The Fifth International Workshop on Static Analysis and Systems Biology (SASB 2014)

SAS workshop, 10 September 2014, Munich, Germany.

Contact: sasb2014@easychair.org

Novotel München City
Hochstr. 11
81669 München
Germany

The post-proceedings are published online in a special issue of ENTCS

Objectives

SASB aims at promoting discussions and collaborations between biologists (modelers), computer scientists and applied-mathematicians interested in designing or using methods to reduce the complexity of modeling, simulating or analyzing biological systems.

Static analysis refers to a wide range of techniques for characterizing and identifying important features from a model without its exhaustive execution. Static analysis is used for helping the design of models, the test of models against experimental data, and the prediction of behaviors. Static analysis may involve, for instance, modeling paradigms, such as rule-based modeling, that ease the characterization of the behaviors of a model; abstractions that prevent a full exploration of the potential concrete behaviors; algebraic representations and transformations that ease the computation of various properties; 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.

Scope

The program of SASB 2014 will consist mainly of presentations of refereed papers and invited talks. Contributions are welcomed on all aspects about the use of static analysis methods in Systems Biology, including, but not limited to:

  • static analysis frameworks,
  • model reduction,
  • model decomposition,
  • algebraic representations,
  • state space compaction,
  • abstractions of dynamics,
  • link between topology and dynamics,
  • languages for compact description of biological models,
  • modeling or data integration experiences using static analysis,
  • informal methods (that could be candidate to formalization),
  • challenges for tackling complexity of biological models.

Invited Speakers

Gheorghe Craciun, Department of Mathematics and Department of Biomolecular Chemistry, University of Wisconsin-Madison, USA.

Fabian Theis, Institute of Computational Biology, Helmholtz Zentrum München and Department of Mathematics, Technical University München, Germany.

Preliminary Program

8:30-9:00: Welcome

9:00-10:00: First invited talk

Coffee Break

10:30-12:00: Contributed talks

  • Erwan Bigan, Jean-Marc Steyaert, and Stéphane Douady. On necessary and sufficient conditions for stationary proto-cell growth
  • Vincent Picard, Anne Siegel, and Jeremie Bourdon. Multivariate Normal Approximation for the Stochastic Simulation Algorithm: limit theorem and applications
  • Alan Veliz-Cuba, Boris Aguilar and Reinhard Laubenbacher. Dimension reduction of large sparse AND-NOT networks - slides.

Lunch break

14:00-15:00: Second invited talk

15:00-15:30: Contributed talks
  • Lubos Brim, Juraj Nižnan, and David Šafránek. Compact Representation of Photosynthesis Dynamics by Rule-based Models

Coffee break

16:00-17:00: Contributed talks

  • Jerome Feret. An algebraic approach for inferring and using symmetries in rule-based models - slides.
  • Diana Hermith, Davide Chiarugi, Moreno Falaschi, and Carlos Olarte. Verification of spatial and temporal modalities in biochemical systems - slides.

17:00-17:15: Concluding remarks

Venue and Registration

In 2014, the workshop will take place in Novotel Munich City, situated near the river Isar and close to the city center:

    Novotel München City
    Hochstr. 11
    81669 München
    Germany

The venue is close to the S-Bahn station "Rosenheimer Platz" (compare, e.g., the map at the Novotel web site). In order to reach the Rosenheimer Platz from the Airport, you may take any leaving S-Bahn (S1 or S8). There is an S-Bahn every 10 minutes. The trip takes about 35 minutes and costs about 10 Euro. Tickets can be bought in ticket machines at the airport.

From the Main Railway Station, it is almost as easy to reach the venue: there any S-Bahn in direction "Ostbahnhof" will do.

For registration, please refer to the SAS website.

Submissions

Please visit the submission website.

All submitted papers will be peer-reviewed by the program committee.

Submitted papers should not exceed 12 pages including bibliography, and follow the ENTCS guidelines. Submitted papers may include, in addition, an appendix containing technical details, which reviewers may read or not, at their discretion.

Papers must be written and presented in English, and describe original work that does not substantially overlap with papers that have been published or that are simultaneously submitted to a journal, conference, or workshop with refereed proceedings.

Publication

There is preliminary approval to publish the workshop proceedings in ENTCS.

Previous edition

Important Dates

Papers

Submission Deadline (abstract) 25th May 2014
Submission Deadline (paper) 1st June 2014 15th June 2014
Notification 19th July 2014
Final version TBA

Workshop

Early registration 20th July 2014
Workshop Date 10th September 2014

Organizers

Program Co-Chairs

Heinz Koeppl Technische Universität Darmstadt, Germany
Loïc Paulevé CNRS/LRI, Université Paris-Sud, France

Program Committee

Claudine Chaouyia IGC, Portugal
Gheorghe Craciun University of Wisconsin-Madison, USA
Damien Eveillard Université de Nantes, France
Jérome Feret École Normale Supérieure & Inria, France
Johnatan Hayman University of Cambridge, UK
Ina Koch Goethe University, Germany
Reinhard Laubenbacher University of Connecticut Health Center, USA
Wolfgang Marwan Otto-von-Guericke Universität Magdeburg, Germany
Andrew Phillips Microsoft Research Cambridge, UK
Adrien Richard CNRS/I3S, France
Julio Saez-Rodriguez EMBL-EBI, UK
David Safranek Masaryk University, Czech Republic
Thomas Sauter University of Luxembourg
Andrei Zinovyev Institut Curie, France