Team:Minnesota/Project

From 2009.igem.org

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!align="center"|[[Team:Minnesota|<font color="gold">Home</font>]]
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!align="center"|[[Team:Minnesota/Team|<font color="gold">The Team</font>]]
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!align="center"|[[Team:Minnesota/Project|<font color="gold">The Project</font>]]
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!align="center"|[[Team:Minnesota/Parts|<font color="gold">Parts Submitted to the Registry</font>]]
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!align="center"|[[Team:Minnesota/Modeling|<font color="gold">Modeling</font>]]
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!align="center"|[[Team:Minnesota/Notebook|<font color="gold">Notebook</font>]]
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|You can write a background of your team here.  Give us a background of your team, the members, etc.  Or tell us more about something of your choosing.
|You can write a background of your team here.  Give us a background of your team, the members, etc.  Or tell us more about something of your choosing.
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!align="center"|[[Team:Minnesota|<font color="gold">Home</font>]]
 
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!align="center"|[[Team:Minnesota/Team|<font color="gold">The Team</font>]]
 
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!align="center"|[[Team:Minnesota/Project|<font color="gold">The Project</font>]]
 
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!align="center"|[[Team:Minnesota/Parts|<font color="gold">Parts Submitted to the Registry</font>]]
 
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!align="center"|[[Team:Minnesota/Modeling|<font color="gold">Modeling</font>]]
 
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!align="center"|[[Team:Minnesota/Notebook|<font color="gold">Notebook</font>]]
 
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Revision as of 17:23, 3 June 2009

Home The Team The Project Parts Submitted to the Registry Modeling Notebook
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Team Example 2





Contents

Computational Tools

Both Designer and Wiki can be found via the SynBioSS home page.

SynBioSS Designer

SynBioSS Designer is an application for the automatic generation of sets of biomolecular reactions. This software allows a user to input the molecular parts involved in gene expression and regulation (e.g. promoters, transcription factors, ribosomes, etc.) The software then generates complete networks of reactions that represent transcription, translation, regulation, induction and degradation of those parts. To facilitate the creation of detailed kinetic models of synthetic gene networks composed of BioBricks, we have adapted SynBioSS Designer to automatically generate a kinetic model from a construct composed entirely of BioBricks. A NetCDF or SBML file is generated for simulations.

SynBioSS Wiki

The inaccessibility of requisite kinetic data complicates the generation of detailed mechanistic models. We address this barrier by creating a web accessible database curated by users in a “Wiki” format. SynBioSS Wiki is a significant extension of the open-source Mediawiki software. The Wiki stores reaction kinetic data in a formatted and searchable scheme with references to the relevant literature. This framework allows for the input of reactions whose rates are described either by elementary first & second order rate equations or any arbitrarily complex rate equation defined using MathML (e.g. Hill type reactions). Reactions may be searched via participating molecules which may be proteins, DNA sequences, small molecules, etc. Once located, reactions of interest (along with their associated kinetic data) may be collected. The completed model may be exported in SBML format for additional editing or simulation.

It is also through the SynBioSS Wiki databases that SynBioSS Designer can access and proliferate kinetic information related to the simulation of BioBricks, thus extending the utility of the database for the benefit of the greater modeling community. To jumpstart the process, we have entered the known biomolecular interactions in the expression and regulation of well-studied operons, such as the lactose, the tetracycline and the arabinose operons.


The Experiments

Part 3

Results