1. National Resource for Cell Analysis and Modeling Ann Cowan & Raquell Holmes Service, Dissemination, and Training

2. National Resource for Cell Analysis and Modeling SERVICE Feb-0910-Jan Total Registered VCell Users12,364 13,249 Users Who Ran Simulations2,224 2,526 Currently Stored Models29,117 34,402 Currently Stored Simulations160,539 183,399 Publicly Available Models687 712 Publicly Available Simulations2,377 2,778

3. National Resource for Cell Analysis and Modeling SERVICE Feb-0910-JanNEW Total Registered VCell Users12,364 13,249885 Users Who Ran Simulations2,224 2,526302 Currently Stored Models29,117 34,4025,285 Currently Stored Simulations160,539 183,39922,860 Publicly Available Models687 71629 Publicly Available Simulations2,377 2,778401

4. National Resource for Cell Analysis and Modeling SERVICE

5. National Resource for Cell Analysis and Modeling Recent Publications by Users Design of versatile biochemical switches that respond to amplitude, duration, and spatial cues. Lipshtat, A., G. Jayaraman, J.C. He, and R. Iyengar. Proceedings of the National Academy of Sciences. 107:1247-1252, 2010. Modeling Spatial and Temporal Dynamics of Chemotactic Networks Liu Yang and Pablo A. Iglesias Chemotaxis: Methods and Protocols, Methods in Molecular Biology, vol. 571, pp. 489-505, 2009. A genetically encoded reporter of synaptic activity in vivo. Dreosti E, Odermatt B, Dorostkar MM, Lagnado L.. Nat Methods. 2009 6:883-9. Subcellular dynamics of type II PKA in neurons. Zhong, H., G.M. Sia, T.R. Sato, N.W. Gray, T. Mao, Z. Khuchua, R.L. Huganir, and K. Svoboda. Neuron. 62:363-374, 2009. Intracellular fluid flow in rapidly moving cells Kinneret Keren, Patricia T. Yam, Anika Kinkhabwala, Alex Mogilner & Julie A. Theriot Nature Cell Biology 11, 1219 - 1224 (2009) Affinity for phosphatidylinositol 4,5-bisphosphate determines muscarinic agonist sensitivity of Kv7 K+ channels Ciria C. Hernandez, Bjorn Falkenburger, and Mark S. Shapiro J. Gen. Physiol. 2009;134 437-448 A Tridimensional Model of Proangiogenic Calcium Signals in Endothelial Cells Luca Munaron The Open Biology Journal, 2009, 2, 114-129 Publication Persistent cAMP-Signals Triggered by Internalized G-Protein-Coupled Receptors. Calebiro D, Nikolaev VO, Gagliani MC, de Filippis T, Dees C, Tacchetti C, Persani L, Lohse MJ. PLoS Biol. 2009 A model of action potentials and fast Ca2+ dynamics in pancreatic beta-cells. Fridlyand LE, Jacobson DA, Kuznetsov A, Philipson LH. Biophys J. 2009 Apr 22;96(8):3126-39. Energetic requirements for processive elongation of actin filaments by FH1FH2-formins Aditya S. Paul and Thomas D. Pollard J. Biol. Chem. 284:12533-40, 2009. SERVICE

6. National Resource for Cell Analysis and Modeling NRCAM Publications SERVICE An open model of actin dendriticnucleation Ditlev JA, Vacanti NM, Novak IL, Loew LM.. 2009 Biophys J. 96:3529-42. CLIP-170-dependent capture of membrane organelles by microtubules initiates minus-end directed transport. Lomakin AJ, Semenova I, Zaliapin I, Kraikivski P, Nadezhdina E, Slepchenko BM, Akhmanova A, Rodionov V. 2009 Dev Cell. 17(3):323-33. Diffusion in cytoplasm: effects of excluded volume due to internal membranes and cytoskeletal structures. Novak IL, Kraikivski P, Slepchenko BM. 2009 Biophys J. 97:758-67. Model-based global analysis of heterogeneous experimental data using gfit. Levin MK, Hingorani MM, Holmes RM, Patel SS, Carson JH. 2009 Methods Mol Biol. 500:335-59. Molecular machines or pleiomorphic ensembles: signaling complexes revisited. Mayer BJ, Blinov ML, Loew LM. 2009 J Biol. 8:81.

7. National Resource for Cell Analysis and Modeling Release : VCell 4.6 Released 6-2-09 Beta : VCell 4.7 Released 6-26-09 Alpha : Internal release 1-2 times weekly Release 4.6 Implementation of Global Parameters for BioModels. Resources: Links to BioModels database Protein Subcellular Location Image Database (PSLID) import and data handling in FieldData Allow membrane field data from simulation results Improved spatial data analysis for ROIs. Predefined ROIs for existing spatial compartments. ROIs from user defined Boolean functions. ROIs from user drawn polygons. CVODE solver used for Optimization in parameter estimation. Support for both Intel and G5 macs. Basic CellML import into MathModels. Added sort and search functions to Math Viewer and Math Model editor. Feature and Membrane sizes available for use in expressions in non-spatial models SERVICE Beta (4.7) Solvers New combined CVODE/IDA solver for compartmental simulations. New fully implicit finite volume solver for spatial simulations. Improved solvers to handle user-defined discontinuities. Initial Conditions Advection (Velocity) added to Initial conditions in BioModels Initial conditions can be specified in terms of other model parameters, reserved symbols and species. Geometry New assistant dialog for creating analytic shapes in geometry editor User Interface Expression editors: Improved with auto-complete text Data Export: Variables separated into membrane and volume variables Simulation Editor/Advanced: New output option for semi-implicit solvers Application menu added to main menu Display of application methods (deterministic/stochastic) and geometric dimensions (compartmental/1D/2D/3D)

8. National Resource for Cell Analysis and Modeling Shared instrumentation grant likely funded (Moraru, co-PI) 10.2 TFlop cluster Will bring HPC facilty to >14 TFlops of processing power and >6 TB of distributed memory

9. National Resource for Cell Analysis and Modeling DISSEMINATION

10. National Resource for Cell Analysis and Modeling

12. DISSEMINATION

13. National Resource for Cell Analysis and Modeling Two Courses >11 lectures with exercises

14. National Resource for Cell Analysis and Modeling

15. Existing Course Content on TWiki Lecture Materials: Slide images from lectures and exercises by Mogilner and Dey.

16. National Resource for Cell Analysis and Modeling Courses using resources Bill Lytton: SUNY Downstate Jason Haugh: NC State University Alex Mogilner: University of California at Davis Joel Stiles: Pittsburgh Supercomputing Center Students make use of data and lessons for projects.

17. National Resource for Cell Analysis and Modeling Documentation for 4.7 Tutorials: Four pdfs, 32 pages, 70 images; User Guide: 13 chapters, 78 pages, 140 images New record keeping of images will be linked to Java Classes

18. National Resource for Cell Analysis and Modeling DISSEMINATION Presence in the Community ASCB (2008 Saturday Education Workshop) Biophysics NRCAM booth; tutorial SC09 (NRCAM booth, Conference Comm.) ICSB09 tutorial Grace Hopper Celebration of Women in Computing

19. National Resource for Cell Analysis and Modeling TRAINING

20. National Resource for Cell Analysis and Modeling Graduate Program Approval In Progress! 1)Executive Committee of the Graduate School; 2)Dean of Councils 3)Board of Trustees (Feb. 18) 4)State Department of Higher Education

21. National Resource for Cell Analysis and Modeling ADMINISTRATION