1. National Resource for Cell Analysis and Modeling Scientific Advisory Board Meeting Nov. 18, 2015 Advisors: Reka Albert, Gary Bader, Phil Colella, Jason Haugh, Ravi Iyengar, Jon Lederer, Thomas Pollard

2. Agenda

3. The Team Les Loew – Co-PI; Biophysical Mechanisms Boris Slepchenko – Co-PI, Numerical Algorithms Jim Schaff – Co-PI, Data Driven Modeling Ion Moraru – Co-PI, Computational Infrastructure and Model Building Blocks Ann Cowan – Co-PI, Dissemination, Service, Training Michael Blinov – Rule-based modeling and pathway integration *Sofya Borinskaya – Graduate Student Ed Boyce – Software Developer – Visualization (100% institutional support) John Carson – Co-I, Biophysical Mechanisms Jeff Dutton – System Manager and Support (100% Institutional support) Fei Gao – Software Consultant Steven King – System admin and support (100% Institutional support) Susan Krueger – Website Developer, User facility Olena Marchenko – Graduate student Frank Morgan – Software Developer (50% Institutional Support) Masoud Nickaeen – Mechanics and moving boundaries Diana Resasco – Numerics *Mark Rigatti – Graduate Student Vladimir Rodionov – Co-I, Biophysical Mechanisms *Dan Vasilescu - Software developer Gerard Weatherby – Software developer *Ronghua Yang – Graduate student Karen Zucker – Program Coordinator (funded through Institutional support) (*supported via collaborative grants)

4. Ann CowanMichael BlinovIon MoraruBoris SlepchenkoJim Schaff Fei Gao Les Loew Diana ResascoMasoud Nickaeen The VCell Team Karen ZuckerFrank MorganGerard WeatherbyDan Vasilescu Jeff Dutton Susan Krueger

5. The Virtual Cell Project 5,000 users have built models Graphical interface for biologists & physical scientists Reactions, diffusion, advection, membrane transport, electrophysiology Compartmental (ODE), spatial (PDE), deterministic and stochastic simulations Searchable model database Pathway database support Rule-based modeling Experimental data integration Virtual Microscopy

6. VCell User Interface BioModel Navigator BioModel Element (Reaction Diagram) Selection Details (Rate Expression) Database Resources

7. Highlights of Progress Since February Ver 6.0 is days away SpringSaLaD (Springs Sites and Langevin Dynamics) –Ver 1 released –Paper at minor rev Moving Boundaries –Paper published VCell EBChombo Enhancements Hybrid Stochastic/Determistic Spatial –Testing complete –Paper submitted Rule-based abstractions and gui –Molecules, Rules, Observables –Network-free simulator (NFSim) Major upgrades in Computational Infrastructure

8. Usage Usage 2015 Total Registered VCell Users Users Who Ran Simulations Currently Stored Models Currently Stored Simulations Publicly Available Models Feb. 18,038 4,651 65,412 390,835 791 Nov. 18,833 5,051 69,647 420,733 849

9. Highlights of proposed TR&D Projects 1.New mesoscale physics for multimolecular interactions in subcellular volumes 2.New solvers for mechanics, deforming geometries and electrophysiology 3.New computer science for large models and kinematics 4.New data structures for connecting complex dynamic microscopy imaging experiments to models

10. The Technology Development Process Cell Biology DBPs Users Biology to Physics Physics to Numerics Biophysics to Software Data-Driven Modeling DeveloperCommunity Prototype Code Virtual Cell Standalone Applications Drivers: TR&D: Products: