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National Resource forCell Analysis and Modeling

Scientific Advisory Board MeetingNov. 18, 2015

Advisors: Reka Albert, Gary Bader, Phil Colella, Jason Haugh, Ravi Iyengar, Jon Lederer, Thomas Pollard

Agenda

The TeamLes Loew Co-PI; Biophysical MechanismsBoris Slepchenko Co-PI, Numerical Algorithms Jim Schaff Co-PI, Data Driven ModelingIon Moraru Co-PI, Computational Infrastructure and Model Building BlocksAnn 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 ConsultantSteven King System admin and support (100% Institutional support)Susan Krueger Website Developer, User facility Olena Marchenko Graduate studentFrank Morgan Software Developer (50% Institutional Support) Masoud Nickaeen Mechanics and moving boundariesDiana Resasco Numerics *Mark Rigatti Graduate Student Vladimir Rodionov Co-I, Biophysical Mechanisms *Dan Vasilescu - Software developerGerard Weatherby Software developer*Ronghua Yang Graduate studentKaren Zucker Program Coordinator (funded through Institutional support) (*supported via collaborative grants) 3

Ann Cowan

Michael BlinovIon MoraruBoris SlepchenkoJim SchaffFei GaoLes LoewDiana ResascoMasoud Nickaeen

The VCell Team

Karen Zucker

Frank Morgan

Gerard Weatherby

Dan Vasilescu

Jeff Dutton

Susan Krueger

4The Virtual Cell Project

5,000 users have built modelsGraphical interface for biologists & physical scientistsReactions, diffusion, advection, membrane transport, electrophysiologyCompartmental (ODE), spatial (PDE), deterministic and stochastic simulationsSearchable model databasePathway database supportRule-based modelingExperimental data integrationVirtual Microscopy

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VCell User InterfaceBioModelNavigatorBioModel Element(Reaction Diagram)Selection Details(Rate Expression)DatabaseResources

Highlights of Progress Since FebruaryVer 6.0 is days awaySpringSaLaD (Springs Sites and Langevin Dynamics)Ver 1 releasedPaper at minor revMoving BoundariesPaper publishedVCell EBChombo EnhancementsHybrid Stochastic/Determistic SpatialTesting completePaper submittedRule-based abstractions and guiMolecules, Rules, ObservablesNetwork-free simulator (NFSim)Major upgrades in Computational Infrastructure

Usage

2015

Total Registered VCell UsersUsers Who Ran SimulationsCurrently Stored ModelsCurrently Stored SimulationsPublicly Available Models

Feb.18,0384,65165,412390,835791Nov.18,8335,05169,647420,7338498Highlights of proposed TR&D ProjectsNew mesoscale physics for multimolecular interactions in subcellular volumesNew solvers for mechanics, deforming geometries and electrophysiologyNew computer science for large models and kinematicsNew data structures for connecting complex dynamic microscopy imaging experiments to models

The Technology Development Process

Cell BiologyDBPs UsersBiology to PhysicsPhysics toNumericsBiophysics to SoftwareData-DrivenModelingDeveloperCommunityPrototypeCodeVirtual CellStandaloneApplicationsDrivers:TR&D:Products:

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