Team:Edinburgh/Software

From 2008.igem.org

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[http://www.ehmn.bioinformatics.ed.ac.uk/igem/ MGEC: Modeling Genetically Engineered Circuits]
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== Objective ==
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== Software Overview ==
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Make the generating of models for engineered gene circuits easier for Biologist
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== Background ==
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Our software is a drag-droppable web tool for model creation. Through our website, the users can select parts from the MIT registry (and other databases such as RegulonDB) and add them to a modelling basket. Once they add all the parts for a designed circuit and click "check out", a model in SBML format for the circuit will be automatically generated.
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Many software tools (such as Copasi and SimBiology) are available for simulation and analysis of biological circuits using mathematical models. However, most tools require the users to convert a designed circuit into a set of reaction equations for modeling. For Biologists who has no experience on modeling, this process is not straightforward. Therefore we developed a web tool called MGEC (Modeling Genetically Engineered Circuits) to address this issue. Through MGEC, one only needs to tell which genes and promoters are assembled to form their gene circuit, a preliminary model in SBML format will be automatically generated for the circuit. This model can then be analyzed in other software such as Copasi for further improvement.
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Have a try of our software, see here.
 
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== Software Requirements ==
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== Design of MGEC ==
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'''Database'''
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There are some software that can be used to build model, such as copasi, but these softwares need some grammers, which are not convenient for biologists. In our tool, the only thing users need to do is select the parts. Then the model in SBML format will be generated automatically.  
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A key technology used for engineering gene circuit in Synthetic Biology researches and iGEM competition is the recombination of genes with different promoters. Therefore the focus of MGEC is also on the promoters which link the signal, transcription factor with the regulated genes. We developed a database for E. coli promoters which includes the information on:  transcription factor which binds to the promoter, cofactors or other signals which active or deactive the TF, corresponding MIT registry ID (if any) etc.  
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When biologists are trying to build a model, they need to search a lot of information. Our tool has a database, which includes data from all kinds of biodatabases.
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'''Web Interface'''
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A web interface is designed which allows the users to type in the promoter name and the name of the gene which is assembled with the promoter. Many promoter-gene pairs can be input one by one for generating a complex circuit. Alternatively, if a promoter is not in the database, the users can type in directly the name of the transcription factor binding to the promoter.
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== Software Design ==
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'''Model generation'''
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Interface Layer
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For each pair two reaction equations will be generated for the model (In the future version, users will have options to generate model with different set of reactions). One is for the production of the gene product where the corresponding TF is the modifier. Another is for the degradation of the gene product.  Hill equation is used for the kinetic equation of the production process and mass action kinetics for the degradation. Once all the promoter-gene pairs forming the circuit are added, a model in SBML format can be generated by pressing the “Create Model” button.
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Database Layer
 
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Processing layer
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== Features ==
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1. as a web tool, no download required, easy to use than complex software tools
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== Software Test ==
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2. the users can directly type in the MIT registry parts IDs used in their circuit design to build a model. This is especially useful for the iGEM teams.
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3. generating models in SBML format which is supported by over one hundred software tools for model analysis
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4. the users have options to generate models with different complexity for the same circuit (to be completed)
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5. supported by a background database which includes literature based kinetic information (such as kinetic equations and parameter values) for the regulatory parts,  thus allowing users building models based on previously published data. (to be completed)
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== Further improvements ==
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1. currently only support one gene is regulated by one transcription factor through binding in the promoter region.  Support for combination regulation will be added later.
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2. the users still need other software tools for modelling analysis. We are developing a sister website called SBML toolsets which includes functions for SBML model editor, visualization, time course simulation, steady state analysis and parameter sensitivity analysis etc. Through these two site, the users will be able to do all the model related analysis on line.
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3. support for metabolic pathways and signal transduction pathway models will also be added

Revision as of 20:39, 6 October 2008

[http://www.ehmn.bioinformatics.ed.ac.uk/igem/ MGEC: Modeling Genetically Engineered Circuits]

Contents

Objective

Make the generating of models for engineered gene circuits easier for Biologist

Background

Many software tools (such as Copasi and SimBiology) are available for simulation and analysis of biological circuits using mathematical models. However, most tools require the users to convert a designed circuit into a set of reaction equations for modeling. For Biologists who has no experience on modeling, this process is not straightforward. Therefore we developed a web tool called MGEC (Modeling Genetically Engineered Circuits) to address this issue. Through MGEC, one only needs to tell which genes and promoters are assembled to form their gene circuit, a preliminary model in SBML format will be automatically generated for the circuit. This model can then be analyzed in other software such as Copasi for further improvement.


Design of MGEC

Database

A key technology used for engineering gene circuit in Synthetic Biology researches and iGEM competition is the recombination of genes with different promoters. Therefore the focus of MGEC is also on the promoters which link the signal, transcription factor with the regulated genes. We developed a database for E. coli promoters which includes the information on: transcription factor which binds to the promoter, cofactors or other signals which active or deactive the TF, corresponding MIT registry ID (if any) etc.

Web Interface

A web interface is designed which allows the users to type in the promoter name and the name of the gene which is assembled with the promoter. Many promoter-gene pairs can be input one by one for generating a complex circuit. Alternatively, if a promoter is not in the database, the users can type in directly the name of the transcription factor binding to the promoter.

Model generation

For each pair two reaction equations will be generated for the model (In the future version, users will have options to generate model with different set of reactions). One is for the production of the gene product where the corresponding TF is the modifier. Another is for the degradation of the gene product. Hill equation is used for the kinetic equation of the production process and mass action kinetics for the degradation. Once all the promoter-gene pairs forming the circuit are added, a model in SBML format can be generated by pressing the “Create Model” button.


Features

1. as a web tool, no download required, easy to use than complex software tools

2. the users can directly type in the MIT registry parts IDs used in their circuit design to build a model. This is especially useful for the iGEM teams.

3. generating models in SBML format which is supported by over one hundred software tools for model analysis

4. the users have options to generate models with different complexity for the same circuit (to be completed)

5. supported by a background database which includes literature based kinetic information (such as kinetic equations and parameter values) for the regulatory parts, thus allowing users building models based on previously published data. (to be completed)


Further improvements

1. currently only support one gene is regulated by one transcription factor through binding in the promoter region. Support for combination regulation will be added later.

2. the users still need other software tools for modelling analysis. We are developing a sister website called SBML toolsets which includes functions for SBML model editor, visualization, time course simulation, steady state analysis and parameter sensitivity analysis etc. Through these two site, the users will be able to do all the model related analysis on line.

3. support for metabolic pathways and signal transduction pathway models will also be added