Team:Minnesota/ProjectComparator

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.

Comparator Project


Control systems are an integral component of almost all aspects of life. Whether it is in industrial, biological, or chemical applications, controllers provide a way to keep systems functioning properly. A vital part of any control system is the comparator. This component compares a set point value and a measured value, and determines which is larger. It then sends the appropriate signal to the rest of the system. In typical applications, this system is electronic. However, our team set out to create a comparator using only genetic components. This comparator could potentially be used as part of a new, solely biological control system that could be used to treat many diseases afflicting humans, for example diabetes. This comparator could compare a diabetics blood sugar to what it should be, and send this result to a control system that could compensate.

In order to undertake this task, a system involving six genes was designed. For our system, the two inputs (one representing the set point and one representing the measured value) are IPTG and aTc. These inputs will activate the transcription of the LacI and TetR proteins, and set in motion the rest of the system to produce the outputs. Depending on the amounts of the two inducer molecules added to the system, either green fluorescent protein(GFP) or red fluorescent protein(RFP) will be produced. The actual design of the system can be seen below. In order to complete this project, a total of six genes will have to be cloned into plasmids, and two new BioBrick parts will be produced. One will be a TetR and p22 mnt dual-repressed promoter, and the other will be a LacI and lambdaphage cI dual-repressed promoter. This project will pave the way for other parts of a true genetic PID controller to be produced, which could be an exciting scientific development in the near future.

Relevant Papers
{| Protocol Papers

Basic BioBrick Design
 * [[Media:BacterialcultureMN.pdf|Bacteria Culture Protocols]]
 * [[Media:PCRtutorialMN.pdf|PCR Tutorial]]
 * [[Media:SubcloningMN.pdf|Subcloning]]
 * [[Media:TransformationsMN.pdf|Transformations]]
 * [[Media:Western_blottingMN.pdf|Western Blotting 1]]
 * [[Media:WesternblotMN.pdf|Western Blotting 2]]
 * [[Media:TransformationsMN.pdf|Transformations]]
 * [[Media:Western_blottingMN.pdf|Western Blotting 1]]
 * [[Media:WesternblotMN.pdf|Western Blotting 2]]
 * [[Media:Western_blottingMN.pdf|Western Blotting 1]]
 * [[Media:WesternblotMN.pdf|Western Blotting 2]]
 * [[Media:WesternblotMN.pdf|Western Blotting 2]]

Combinatorial Promoters Papers
 * [[Media:Biobricks vector designMN.pdf|BioBrick Vector Design Paper]]
 * [[Media:Biobricks vector designMN.pdf|BioBrick Vector Design Paper]]

p22 mnt Papers
 * [[Media:ModularANDgateMN.pdf|Modular AND Gate]]
 * [[Media:CisRegulatoryInputMN.pdf|cis Regulatory Input]]
 * [[Media:CombinatorialpromotersMN.pdf|Combinatorial Promoters]]
 * [[Media:DirectedEvolutionofAraCMN.pdf|Directed Evolution of AraC]]
 * [[Media:CombinatorialpromotersMN.pdf|Combinatorial Promoters]]
 * [[Media:DirectedEvolutionofAraCMN.pdf|Directed Evolution of AraC]]
 * [[Media:DirectedEvolutionofAraCMN.pdf|Directed Evolution of AraC]]
 * [[Media:DirectedEvolutionofAraCMN.pdf|Directed Evolution of AraC]]

Light Sensor Papers
 * [[Media:Mnt01MN.pdf|DNA binding specificity of the Arc and Mnt repressors]]
 * [[Media:Mnt02MN.pdf|Bacteriophage P22 Mnt Repressor]]
 * [[Media:P22mntMN.pdf|The Bacteriophage P22 Arc and Mnt Repressors]]
 * [[Media:Mnt02MN.pdf|Bacteriophage P22 Mnt Repressor]]
 * [[Media:P22mntMN.pdf|The Bacteriophage P22 Arc and Mnt Repressors]]
 * [[Media:P22mntMN.pdf|The Bacteriophage P22 Arc and Mnt Repressors]]


 * [[Media:Chevalier_light_sensorMN.pdf|Chevalier Light Sensor]]
 * [[Media:Young_light_sensor_reviewMN.pdf|Young Light Sensor]]
 * [[Media:Young_UV_light_sensor_caged_IPTGMN.pdf|Young Light Sensor (caged IPTG)]]
 * [[Media:Young_light_sensor_reviewMN.pdf|Young Light Sensor]]
 * [[Media:Young_UV_light_sensor_caged_IPTGMN.pdf|Young Light Sensor (caged IPTG)]]
 * [[Media:Young_UV_light_sensor_caged_IPTGMN.pdf|Young Light Sensor (caged IPTG)]]