SASB 2018

Static Analysis in Systems Biology, affiliated with Static Analysis Symposium, 28.8.2018

Objectives

SASB is a one-day workshop, affiliated with the Static Analysis Symposium , aimed at promoting discussions and collaborations at the intersection between formal methods, static analysis, programming languages, mathematical modelling and systems and synthetic biology of natural and engineered systems. It is important to note that, despite the name of the workshop, we are not limiting the program to work in static analysis, but rather are open to submissions in all of the topics we have listed. See last year's edition

Scope

The program of SASB 2018 will consist of invited talks, presentations of refereed talks, and presentations of refereed papers. Contributions are welcome on all aspects of modeling languages and associated analysis techniques, including static analysis of natural biological systems and the design, specification and verification of engineered biological and chemical systems. This includes, but is not limited to:

  • static analysis frameworks and tools,
  • equivalences and equivalence checking techniques,
  • model reduction and decomposition techniques based on static analysis,
  • state space compaction based on static analysis,
  • links between topology and dynamics,
  • constraint-based and stoichiometric analysis,
  • languages for compact description of biological models,
  • formalisms for description of biological networks,
  • programming languages for molecular devices,
  • static analysis in verification of molecular devices design,
  • standards for models and their annotation,
  • case studies and method applications,
  • informal methods (that could be candidate to formalization).

Program

9-10Carsten WiufGraphs and the dynamics of reaction networks, abstract
10-10.30coffee breakcoffee break
10.30-11Matej Troják, David Šafránek, Luboš Brim, Jakub Šalagovič and Jan ČervenýExecutable Biochemical Space for Specification and Analysis of Biochemical Systems (time-slot changed from 16h)
11-11.30Hans-Michael KaltenbachA unified view on bipartite species-reaction graphs and their relation to interaction graphs and qualitative dynamics of chemical reaction networks
11.30-12Matej HajnalToward Model Selection by Formal Methods
12-13.30lunchlunch
13.30-14.30María Rodríguez MartínezFrom Big Data to mechanistic models: quantitative approaches to understand the healthy and cancerous cellular behavior
14.30-15coffee breakcoffee break
15-15.30Andreea Beica, Jérôme Feret and Tatjana Petrov

Tropical Abstraction of Biochemical Reaction Networks with Guarantees

15.30-16Pierre Boutillier, Aurélie Faure de Pebeyre and Jérôme Feret 

Proving the absence of unbounded polymers in rule-based models

16-16.30Xinwei Chai, Tony Ribeiro, Morgan Magnin, Olivier Roux and Katsumi Inoue

Static Analysis and Stochastic Search for Reachability Problem  (time-slot changed from 10.30)

16.30-17Thomas Wright and Ian StarkModelling Patterns of Gene Regulation in the Bond Calculus
17final word

Registration

Please register via the SAS conference website

Invited Speakers

Dr. Maria Rodriguez Martinez, IBM Research, Zurich, Switzerland.
Prof. Carsten Wiuf, Department of Mathematical Sciences, University of Copenhagen, Denmark.

Important Dates

 Paper abstracts due

15st July, 2018 (AoE) (extended)

Paper and presentation submissions due 

22nd July, 2018 (AoE) (extended)

Paper and presentation notificationsAugust 2, 2018

Submission

Chairs Full papers should be at most 12 pages, ENTCS format, excluding references. Extended abstracts (for presentation-only submissions) should be at most three pages, excluding references. Submission via EasyChair will be announced soon.  

Organisation

 Program Chairs
 contact:  sasb2018 at uni-konstanz dot de 

Tatjana PetrovUniversity of Konstanz
Ankit GuptaETH Basel

Program Committee

Lea PopovicConcordia University, Canada
Verena WolfSaarland University, Germany
David ŠafranekMasaryk University, Czech Republic
Jean KrivineIRIF, France
Jerome FeretINRIA, France
Luca CardelliMicrosoft, UK
Ashutosh GuptaTIFR, India
John BachmanHarvard University, USA
Loic PauleveCNRS/LRI, France
Heinz KoepplTU Darmstadt, Germany
Nicola PaolettiStony Brook University, USA
Hans-Michael KaltenbachETH Zurich, Switzerland
Natasa Miskov-ZivanovUniversity of Pittsburgh, USA
Eugenio CinquemaniINRIA, France