tinker-cell.blogspot.com

TinkerCell Updates

TinkerCell is a Computer-Aided Design software tool for Synthetic Biology that promotes collaboration through its plugin interface. This blog is used to keep notes on updates to the project. Wednesday, May 30, 2012. Graphs of the Nodes Tree and Connections Tree ontologies. Thursday, December 8, 2011. Running TinkerCell from USB. To store all the settings in a USB drive, do this:. Use Settings - "Export current settings" to export "settings.ini". What exactly is this doing? Careful when using dual-monitor.

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TinkerCell Updates | tinker-cell.blogspot.com Reviews

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TinkerCell is a Computer-Aided Design software tool for Synthetic Biology that promotes collaboration through its plugin interface. This blog is used to keep notes on updates to the project. Wednesday, May 30, 2012. Graphs of the Nodes Tree and Connections Tree ontologies. Thursday, December 8, 2011. Running TinkerCell from USB. To store all the settings in a USB drive, do this:. Use Settings - Export current settings to export settings.ini. What exactly is this doing? Careful when using dual-monitor.

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6 for the code

7 new tutorials

8 coupled oscillator modules

9 sequence annotation widget

10 older posts

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TinkerCell Updates | tinker-cell.blogspot.com Reviews

https://tinker-cell.blogspot.com

TinkerCell is a Computer-Aided Design software tool for Synthetic Biology that promotes collaboration through its plugin interface. This blog is used to keep notes on updates to the project. Wednesday, May 30, 2012. Graphs of the Nodes Tree and Connections Tree ontologies. Thursday, December 8, 2011. Running TinkerCell from USB. To store all the settings in a USB drive, do this:. Use Settings - "Export current settings" to export "settings.ini". What exactly is this doing? Careful when using dual-monitor.

INTERNAL PAGES

tinker-cell.blogspot.com

1

TinkerCell Updates: 12/01/2008 - 01/01/2009

http://tinker-cell.blogspot.com/2008_12_01_archive.html

TinkerCell is a Computer-Aided Design software tool for Synthetic Biology that promotes collaboration through its plugin interface. This blog is used to keep notes on updates to the project. Tuesday, December 30, 2008. The ModuleTool uses a new class of connector called ModuleConnectionGraphicsItem. This connection always uses straight line and contains a merge-handle commmand inside. It does not have a handle. . Subscribe to: Posts (Atom). Click on image for summary. Subscribe in a reader.

2

TinkerCell Updates: 07/01/2009 - 08/01/2009

http://tinker-cell.blogspot.com/2009_07_01_archive.html

TinkerCell is a Computer-Aided Design software tool for Synthetic Biology that promotes collaboration through its plugin interface. This blog is used to keep notes on updates to the project. Sunday, July 19, 2009. Core Editor is designed to be the base class for any coding/scripting widget. It is borrowed from Qt's example set. The AntimonyTool uses libAntimony. To parse the text in the current TextEditor and calls setItems(.) in the current TextEditor upon. Saturday, July 18, 2009. 160;and symbols table.

3

TinkerCell Updates: 01/01/2009 - 02/01/2009

http://tinker-cell.blogspot.com/2009_01_01_archive.html

TinkerCell is a Computer-Aided Design software tool for Synthetic Biology that promotes collaboration through its plugin interface. This blog is used to keep notes on updates to the project. Friday, January 16, 2009. Genetic Networks and Hill Equations. 160;plugin keeps track of how the genetic parts, such as promoters, coding sequence, etc. are moved. Whenever coding parts are placed downstream. 160;of a promoter, the coding parts will receive an Assignment rule. 160;refers to the the activity. Indiv = ...

4

TinkerCell Updates: 03/01/2009 - 04/01/2009

http://tinker-cell.blogspot.com/2009_03_01_archive.html

TinkerCell is a Computer-Aided Design software tool for Synthetic Biology that promotes collaboration through its plugin interface. This blog is used to keep notes on updates to the project. Monday, March 16, 2009. Highlighting and Label items on the screen. The CLabelsTool allows labeling and highlighting (drawing circles) on objects on the screen. It also provides convenient C/Python API functions, allowing C and Python programs to label and/or highlight items on the screen. . Saturday, March 14, 2009.

5

TinkerCell Updates: New Tutorials

http://tinker-cell.blogspot.com/2011/11/new-tutorials.html

TinkerCell is a Computer-Aided Design software tool for Synthetic Biology that promotes collaboration through its plugin interface. This blog is used to keep notes on updates to the project. Thursday, November 10, 2011. Subscribe to: Post Comments (Atom). Click on image for summary. Subscribe in a reader. Simple template. Powered by Blogger.

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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...

tinkercell.com

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).

tinkercell.com

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.

tinkercell.com

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.

tinkercell.com

Screenshots - TinkerCell

http://www.tinkercell.com/screenshots

Syn Bio. @ UW. Networks, Cells, and Computation.

tinkercell.com

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.

tinkercell.com

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.

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TinkerCell Updates

TinkerCell is a Computer-Aided Design software tool for Synthetic Biology that promotes collaboration through its plugin interface. This blog is used to keep notes on updates to the project. Wednesday, May 30, 2012. Graphs of the Nodes Tree and Connections Tree ontologies. Thursday, December 8, 2011. Running TinkerCell from USB. To store all the settings in a USB drive, do this:. Use Settings - "Export current settings" to export "settings.ini". What exactly is this doing? Careful when using dual-monitor.

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