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.
The program of SASB 2017 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:
Registration is now open here. Please make sure to specify you are registering for the SASB workshop!
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. Please submit on Easy here.
| Paper abstracts due | July 1, 2017 (AoT) |
| Papers and presentation submissions due (extended!) | July 8, 2017 (AoT) |
| Paper and presentation notifications | August 2, 2017 |
| Matt Might | Strategist in the Executive Office of the President, Director of the Hugh Kaul Precision Medicine Institute (UAB) |
Contact: sasb2017-chairs [at] cs [dot] cmu [dot] edu.
| Jean Yang | Carnegie Mellon University |
| John A. Bachman | Harvard Medical School |
| Luca Cardelli | Microsoft Research |
| Eric Deeds | University of Kansas |
| James Faeder | University of Pittsburgh |
| Jérôme Feret | INRIA Paris |
| Ben Hall | University of Cambridge |
| Jean Krivine | Université Paris Diderot |
| Nicola Paoletti | Stony Brook University |
| Loic Paulevé | CNRS and LRI |
| Tatjana Petrov | IST Austria |
| Amaury Pouly | MPI-SWS |
| Ovidiu Radulescu | Université de Montpellier 2 |
| David Safranek | Masaryk University |
| Qinsi Wang | Carnegie Mellon University |
| Paolo Zuliani | Newcastle University |
| 8:30-9:00 | Arrival, registration, breakfast | ||
| 9:00-10:00 | Invited talk: Winning the war on error: Solving the Halting Problem and curing cancer (Matt Might) | slides | |
| 10:00-10:15 | Discussion/coffee break | ||
| Session 1 | |||
| 10:15-10:35 | Explanation of drug effects using a mechanistic model automatically assembled from natural language, databases, and literature (John A. Bachman, Benjamin Gyori and Peter Sorger) | slides | |
| 10:35-10:55 | A tool for automated inference in rule-based biological models (Chelsea Voss, Jean Yang, and Walter Fontana) | slides | |
| 10:55-11:10 | Discussion/coffee break | ||
| Session 2 | |||
| 11:10-11:30 | Syntax-guided optimal synthesis for chemical reaction networks (Luca Cardelli, Milan Ceska, Martin Martin Fränzle, Marta Kwiatkowska, Luca Laurenti, Nicola Paoletti and Max Whitby) | extended abstract / related paper | slides |
| 11:30-11:50 | Towards personalized verification and synthesis for the artificial pancreas (Taisa Kushner, Sydney Keenan, David Bortz, David Maahs and Sriram Sankaranarayanan) | extended abstract | |
| 11:50-1:30 | Lunch | ||
| Session 3 | |||
| 1:30-1:50 | Causal analysis of rule-based models through counterfactual reasoning (Jonathan Laurent, Jean Yang, and Walter Fontana) | slides | |
| 1:50-2:10 | SAT solving for vesicle traffic systems in cells (Ashutosh Gupta, Ankit Shukla, Mandayam Srivas and Mukund Thattai) | slides | |
| 2:10-2:30 | Computing similarity between multiscale biological systems under uncertainty (Krishnendu Ghosh) | slides | |
| 2:30-2:45 | Discussion/coffee break | ||
| Session 4 | |||
| 2:45-3:05 | Using alternative sums to express the occurrence number of extended patterns in site-graphs (Jerome Feret and Ferdinanda Camporesi) | paper | |
| 3:05-3:25 | Visualizing model architecture (John A.P. Sekar and James R. Faeder) | slides | |
| 3:25-3:45 | Translating BNGL models into Kappa our experience (Kim Quyen Ly) | extended abstract | slides |
| 3:45-4:00 | Discussion/coffee break | ||
| Session 5 | |||
| 4:00-4:20 | Biochemical Space: A framework for formal description and annotation of complex biological processes (Matej Troják, David Šafránek, Jakub Šalagovič, Františka Romanovská and Matej Hajnal) | extended abstract | slides |
| 4:20-4:40 | When rule-based models need to count (Pierre Boutillier and Ioana Cristescu) | draft | slides |
| 4:40 | Closing remarks | ||