The Seventh International Workshop on Static Analysis and Systems Biology (SASB 2016)

SAS workshop, 7 September 2016, Edinburgh, UK

This event is supported by The Scottish Informatics & Computer Science Alliance (SICSA).


SASB is a one day workshop that aims at promoting discussions and collaborations at the intersection inbetween the specific field of formal methods covering modelling languages and static analysis, and the following fields: (i) systems biology targetting a system-level understanding of biological systems, (ii) synthetic biology targetting functional modifications to naturally occurring systems, (iii) molecular programming and development of engineered biological and chemical systems.

The workshop targets biological networks and executable models of biological systems and molecular devices, focusing on their formal specification and static analysis. A special emphasis is given to rule-based or process-algebraic languages that have the advantage of compact representation and provide a robust tool for systems and synthetic biology as well as a good base for molecular programming languages.

Since the state space explodes combinatorially with number of possible states of biochemical substances, static analysis allows investigation of important features from a model without its exhaustive execution. In particular, it allows to pre-process molecular programs and optimise their implementation in DNA; ease characterization of the behaviors of a model; abstractions that prevent a full exploration of the potential concrete behaviors; model reductions, that decrease the dimension of a model while preserving important behaviors; characterization of dynamical properties with respect to the topology of the model; etc. All these features empower and strengthen applicability and efficiency of dynamical analysis and verification.


The program of SASB 2016 will consist of invited talks, oral-only presentations and presentations of refereed papers. Work-in-progress and tool presentations will be organised at the poster session. Contributions are welcome on all aspects about modelling languages and techniques employing static analysis targetting natural biological systems and specification, design and verification of engineered biological and chemical systems, including, but 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).

Invited Speakers

Venue and Registration

In 2016, the workshop will take place in Edinburgh, Scotland.

  • Registration (select Workshops only if you do not plan to stay at the hosting SAS conference);
  • detailed information for venue, accomodation and collocated events.

Previous edition

Important Dates


Paper Submission Deadline (paper) 5th July 2016  11th July 2016 (closed)
Paper Notification 10th August 2016
Poster and Oral Presentation Submission 12th August 2016
Poster and Oral Presentation Notification 15th August 2016


Workshop Date 7th September 2016


8:55-9:00: Opening

9:00-10:00: Invited Talk

  • Jane Hillston. Dealing with Uncertainty in Formal Models of Biological Processes

Coffee Break

10:30-11:50: Full Contributions

  • Jerome Feret and Kim Quyen Ly. Reachability analysis via orthogonal sets of patterns
  • Pedro Varela, Ines Lynce, Vasco Manquinho, Claudine Chaouiya and Pedro T. Monteiro. SAT-based identification of stable states in composed Boolean regulatory networks
  • Célia Biane, Franck Delaplace and Tarek Melliti. Abductive Network Action Inference for Targeted Therapy
  • Juraj Kolčák, David Šafránek, Stefan Haar and Loïc Paulevé. Unfolding of Parametric Logical Regulatory Networks

11:50-12:00: Oral-Only Contribution

  • Diana-Elena Gratie. Extended Composition Colored Petri Nets for Model Refinement

Lunch Break

13:30-14:30: Invited talk

14:30-14:50: Full Contribution

  • Ricardo Honorato-Zimmer, Andrew Millar, Gordon Plotkin and Argyris Zardilis. Chromar, a rule-based language of parameterised objects

14:50-15:00: Oral-Only Contribution

  • Luca Cardelli, Mirco Tribastone, Max Tschaikowski and Andrea Vandin. Quantitative Abstractions for Continuous Models of Biological Systems

Coffee Break

15:30-16:30: Invited talk

  • Eugenio Cinquemani. Inference of regulatory networks from time-series reporter gene data: The case of promoter regulation in the E.coli motility network

16:30-16:50: Full Contribution

  • Guillaume Terradot, Andrea Weisse and Vincent Danos. Survival of the Fattest: The trade-offs underlying the evolution of storage

16:50-17:00: Oral-Only Contribution

  • Ken Chanseau Saint-Germain and Jerome Feret. Conservative numerical approximations of the differential semantics in rule-based models

17:00-18:00: Poster Session

18:00: Reception & Discussion (joint with other workshops)


Program Co-Chairs

Guido Sanguinetti School of Informatics, University of Edinburgh; Edinburgh, UK
David Šafránek Faculty of Informatics, Masaryk University; Brno, Czech Republic

Program Committee

Reka Albert Pennsylvania State University, USA
Gulio Caravagna University of Edinburgh, UK
Luca Cardelli Microsoft Research, Cambridge, UK
Claudine Chaouyia IGC, Oeiras, Portugal
Eugenio Cinquemani IBIS, INRIA Grenoble, France
Vincent Danos École Normale Supérieure, CNRS, France
François Fages INRIA Rocquencourt, France
Jérôme Feret École Normale Supérieure, Inria, France
Vashti Galpin University of Edinburgh, UK
Jane Hilston University of Edinburgh, UK
Gethin Norman University of Glasgow, UK
Nicola Paoletti University of Oxford, UK
Loïc Paulevé CNRS/LRI, Université Paris-Sud, France
Ion Petre Åbo Akademi Turku, Finland
Tatjana Petrov IST, Austria
Andrew Phillips Microsoft Research, Cambridge, UK
David A. Rosenblueth Universidad Nacional Autonoma de Mexico, Mexico
Thomas Sauter University of Luxembourg, Luxembourg
Chris Thachuk California Institute of Technology
Mirco Tribastone IMT Institute for Advanced Studies Lucca, Italy
Paolo Zuliani Newcastle University, UK