Workshops

Summer 2015

Dynamic Biological Modeling: Abstractions, Algorithms & Logic

Aug 10, 2015 to Aug 14, 2015

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Click on the titles of individual talks for abstract and slides (if applicable).

Please note that this schedule is subject to change. All events take place in the Calvin Lab Auditorium.

Monday, August 10th, 2015
9:00 am–9:20 am		Coffee and Check-In
9:20 am–9:30 am		Opening Remarks
9:30 am–10:30 am		Computational Modeling Animal Development: Towards a Whole Embryo Model of the Nematode Caenorhabditis Elegans Alex Hajnal, University of Zürich
10:30 am–11:00 am		Break
11:00 am–12:00 pm		Questions & Challenges in Immunology Russell Vance, UC Berkeley
12:00 pm–1:30 pm		Lunch
1:30 pm–2:30 pm		Systems Biology of ncRNA– From Biology to Networks to Targets Prahlad Ram, UT MD Anderson Cancer Center
2:30 pm–3:00 pm		Break
3:00 pm–4:00 pm		Questions & Challenges in Cancer Biology Gerard Evan, University of Cambridge
4:15 pm–5:00 pm		Discussion and/or Breakout Sessions
5:00 pm–6:00 pm		Reception

Tuesday, August 11th, 2015
9:00 am–9:30 am		Coffee and Check-In
9:30 am–10:30 am		Challenges in Integrative Modeling of Gene Regulation, Protein Signaling, and Metabolism Ernest Fraenkel, Massachusetts Institute of Technology
10:30 am–11:00 am		Break
11:00 am–12:00 pm		What We Can Learn from Single-Cell Data Calin Guet, IST Austria
12:00 pm–1:30 pm		Lunch
1:30 pm–2:30 pm		What We Can Measure Today, Tomorrow, and Which Experiments are Useful for Model Inference Alejandro Wolf-Yadlin, University of Washington
2:30 pm–3:00 pm		Break
3:00 pm–3:30 pm		Next Steps in Functional Genomics Lior Pachter, UC Berkeley
3:30 pm–4:00 pm		Mapping Cell Network Signaling to Clinical Outcomes Amina Qutub, Rice University
4:15 pm–5:00 pm		Discussion and/or Breakout Sessions

Wednesday, August 12th, 2015
9:00 am–9:30 am		Coffee and Check-In
9:30 am–10:30 am		Successes and Challenges in Executable Biology Jasmin Fisher, Microsoft Research & University of Cambridge
10:30 am–11:00 am		Break
11:00 am–12:00 pm		Opportunities in Executable Biology: Modeling Transcriptional Regulation with New Types of High-Throughput Data Nir Yosef, UC Berkeley
12:00 pm–1:30 pm		Lunch
1:30 pm–2:00 pm		Synthesis of Executable Models Ras Bodik, University of Washington
2:00 pm–2:45 pm		How to Build a Living Cell in Software (Or: Can We Computerize a Bacterium?) Tom Henzinger, IST Austria
2:45 pm–3:15 pm		Break
3:15 pm–4:00 pm		Rule-Based Modeling of Graph-Like Systems Sandro Stucki, Ecole Polytechnique Federale de Lausanne (EPFL)
4:15 pm–5:00 pm		Discussion and/or Breakout Sessions

Thursday, August 13th, 2015
9:00 am–9:30 am		Coffee and Check-In
9:30 am–10:00 am		Challenges in Formal Reasoning About Signaling Networks Carolyn Talcott, SRI International
10:00 am–10:30 am		Parallel Composition in Biology Nir Piterman, University of Leicester
10:30 am–11:00 am		Break
11:00 am–11:30 am		Successes and Challenges of Modelling and Verification at the Nanoscale Marta Kwiatkowska, University of Oxford
11:30 am–12:00 pm		Dynamical Systems Biology Oded Maler, CNRS-VERIMAG
12:00 pm–1:30 pm		Lunch
1:30 pm–2:00 pm		Combining Computational Modelling with Experimentation to Understand Immune System Function Mark Coles, University of York
2:00 pm–2:30 pm		Questions and Challenges in Tissue and Whole Organ Modeling Radu Grosu, Technical University of Vienna
2:30 pm–3:00 pm		Break
3:00 pm–3:30 pm		Challenges in Network Biology Roded Sharan, Tel Aviv University
3:30 pm–4:00 pm		Levels of Abstraction: From Stochastic to Continuous to Discrete David Dill, Stanford University
4:15 pm–5:00 pm		Discussion and/or Breakout Sessions

Friday, August 14th, 2015
9:00 am–9:30 am		Coffee and Check-In
9:30 am–10:30 am		Summary and Observations Dick Karp, UC Berkeley
10:30 am–11:00 am		Break
11:00 am–12:00 pm		Towards the Roadmap to Executable Biology Moshe Vardi, Rice University