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CompuCell3D / SBW Integration Posted by: FrankBergmann
Video duration: 305 seconds In this video Compucell3D will simulate about a hundred cells. For each of these cells SBW (http://sys-bio.org/ ) will simulate an osillating network. These oscillations influence the compucell simulation, by influencing how much the cells 'like' each other. This proof-of-concept implementation uses compucell3D, sbw, mono, python, qt on Ubuntu 6.06 Related: biology, compucell3d, sbw, sys-bio.org, systems, workbench |
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Brusselator Reaction Diffusion System in 3D Posted by: FrankBergmann
Video duration: 116 seconds This video was one of the results of my thesis project, on simulation and visualization of 3D reaction diffusion systems. Have a look; Related: diffusion, reaction, sbw, thesis |
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Systems Biology Workbench Posted by: FrankBergmann
Video duration: 49 seconds The SBW team just released SBW 2.7.6 for Windows, Linux and OSX. More under http://sys-bio.org Related: biology, jarnac, jdesigner, osx, sbw, systems, workbench |
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JDesigner Tutorial 1 - Basic Skills Posted by: FrankBergmann
Video duration: 202 seconds This tutorial shows basic skills using JDesigner. For more information also see our website at http://sys-bio.org Related: jdesigner, sbw, tutorials |
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JDesigner Tutorial: Building an Oscillator Posted by: FrankBergmann
Video duration: 302 seconds This tutorial of JDesigner (http://sys-bio.org/ ) shows how to build a more complex reaction network (the brusselator). Includes adding nodes and reactions, changing rate constants, adding user defined rate law and using sliders to study the effect of parameters on the simulation. Related: biology, jdesigner, sbw, sys-bio.org, systems, workbench |
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Jarnac Tutorial 1 Posted by: FrankBergmann
Video duration: 250 seconds This tutorial shows how to create a basic pathway using Jarnac. For more information be sure to check out http://sys-bio.org Related: jarnac, sbw, tutorial |
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JDesigner Tutorial 1 - Basic Skills (part 2) Posted by: FrankBergmann
Video duration: 272 seconds This tutorial shows basic skills using JDesigner. For more information also see our website at http://sys-bio.org Related: jdesigner, sbw, tutorials |
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JDesigner Tutorial 2 - Simple Branch Posted by: FrankBergmann
Video duration: 177 seconds This tutorial shows how to model a simple branch. For more information also see our website at http://sys-bio.org Related: jdesigner, sbw, tutorials |
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JDesigner Tutorial 3 - Simple Cycle Posted by: FrankBergmann
Video duration: 195 seconds This tutorial shows how to model a simple cycle using JDesigner. For more information also see our website at http://sys-bio.org Related: jdesigner, sbw, tutorials |
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JDesigner Tutorial 4 - Bistable Systems Posted by: FrankBergmann
Video duration: 183 seconds This tutorial shows how to model true bistable systems using JDesigner. For more information also see our website at http://sys-bio.org Related: jdesigner, sbw, tutorials |
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JDesigner Tutorial 5 - Oscillators and Sliders Posted by: FrankBergmann
Video duration: 218 seconds This tutorial shows how to build an oscillating model, and how to simulate it using JDesigner. For more information also see our website at http://sys-bio.org Related: jdesigner, sbw, tutorials |
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JDesigner Tutorial: Building a Simple model Posted by: FrankBergmann
Video duration: 180 seconds In this tutorial we show how to build a simple model using JDesigner (http://sys-bio.org ). Related: biology, jdesigner, sbw, sys-bio.org, systems, workbench |
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Jarnac Tutorial 3 Posted by: FrankBergmann
Video duration: 220 seconds This tutorial shows how to model a simple cycle. For more information, see also our website at http://sys-bio.org Related: jarnac, sbw, tutorial |
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Jarnac Tutorial 4 Posted by: FrankBergmann
Video duration: 128 seconds this tutorial shows how to model true bistable systems. For more information be sure to see our website at: http://sys-bio.org Related: jarnac, sbw, tutorial |
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Jarnac Tutorial 5 Posted by: FrankBergmann
Video duration: 131 seconds Reaction Stiochiometry and Oscillators. For more information see also our website: http://sys-bio,org Related: jarnac, sbw, tutorial |
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3D Timecourse Simulation Posted by: FrankBergmann
Video duration: 30 seconds Here a video of a 3D Timecourse Simulation prototype I've created. For more information see: http://public.kgi .edu/~fbergman/Simul ate3D.htm Related: biology, sbml, sbw, systems |
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Jarnac Tutorial 2 Posted by: FrankBergmann
Video duration: 117 seconds This tutorial shows how to model a simple branch. For more information, see also our website at http://sys-bio.org Related: jarnac, sbw, tutorial |
