flight to Basel. At first, I thought Basel airport is in Switzerland (as one would expect), but it was in France. There we took Flixbus connection directly to Freiburg, where we had to walk approximately 20 minutes to our hotel. The entire journey took us about 9 hours.
Tuesday 28.8.
The official start of the workshop was at 9 am, however, the registration desk was opened from 8 am.
The workshop started by the first invited talk with title Graphs and the dynamics of reaction networks given by Carsten Wiuf. The first part was basically about the translation of reaction networks to graphs and reducing the network by adding species to rate instead (non-interacting ones). It works only for mass action kinetics. Generally, from the dynamic point of view, nothing has changed, the variable is just added to the rate explicitly. Finally, we is end up with a linear network. The second part was generally about model reductions (removing intermediate and catalyst species) and the properties they hold.
After a short break, there was the first session of presenting accepted contributions. There were three presentations in a row, each of length 30 minutes. I had the first presentation with title Executable Biochemical Space for Specification and Analysis of Biochemical Systems. I have enjoyed the talk, 30 minutes is enough time to actually say something without hurry and too precise preparation. After the presentation, there were few relevant questions about the level of abstraction the language uses. The short discussion concluded that our language is not context-free when it comes to complex dissociation and formation.
The next talk was given by Hans-Michael Kaltenbach. He was talking about A unified view on bipartite species-reaction graphs and their relation to interaction graphs and qualitative dynamics of chemical reaction networks. It was basically about conversion from reactions through Jacobian matrix to interaction networks.
The talk was interrupted by the fire alarm. At first, we didn't know whether it is real or not, but then we packed our stuff and left the building. The alarm was incredibly loud, almost painful for the ears.
After 30 minutes we returned inside and the workshop continued. Matej gave the next talk about Toward Model Selection by Formal Methods. It was very well-structured with a good summary in the end. Despite the fact the work was quite preliminary, it induces a few questions and discussions. A big plus was that it was very interactive.
A short break for lunch followed. It was nothing special; it was mostly pastry, no cooked food.
After refreshment, there was second invited talk given by María Rodríguez Martínez about From Big Data to mechanistic models: quantitative approaches to understand the healthy and cancerous cellular behaviour. The general idea was extracting modelling information from texts (similar to INDRA) and discovering molecular interactions. The second part was different; it was about predictive models for patient stratification. In the third part, these two approaches were combined. The drawback of the presentation was that it showed up that the classification of predictive models was not very successful.
Andreea Beica started the second session of presenting accepted contributions in joint work with Jérôme Feret and Tatjana Petrov: Tropical Abstraction of Biochemical Reaction Networks with Guarantees. The primary goal of the work were reductions on the level of ODEs for reaction networks using abstraction and numerical approximation. It was done by bounding the derivations of variables by calculation of quasi-steady state. The rest of the talk rest was just about finding minimal bound by refinement using mass invariant.
The next speaker was Jérôme Feret. His presentation with title Proving the absence of unbounded polymers in rule-based models started with a nice introduction to rule-based modelling. He mentioned computational challenges and static analysis as a way to avoid it followed by an intro to Kappa language. Then he was talking about an approach for detecting potential unbounded polymers using interaction network (similar to contract map). It was done by finding some patterns using graphs of the links.
Xinwei Chai presented the topic Static Analysis and Stochastic Search for Reachability Problem. It was basically about solving reachability problem for Boolean networks (or some similar structure). It is quite frequent that there is an unknown answer or the reachability problem, he is trying to focus on such cases.
The last talk was given by Thomas Wright about Modelling Patterns of Gene Regulation in the Bond Calculus. Thomas provided a sum up of different languages for biochemical modelling. The talk was about process algebra and some case studies.
After that we had 20 minutes to drop our stuff in the hotel, then there was an official conference dinner. Well, "dinner". There was again no warm food, just some pastry. It was also joined by other people from a parallel workshop (TAPAS). We have decided to go for a real dinner in a restaurant. We found a place and had an excellent dinner. It was about 25€ each, which was not that bad. After the dinner, we went to the hotel.
Complete album from the entire day.
Wednesday 29.8.
We woke up late, and then we bought breakfast in a shop. It was two croissants for 1€, while breakfast in the hotel was for 17€.
After breakfast, we went to Schloßbergturm, which was a tower above a hill above the city. The view was wonderful, it was possible to see the entire city.
From the hill, we got to the city centre (AltStadt), where we have seen a nice cathedral. Before the lunch, we were walking around the city. After lunch we wanted to do some work, the plan was to take our laptops to a park nearby. However, there was a storm. But it didn't take very long, after that we went for a coffee as planned.
Complete album from the entire day.
Thursday 30.8.
The last day we had to check out from the hotel till 12 pm. It was much colder and rainy in the morning, but we went for a walk. We visited a botanical garden nearby.
After the checkout, we went for lunch, ice cream, and slowly marched to the bus stop. From there we took a Flixbus again to Basel airport to catch out flight to Vienna. We arrived in Brno at midnight.
Complete album from the entire day