SASB 2019

10th International Workshop on Static Analysis for Systems Biology

October 8
Porto, Portugal


News:
  • SASB Program available!
  • Joint day with FM4BioMed tutorial in the morning and SASB in the afternoon
  • The registration to SASB includes also the participation in FM4BioMed
  • Unfortunately, FM4BioMed tutorial was canceled. SASB workshop will continue as a standalone workshop as initially planned!
  • Attention: as you can see on FM'19 website, our venue is located at Hotel Vincci Porto!

Objective

SASB is a one-day workshop aimed at promoting discussions and collaborations at the intersection between programming languages, formal methods, static analysis, 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.

Previous workshops have been held in:

SASB 2019 will be co-located with SAS 2019, both being part of the FM'19 world congress.

Scope

The program of SASB 2019 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)

This workshop welcomes work in progress, overviews of more extensive work, programmatic or position papers and tool presentations.

Proceedings and post-proceedings

The workshop will have informal proceedings, posted on its web page.

Revised versions of selected papers will be published after the workshop by Springer in a volume of its Lecture Notes in Computer Science (LNCS), which will collect contributions to some workshops and symposia co-located with FM 2019. Condition for inclusion in the post-proceedings is that at least one of the co-authors has presented the paper at the Workshop.

Submission instructions

Please submit your regular paper (up to 15 pages), short paper (up to 6 pages), or extended abstract (2 pages), in LNCS style, via the SASB 2019 author interface of EasyChair.

All submissions will be peer-reviewed by at least three members of the program committee for quality and relevance.

Important Dates

  • Submission deadline: June 30 * extended * July 14
  • Notification of acceptance: July 31
  • Final version due: 02 September
  • Workshop: 8 October

LNCS special issue dates

  • Submission deadline: October 20
  • Notification of acceptance: November 11
  • Final version due: November 27

Invited Speakers

Program

12:30 - 14:00
Lunch
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14:00 - 14:45
Miguel P. Rocha (Keynote speaker)
Modeling and optimizing metabolism with constraint-based and pathway analysis methods
14:45 - 15:05
Sébastien Légaré
Biochemical pathways from causal cores in rule-based modelling
15:05 - 15:30
Coffee break
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15:30 - 15:55
Matej Troják, David Šafránek, Jan Červený, Lubos Brim, Lukrécia Mertová
Specification and Analysis of Biochemical Systems in BCSL
15:55 - 16:20
Gareth Molyneux, Viraj Brian Wijesuriya, Alessandro Abate
Bayesian Verification of Chemical Reaction Networks
16:20 - 17:05
Anne Siegel (Keynote speaker)
Learning boolean regulations based on prior-knowledge data: a logical-based viewpoint

Abstract: Many technologies have been developed to infer Boolean regulations from prior knowledge network and experimental data. Most of them consist in solving optimization problems with different approaches, from constrains-based approaches to genetic algorithms. However, most of the methods provide no guarantee of exhaustivity in the reported models. In this talk, we will review how the underlying optimization problems can be approximated with combinatorial optimization problem and then be solved by logical-based approaches in order to guarantee exhaustivity. Exhaustivity is obtained by performing abstraction of the underlying dynamics and then model-check the resulting models according to the data specificities. We will illustrate how this approach depends on the data measured, from static phosphoproteomic data to time-series metabolism data.

17:05 - 17:30
Evan Becker, Kara Bocan, Natasa Miskov-Zivanov
Nested Event Representation for Automated Assembly of Cell Signaling Network Models
17:30 - 17:50
Yvan Sraka and Jérôme Feret
Kappa Site-graph Patterns Equations Resolution

Venue and Registration

Please see the main main FM'19 page for details.

Organizers

Program chairs

Program Committee

  • Lea Popovic - Concordia University, Canada
  • Verena Wolf - Saarland University, Germany
  • David Šafranek - Masaryk University, Czech Republic
  • Tatjana Petrov - University of Konstanz
  • Jerome Feret - INRIA, France
  • Luca Cardelli - Microsoft, UK
  • Ashutosh Gupta - TIFR, India
  • John Bachman - Harvard University, USA
  • Loic Pauleve - CNRS/LRI, France
  • Heinz Koeppl - TU Darmstadt, Germany
  • Nicola Paoletti - Stony Brook University, USA
  • Hans-Michael Kaltenbach - ETH Zurich, Switzerland
  • Natasa Miskov-Zivanov - University of Pittsburgh, USA
  • Eugenio Cinquemani - INRIA, France
  • Thomas Sauter - University of Luxembourg

Contact
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