Team:Newcastle University/Software

From 2008.igem.org

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{{:Team:Newcastle University/Template:UnderTheHome|page-title=[[Team:Newcastle University/Software|Software]]}}
{{:Team:Newcastle University/Template:UnderTheHome|page-title=[[Team:Newcastle University/Software|Software]]}}
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Our software consists of four main modules which communicate via Web services. One person was Lead Developer for each module, but the developers worked in the same lab, and had frequent formal and informal discussions in order to develop software which works together and provides the necessary functionality.
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Our software consists of four main modules, each providing distinct functionality. These communicate with each other, and with external applications, via Web services. One person was Lead Developer for each module, but the developers worked in the same lab, and had frequent formal and informal discussions in order to develop software which works together and provides the necessary functionality.
==Components==
==Components==
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[[Image:Ncl-software.png|thumb|left|500px|Schematic of the components of the software system. The workbench contains parts provided by the parts repository, and constraints provided by the constraints repository. Parts are selected by the user to create an initial structure for the genetic circuit.  Constraints define whether these parts can fit together. The workbench outputs this user defined structure to the evolutionary algorithm, which evolves the circuit by requesting different parts from the parts repository, and generates a fitness value of the mutated circuit using values provided by the constraints repository. Using part model s provided a composite model could be formed. The fittest composite model is output to the model to sequence converter, which uses the parts to derive the sequence of the construct and how they fit together to give an overall nucleotide sequence.]]
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[[Image:Ncl-software.png|thumb|left|500px|Schematic of the components of the software system. The workbench contains parts provided by the parts repository, and constraints provided by the constraints repository. Parts are selected by the user to create an initial structure for the genetic circuit.  Constraints define whether these parts can fit together. The workbench takes a user defined structure, together with a desired behavior, and presents this to the evolutionary algorithm. The evolutionary algorithm evolves potential solutions, starting with the provided structure. It generates a range of potential solutions by requesting different parts from the parts repository, assembling them according to information retrieved from the constraints repository, and assessing the fitness value of the mutated circuit based upon how well this satisfies the objective. Once an acceptable regulatory network has been discovered, this model is sent to the model-to-sequence converter, which uses the parts to derive a DNA sequence that encodes the necessary behaviour, while satisfying sequence constraints, such as avoiding long duplicate regions, or low-complexity regions.]]
===Workbench (Morgan)===
===Workbench (Morgan)===
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===Parts Repository (Megan)===
===Parts Repository (Megan)===
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The Parts Repository stores information from the literature and various databases about biological parts such as promoters, ribosomal binding sites and protein coding regions.
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The Parts Repository stores information from the literature and various databases about biological parts such as promoters, ribosomal binding sites and protein coding regions. As well as biological information, this includes fragments of CellML that facilitate incorporation of the part into a larger simulation.
'''[[Team:Newcastle University/Parts Repository|Parts Repository]]'''
'''[[Team:Newcastle University/Parts Repository|Parts Repository]]'''
===Constraints Repository (Nina)===
===Constraints Repository (Nina)===
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The Constraints Repository stores information about how parts work together, and associated parameters such as binding affinities, POPS, etc., where these are known. Populated from the literature and hard-won knowledge from advisors.
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The Constraints Repository stores information about how parts work together, and associated parameters such as binding affinities, POPS, etc., where these are known. This was populated from the literature and by extracting hard-won knowledge from advisors.
'''[[Team:Newcastle University/Constraints Repository|Constraints Repository]]'''
'''[[Team:Newcastle University/Constraints Repository|Constraints Repository]]'''

Revision as of 17:52, 29 October 2008

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Newcastle University

GOLD MEDAL WINNER 2008

Home Team Original Aims Software Modelling Proof of Concept Brick Wet Lab Conclusions


Home >> Software

Our software consists of four main modules, each providing distinct functionality. These communicate with each other, and with external applications, via Web services. One person was Lead Developer for each module, but the developers worked in the same lab, and had frequent formal and informal discussions in order to develop software which works together and provides the necessary functionality.

Components

Schematic of the components of the software system. The workbench contains parts provided by the parts repository, and constraints provided by the constraints repository. Parts are selected by the user to create an initial structure for the genetic circuit. Constraints define whether these parts can fit together. The workbench takes a user defined structure, together with a desired behavior, and presents this to the evolutionary algorithm. The evolutionary algorithm evolves potential solutions, starting with the provided structure. It generates a range of potential solutions by requesting different parts from the parts repository, assembling them according to information retrieved from the constraints repository, and assessing the fitness value of the mutated circuit based upon how well this satisfies the objective. Once an acceptable regulatory network has been discovered, this model is sent to the model-to-sequence converter, which uses the parts to derive a DNA sequence that encodes the necessary behaviour, while satisfying sequence constraints, such as avoiding long duplicate regions, or low-complexity regions.

Workbench (Morgan)

The Workbench is a graphical front end that allows circuits to be designed by hand, using drag-and-drop of icons, and drawing upon the Parts Repository and the Constraints Repository. The designed circuits can then be sent to the EA to be further refined.

Workbench

Parts Repository (Megan)

The Parts Repository stores information from the literature and various databases about biological parts such as promoters, ribosomal binding sites and protein coding regions. As well as biological information, this includes fragments of CellML that facilitate incorporation of the part into a larger simulation.

Parts Repository

Constraints Repository (Nina)

The Constraints Repository stores information about how parts work together, and associated parameters such as binding affinities, POPS, etc., where these are known. This was populated from the literature and by extracting hard-won knowledge from advisors.

Constraints Repository

Evolutionary Algorithm (Mark)

The EA takes parts from the Parts Repository, assembles them randomly, but using constraints from the Constraints Repository, and evaluates the "fitness" of the resulting circuit depending on a desired input:output mapping. Equivalent parts with different parameters are swapped in and out at random, and fitter circuits selected in an iterative manner.

Evolutionary Algorithm


Download

The software for the above projects is available on the Synthetic Biology at Newcastle homepage. Due to the size of the projects, they could not be placed on the iGEM wiki.

Lab Journal

Combined Dry Lab Journal