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Ann Cowan & Raquell Holmes

Ann Cowan & Raquell Holmes. Service, Dissemination, and Training. SERVICE. SERVICE. SERVICE.

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Ann Cowan & Raquell Holmes

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  1. Ann Cowan & Raquell Holmes Service, Dissemination, and Training

  2. SERVICE

  3. SERVICE

  4. SERVICE • 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. Recent Publications by Users

  5. 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) SERVICE • 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 Release : VCell 4.6 Released 6-2-09 Beta : VCell 4.7 Released 6-26-09 Alpha : Internal release 1-2 times weekly

  6. 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

  7. DISSEMINATION

  8. DISSEMINATION

  9. Two Courses • >11 lectures with exercises

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

  11. 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

  12. TRAINING

  13. Graduate Program Approval In Progress! • Executive Committee of the Graduate School; • Dean of Councils • Board of Trustees (Feb. 18) • State Department of Higher Education

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