Workshop on Systems Biology and Formals Methods (SBFM'12)


This workshop will bring together researchers who are interested in developing and applying novel computational methods to the modeling, simulation, and analysis of complex biological systems.

Workshop participants will encompass a diverse group of scientists including experimental biologists, physical scientists, mathematicians, and computer scientists.

The emphasis is on modeling and methods aimed at mechanistic understanding of the biochemical of protein-protein interaction networks, the process by which cells process information and respond to their environment, which has critical applications for the prevention and treatment of disease.

A unifying theme of the workshop is the use of so-called "rule-based" languages and tools, such as Kappa and BioNetGen, for specifying and simulating complex biological models in a scalable way. These methods open the possibility of simulating and analyzing cellular networks based on mechanistic principles on a much broader scale than was previously possible. They also create new challenges and opportunities, which will be a central theme of the workshop. These include identifying the key emergent properties of signaling networks that should be captured by models, automating the process of property determination and verification using formal methods such as abstract interpretation and model checking, developing sound methods for model abstraction to reduce model complexity, expanding formal biological languages to encompass greater complexity and realism, developing new approaches for visualizing models and simulation results, and developing improved Monte Carlo simulation methods.

The workshop is sponsored by the NSF Expeditions in Computing Project, "Computational Modeling and Analysis for Complex Systems", which aims to expand and apply formal methods for automated hardware and software validation to challenge problems in biology, pancreatic cancer and atrial fibrillation, in which molecular signaling plays a central role.

In conclusion, the workshop will provide a forum for discussion of biological modeling and model-based analysis, with the goal of deepening the fruitful collaboration between biologists and computational researchers.

Publication of conference proceedings is anticipated and the potential occurrence and structure of future meetings on this theme will be discussed.


Patrick Cousot, James Faeder, Jérôme Feret

Thanks to Laura Bundesen, Gloria Clivilles-Ramos, and Elizabeth Rodriguez from CIMS, NYU, for their precious help.


Thursday, March 29th, 2012
Friday, March 30th, 2012


Kimmel Center
New York University
60 Washington Square South
New York, NY 10012, USA



Stuart Aitken (Edinburgh University)
Grégoire Altan-Bonnet (Memorial Sloan Kettering Cancer Center)
Bastian Angermann (NIAD, NIH)
Mitra Basu (NSF)
Michael Blinov (University of Connecticut Health Center)
Lily Chylek (Cornell University & Los Alamos National Laboratory)
Edmund Clarke (CMU)
Patrick Cousot (CIMS/NYU & ENS)
Radhia Cousot (CNRS/ENS)
Vincent Danos (Edinburgh University)
Jayajit Das (Nationwide Childrens' Hospital/Ohio State University)
Eric Deeds (University of Kansas)
Thierry Emonet (Yale University)
Jim Faeder (University of Pittsburgh School of Medicine)
Jérôme Feret (INRIA)
Walter Fontana (Harvard Medical School)
Shawn Garbett (Vanderbilt University Medical Center)
Helen Gill (NSF)
Nancy Griffeth (CUNY)
Russ Harmer (CNRS/Université Paris-Diderot)
Jean Krivine (CNRS/Université Paris-Diderot)
Andre Levchenko (Johns Hopkins University)
Carlos F. Lopez (Harvard Medical School)
Martin Meier-Schellersheim (NIAD, NIH)
Bud Mishra (NYU)
Ilya Nemenman (Emory University)
Ovidiu Radulescu (Université de Montpellier 2)
Scott Smolka (Stony Brook)
P.S. Thiagarajan (NUS)
Andreas Witzel (NYU)
Paolo Zuliani (CMU)

Student participants:

John Bachman (Harvard Medical School)
Norman Ferns (INRIA/ENS)
Terri Grosso (CUNY)
Ariful Islam (Stony Brook)
Justin Jee (NYU)
Ilya Korsunsky (NYU)
Abhishek Murthy (Stony Brook)
Loes Olde Loohuis (NYU)
Daniel Packer (NYU)
Harsh Patel (NYU)
Tatjana Petrov (ETH Zurich)
John A. P. Sekar (University of Pittsburgh School of Medicine)
Andrew Sundstrom (NYU)
Qinsi Wang (CMU)
Kai Zhao (CUNY)

Programme, March 29th, 2012, Kimmel Center, Room 909


Light breakfast served


Welcome and Workshop Overview


Model-Checking and Abstraction-Refinement — Edmund Clarke (Computer Science Department, Carnegie Mellon University) — Slides


Statistical Model Checking for Biological Systems — Paolo Zuliani (Computer Science Department, Carnegie Mellon University) — Slides


A brief introduction to rule based modeling — James Faeder (School of Medicine, University of Pittsburgh) — Slides

10:45 Break and Poster Session

Pathways and Abstraction — Bud Mishra (NYU)


Non local causality analysis in rule-based formalisms — Jean Krivine (CNRS/Université Paris-Diderot) — Slides

12:15 Lunch

Modeling how immune responses get reliably established despite unreliable lymphocytes — Grégoire Altan-Bonnet (ImmunoDynamics Group Programs in Computational Biology & Immunology Memorial Sloan-Kettering Cancer Center, New York)


The dynamics of assembly in complex biological networks — Eric Deeds (Center for Bioinformatics and Department of Molecular Biosciences, University of Kansas)


Rule-based modelling of signalling in messenger RNA transcription — Stuart Aitken (Edinburgh University)


A casual introduction to Abstract Interpretation — Patrick Cousot (CIMS, NYU & ENS) — Slides

16:00 Break and Poster Session

Formal model reduction — Jérôme Feret (INRIA) — Slides


Reduction of biochemical networks with multiple time scales — Ovidiu Radulescu (Université de Montpellier 2) — Slides


Coarse-graining stochastic biochemical reaction networks in the adiabatic limit — Ilya Nemenman (Departments of Physics and Biology Emory University) — Slides

Programme, March 30th, 2012, Kimmel Center, Room 909


Light breakfast served


Probabilistic Approximations of ODEs Based Bio-pathways Dynamics — P.S. Thiagarajan (NUS) — Slides


Experimental and computational, rule-based analysis of endothelial cell responses to external and self-imposed cues — Andre Levchenko (Whitaker Institute for Biomedical Engineering, Institute for Cell Engineering, Johns Hopkins University)


Dramatic reduction of dimensionality in large biochemical networks due to strong pair correlations — Jayajit Das (Battelle Center for Mathematical Medicine, The Research Institute at Nationwide Children's Hospital, The Ohio State University) — Slides

10:30 Break and Poster Session

Executable Knowledge — Russ Harmer (CNRS/Université Paris-Diderot)


Modeling, visualizing, and annotating immunoreceptor signaling systems — Lily Chylek (Cornell University & Los Alamos National Laboratory) — Slides

12:15 Lunch

Bisimulation-Based Abstraction of Sodium-Channel Dynamics in Cardiac-Cell Models — Ariful Islam and Abhishek Murthy (Stony Brook University) — Slides


Considering alternate signaling mechanisms in extrinsic apoptosis using models as programs — Carlos F. Lopez (Department of Systems Biology, Harvard Medical School) — Slides


Bringing rule-based modeling to VCell users — Michael Blinov ( University of Connecticut Health Center)

15:30 Break and Poster Session

Rule-based spatially resolved modeling of cellular signaling processes — Bastian R. Angermann (Computational Biology Unit, Laboratory of Systems Biology, NIAD, NIH) — Slides


Statistical physics of communicating processes — Vincent Danos (University of Edinburgh) — Slides

17:15 Wrap-up



The poster size is 40 in x 30 in.

A Quantitative Synthetic Approach to Understanding the Mitochondrial Apoptotic Switch — John Bachman (Harvard Medical School)

Fitting complex protein interaction models to data — Shawn Garbett (Vanderbilt University Medical Center)

Approximate reductions of rule-base models — Tatjana Petrov (ETH Zurich) — Poster

Modular Construction of Rule-Based Models — John A. P. Sekar & James R. Faeder (University of Pittsburgh School of Medicine)

Local Information:


Directions to Kimmel Center

Hotels nearby:

• A block of 10 rooms negotiated at $199 (exclusive of taxes and fees, mention "NYU rate") per night has been reserved at the Holiday Inn, 125 W. 26th St. (between 6th and 7th Avenues), 10001 New York, NY, Hotel Front Desk: 1-212-430-8500, Hotel Fax: 1-212-430-8501
     This hotel is 25 mn by foot from the Kimmel center, 60 Washington Square South. One can also take the F subway towards Coney Island - Stillwell Av, by walking to the 23 St station on 6th Ave, get out at West 4 ST (3mins, 2 stops), and walk to the Kimmel center, 60 Washington Square South (5min)

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• Another block of rooms is reserved at the Club Quarters - Wall Street with a $206 per night rate (exclusive of taxes and fees, mention "NYU rate"). This hotel is located on 52 William Street (Between Wall & Pine Streets), New York, NY 10005, Phone: (212) 269-6400.
     This hotel is 40 mn by foot from the Kimmel center, 60 Washington Square South or 15 mn by metro. Take the 3 subway - 7 Ave Express towards Harlem - 148th St, near the hotel, get off at Park Pl, walk to Chambers St, take A - 8 Ave Express towards Inwood -207 St, get off at West 4th St, and walk to the Kimmel center, 60 Washington Square South.
     A simpler solution (20 to 25mn) is to walk from the hotel to Chamber's St (at Church) take A or C subway uptown and stop at 4 W St.

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• A block of rooms negotiated at $205 per night has been reserved at the Holiday Inn Downtown, 138 Lafayette Street New York, NY 10013, 212-966-8898 (16 mn by foot, one can also take line 6 uptown from Canal St to Bleecker St).

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• Another block of rooms negotiated at $209 per night has been reserved with code NYU at the Sheraton Brooklyn New York Hotel, 228 Duffiled St, 11201 Brooklyn, NY. This hotel is about 20mn away by metro A from Kimmel Center. Walk to W 4 St (4 mn), take A - 8 Avenue Express downtown towards Ozone Park - Lefferts Blvd and stop at Jay St - MetroTech (12mn), walk to Sheraton Brooklyn New York (4 mn).

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• A closer hotel (3mn) is Washington Square Hotel, 103 Waverly Place, New York, NY 10011, Toll-Free: 1.800.222.0418, Phone: 1.212.777.9515, Fax: 1.212.979.8373 — reservations@wshotel.com

Restaurants nearby:

Sustainable Lunch Map (pdf)
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nsfSupported by an Expeditions in Computing award from the National Science Foundation