Main Page
From SynBioSS Wiki
This is the main page for the SynBioSS Wiki. A document describing its design & implementation can be found here.
Contents |
SynBioSS Desktop Simulator
The SynBioSS Desktop Simulator software can be downloaded from Sourceforge.
SynBioSS Designer
The web interface to the SynBioSS Designer can be found here.
A tutorial (with example) to the Designer is provided here and paper discussing the designer and its underlying algorithms is located here.
Getting Started
- To add reactions to a model, visit a particular species' page, such as LacI. To view reactions already added to your model, use the navigation panel on the left.
- Use the search box on the left to find species.
- Need inspiration? You can browse all species or reactions.
- To add species or reactions, use the navigation panel on the left. You must be logged in to add or edit species or reactions.
Examples
You can load some example networks:
- [1] This model is the AND gate of Ramalingam, Tomshine, Maynard, and Kaznessis. The article associated with this sequence has been submitted to Synthetic Biology. Several related NetCDF Files are also provided for download (they can be examined and run in SynBioSS Desktop). Each file describes a different AND Gate promoter configuration:
*[2] TTL NetCDF File (for download) *[3] TLT NetCDF File (for download) *[4] LTT NetCDF File (for download) *[5] LTL NetCDF File (for download)
- [6] This is a model of a bistable switch.
- [7] This model is the oscillator network presented in Tuttle, L. M., H. Salis, J. Tomshine, and Y. N. Kaznessis. 2005. Model-Driven Designs of an Oscillating Gene Network. Biophysical Journal. 89:3873-3883.
- [8] This model is a tetracycline-inducable regulatory network described in Sotiropoulos, V. and Y. N. Kaznessis. 2007. Synthetic tetracyline-inducible regulatory networks: Computer-aided design of dynamic phenotypes. BMC Systems Biology. 1:7.
Bugs?
Please report all bugs or other issues to weed0019(at)umn.edu with the subject "SynBioSS Wiki Bugs".
