tinkercell.com
Tutorials - TinkerCell
http://www.tinkercell.com/tutorials-1/stepbystep
Syn Bio. @ UW. Networks, Cells, and Computation. Tutorials are slow videos that allow you to follow along when using TinkerCell. They do not contain audio. For explanations of different TinkerCell features (with audio), see the Demos. Simulate Simple Bistable System. Light-induced System involving two Phosphorylation Steps. Lac operon and bistability. Create New Symbols in TinkerCell. Use WikiDust to Upload Diagrams to Wiki. Simulate Simple Bistable System. This tutorial will show how to create a NOR gat...
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Download - TinkerCell
http://www.tinkercell.com/downloads-2
Syn Bio. @ UW. Networks, Cells, and Computation. Download WikiDust or Script Editor versions of TinkerCell. If first time, you m. Need to restart TinkerCell once). Download Mac installer (image). Mac version is no longer being updated). Download Ubuntu 64-bit version. After downloading, follow these instructions. Download Ubuntu 32-bit version. After downloading, follow these instructions. If you experience problems with installation, please email admin@tinkercell.com. Download Mac installer (image).
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Old videos - TinkerCell
http://www.tinkercell.com/tutorials-1/video-presentations
Syn Bio. @ UW. Networks, Cells, and Computation. Hiding Model inside Enzymatic Reaction. Connecting parts to make genetic network. Simple demo using a module and a cell. Hiding Model inside Gene Regulation Diagrams. Python scripts and genetic network. Dual Feed Forward Network. Flux Balance and Sensitivity Analysis.
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About Plugins - TinkerCell
http://www.tinkercell.com/plugins
Syn Bio. @ UW. Networks, Cells, and Computation. Plugins currently bundled with TinkerCell:. Currently supported languages: Python, Octave, Ruby (linux only), C, C. If you want to make serious changes to TinkerCell and like C , read this document. If you want to create quick scripts and automatically share it between other TinkerCell users, read this document. Install these plugins and keep them up to date using Subversion.
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Screenshots - TinkerCell
http://www.tinkercell.com/screenshots
Syn Bio. @ UW. Networks, Cells, and Computation.
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Join the team! - TinkerCell
http://www.tinkercell.com/join-the-team
Syn Bio. @ UW. Networks, Cells, and Computation. You can be a core developer, extension developer, plug-in developer, idea generator. TinkerCell can use them all. To join the TinkerCell project. Although not active, you may also choose to join the Google Groups. Deepak Chandran: main developer. Herbert M. Sauro: Deepak's PhD advisor. Saurlo lab members ( www.sys-bio.org. Jeff Johnson: developed WikiDust, a python plugin. Arnaud Gelas: assisted with CMake files. Download Deepak's PhD dissertation.
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Cite - TinkerCell
http://www.tinkercell.com/Home/cite
Syn Bio. @ UW. Networks, Cells, and Computation. Deepak Chandran and Herbert M. Sauro. "Hierarchical Modeling for Synthetic Biology. ACS Synthetic Biology 2012, 1(8), pg. 353-364 DOI: 10.1021/sb300033q URL http:/ pubs.acs.org/doi/abs/10.1021/sb300033q. Deepak Chandran, Frank T Bergmann and Herbert M Sauro. "TinkerCell: modular CAD tool for synthetic biology". Journal of Biological Engineering 2009, 3:19 DOI: 10.1186/1754-1611-3-19.
tinkercell.com
Provide Feedback - TinkerCell
http://www.tinkercell.com/suggestions-bugs
Syn Bio. @ UW. Networks, Cells, and Computation.
tinkercell.com
Demos - TinkerCell
http://www.tinkercell.com/tutorials-1/tutorials
Syn Bio. @ UW. Networks, Cells, and Computation. Ring Oscillator (with sound). Hierarchical modeling (with sound). Bsubtilis bistable system (no sound). TinkerCell for drawing parts. Ring Oscillator (with sound). Hierarchical modeling (with sound). Simple Genetic Enzymatic network. OR Gate on a Plasmid. Bsubtilis bistable system (no sound). Building bistable system from B.subtilis. Building and simulating network using Promoters, RBS, etc. Presentation at CSHL (April 2011). TinkerCell for drawing parts.