Team:Newcastle University/Parts Repository

From 2008.igem.org

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==Parts Repository==
==Parts Repository==
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* Entity Relationship Diagram
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=== Outcomes ===
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[[Image:Erd-big.jpg]]
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The work for the Parts Repository (PR) was concluded on 1 Sept 2008.
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==== CellML models ====
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The PR attempts to completely define a "part", which can be any genetically defined construct. These can include BioBrick parts and devices, as well as independently defined objects like the 2-part quorum sensing systems used in the BugBuster project. As such, the behaviour of each part was defined by a [http://www.cellml.org/ CellML model].
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Some of the models are complete, and others are incomplete. It is suggested to compile the models in [http://cor.physiol.ox.ac.uk/ COR] and to run them in [http://www.cellml.org/tools/pcenv/ PCEnv].
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There are also some components, which are the fragments of CellML code that are associated with each part, and fragments to create complete models from these. They appear as they are stored in the parts repository for access by the iGEM project as a whole.
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==== iGEM java programme ===
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This is an interface that allows easy access to the items stored in the PR database without needing knowledge of the database structure. It is written in Java to access via webservices. The javadoc is available.
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==== Part Sequences ====
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The nucleotide sequences for the parts used in the BugBuster project, to further define the function of a part in the part repository.
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==== Parts Repository ====
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The database repository of genetic parts for bottom-up modelling of synthetic biology. Implemented as a Microsoft Access database.
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* [[Team:Newcastle University/Defining Parts|Progress towards defining Parts]]
* [[Team:Newcastle University/Defining Parts|Progress towards defining Parts]]
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[[Image:Erd-big.jpg|thumb|The Entity Relationship Diagram for the parts repository database]]
* [[Image:Characterisation_of_the_comabcde_pathway_in_s.ppt]]
* [[Image:Characterisation_of_the_comabcde_pathway_in_s.ppt]]
* [[Image:Zipped_parts.zip]]
* [[Image:Zipped_parts.zip]]

Revision as of 13:14, 27 October 2008

Bugbuster-logo-red.png
Ncl uni logo.jpg


Newcastle University

GOLD MEDAL WINNER 2008

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


Home >> Original Aims >> Parts Repository

Parts Repository

Aim:

To develop a system that will define the kinds of parts that make up a biological circuit and their behaviour.

Computers do not know any biology. Many of the other projects involve manipulating data without any need to understand its biological meaning. This module is responsible for capturing biological knowledge and how it relates to that data. So the parts that make up a biological system need to be described in a computationally accessible manner. This system will model the parts that make up the biological circuits. Efforts to define parts are already underway in the BioBricks community, and this project will build upon these.

Objectives:

  • to develop a database that stores clear definitions of the components of a genetic circuit, including:
    • sequences
    • important domains
    • abstract model(s)
    • the ontology of component types
    • provenance back to e.g. BioBrick of origin
  • to develop an API that will provide access to the repository in a standard, easily usable manner

Contributors

Lead: Megan Aylward


Outcomes

The work for the Parts Repository (PR) was concluded on 1 Sept 2008.

CellML models

The PR attempts to completely define a "part", which can be any genetically defined construct. These can include BioBrick parts and devices, as well as independently defined objects like the 2-part quorum sensing systems used in the BugBuster project. As such, the behaviour of each part was defined by a [http://www.cellml.org/ CellML model].

Some of the models are complete, and others are incomplete. It is suggested to compile the models in [http://cor.physiol.ox.ac.uk/ COR] and to run them in [http://www.cellml.org/tools/pcenv/ PCEnv].

There are also some components, which are the fragments of CellML code that are associated with each part, and fragments to create complete models from these. They appear as they are stored in the parts repository for access by the iGEM project as a whole.

= iGEM java programme

This is an interface that allows easy access to the items stored in the PR database without needing knowledge of the database structure. It is written in Java to access via webservices. The javadoc is available.

Part Sequences

The nucleotide sequences for the parts used in the BugBuster project, to further define the function of a part in the part repository.

Parts Repository

The database repository of genetic parts for bottom-up modelling of synthetic biology. Implemented as a Microsoft Access database.


The Entity Relationship Diagram for the parts repository database

Screenshots of the Parts Repository Database

Database screen shot.jpg Relationships.jpg Db.jpg