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Virtual Cell User Guide

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Virtual Cell User Guide 1 INTRODUCTION ............................................................................................................................................. 2 1.1 REGISTRATION ................................................................................................................................................................ 2 1.2 SYSTEM REQUIREMENTS ................................................................................................................................................. 2 1.3 COMPUTER CONFIGURATION ........................................................................................................................................... 2 1.4 USING THE VIRTUAL CELL MODELING AND SIMULATION FRAMEWORK WITH JAVA TECHNOLOGY .......................................... 3 1.5 USER SUPPORT .............................................................................................................................................................. 3 1.6 UNITS USED IN THE VIRTUAL CELL ................................................................................................................................... 3 2 AN OVERVIEW OF THE VIRTUAL CELL DOCUMENTS...................................................................... 4 2.1 BIOMODEL DOCUMENT.................................................................................................................................................... 4 2.2 GEOMETRY DOCUMENT ................................................................................................................................................... 4 2.3 MATH DOCUMENT ........................................................................................................................................................... 4 3. QUICK TOUR OF THE VIRTUAL CELL................................................................................................... 4 3.1 CREATING BIOMODELS ................................................................................................................................................... 4 3.2 DEFINING GEOMETRIES ................................................................................................................................................... 5 3.3 CREATING APPLICATIONS ................................................................................................................................................ 5 3.4 DESCRIBING MATH MODELS ............................................................................................................................................ 6 4. MANAGING YOUR DOCUMENTS ............................................................................................................. 6 4.1 BIOMODELS, GEOMETRIES AND MATH MODELS ................................................................................................................ 7 4.2 APPLICATIONS AND SIMULATIONS..................................................................................................................................... 7 4.3 ALLOWING OTHERS TO VIEW YOUR MODELS ...................................................................................................................... 7 4.4 SAVING ANNOTATIONS .................................................................................................................................................... 7 4.5 COMPARING MODELS ...................................................................................................................................................... 8 4.6 EXPORTING AND IMPORTING MODELS...............................................................................................................................8 5. CREATING BIOMODELS ............................................................................................................................. 9 5.1 SPECIFYING CELLULAR STRUCTURE................................................................................................................................. 9 5.2 SPECIFYING MOLECULAR SPECIES................................................................................................................................... 9 5.3 EDITING PROPERTIES OF MODEL COMPONENTS .............................................................................................................10 5.4 SPECIFYING BIOCHEMICAL REACTIONS...........................................................................................................................10 6. DEFINING GEOMETRIES .......................................................................................................................... 13 6.1 COMPARTMENTAL GEOMETRIES.....................................................................................................................................14 6.2 SPATIAL GEOMETRIES ...................................................................................................................................................14 7. USING APPLICATIONS .............................................................................................................................. 16 7.1 STRUCTURE MAPPING ...................................................................................................................................................16 7.2 INITIAL CONDITIONS.......................................................................................................................................................17 7.3 REACTION MAPPING......................................................................................................................................................17 7.4 ELECTRICAL MAPPING ...................................................................................................................................................18 7.5 GENERATING AND VIEWING THE MATH DESCRIPTION ......................................................................................................18 7.6 SIMULATIONS ................................................................................................................................................................18 8. ACCESSING SIMULATION RESULTS..................................................................................................... 21 8.1 COMPARTMENTAL RESULTS...........................................................................................................................................21 8.2 SPATIAL RESULTS .........................................................................................................................................................22 8.3 3D MEMBRANE SURFACE VIEWER .................................................................................................................................24 9. EXPORTING SIMULATION RESULTS.................................................................................................... 25 9.1 COMPARTMENTAL RESULTS...........................................................................................................................................25 9.2 SPATIAL RESULTS .........................................................................................................................................................25 10. CREATING MATH MODEL DOCUMENTS .......................................................................................... 27 10.1 CREATING NEW MATH MODELS ...................................................................................................................................27 10.2 CREATING MATH MODELS FROM BIOMODELS ...............................................................................................................28 1 1 Introduction The National Resource for Cell Analysis and Modeling has developed the Virtual Cell Modeling and Simulation Framework version 4.1. This unique software platform has been designed to model cell biological processes. This new technology associates biochemical and electrophysiological data describing individual reactions with experimental microscopic image data describing their subcellular locations. Cell physiological events can then be simulated within the empirically derived geometries, thus facilitating the direct comparison of model predictions with experiment. The Virtual Cell consists of a biological and mathematical framework. Scientists can create biological models from which the software will generate the mathematical code needed to run simulations. Mathematicians may opt to use the math framework, based on the Virtual Cell Math Language, for creating their own mathematical descriptions. The simulations are run over the internet on 84 servers with 256 GHz total cpu power and 119Gb total RAM. Currently the storage capacity is 11.7 Tb. Models can be reused, updated and published so they are available to the scientific community. In addition, models may also be privately shared amongst collaborating groups. The data from simulations is stored on the Virtual Cell database server and is easily exported in a variety of formats. Access to the Virtual Cell modeling software is available via the internet using a JAVA based interface. Version 4.0 of the Virtual Cell has been developed using the latest Java 2 SDK technology. 1.1 Registration There is no charge for academic use of the Virtual Cell, however you are required to register. User registration information will aid in serving the Virtual Cell user community. New User Registration-http://vcell.org/vcellR4/login/newuser.jsp
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