Team:Newcastle University/Parts Repository

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Newcastle University

GOLD MEDAL WINNER 2008

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Home >> Original Aims >> Parts Repository

The objectives of this project are:

  • 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

Outcomes

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

Parts Repository

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

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.

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.

CellML models

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.

Download: File:Newcastle-igem2008-CellML-models.zip contains:

  • Alt.promoter.constitutive.cellml
  • Alt.promoter.constitutiveImport.cellml
  • Alt.promoter.inductive.cellml
  • Alt.promoter.inductive3.cellml
  • Alt.promoter.respressive.cellml
  • Alt.protein.cellml
  • Alt.RBS.cellml
  • Bacillus RBS.cellml
  • Basic promoter 2.cellml
  • Basic promoter 3.cellml
  • Basic Promoter.cellml
  • Check comp.cellml
  • CodingRegion.cellml
  • ComD(NoInducSynthWithComEP).cellml
  • ComD.cellml
  • ComDAGAIN.cellml
  • composite2.cellml
  • CompositeModel.cellml
  • constitutive promoter.cellml
  • DNAa.cellml
  • EncodedProtein.cellml
  • example tut3main.cellml
  • example tut3sub..cellml
  • FluxComEP.cellml
  • ftsA.cellml
  • ftsW.cellml
  • HySpank.cellml
  • InitialRBS.cellml
  • minC.cellml
  • NewComD.cellml
  • PbofA.cellml
  • PcotA.cellml
  • Protein.cellml
  • proteinCoding.cellml
  • PspaS.cellml
  • PspollQ.cellml
  • Pxyl.cellml
  • ResponseRegulator.cellml
  • Sensor.cellml
  • Tanscription factor.cellml
  • To join the components together.doc
  • veg.cellml
  • XComDP.cellml
  • zapA.cellml

File:Newcastle-igem2008-CellML-components.zip contains:

  • AgrA.txt
  • AgrC.txt
  • Bind Components.txt
  • CFP.txt
  • Cin-box.txt
  • ComD.txt
  • ComE.txt
  • ConstitutivePromoter.txt
  • DNAa.txt
  • Environment.txt
  • Essentials.txt
  • Footer.txt
  • ftsA.txt
  • ftsW.txt
  • GFP.txt
  • Header.txt
  • HySpank.txt
  • InducablePromoter.txt
  • mCherry.txt
  • minC.txt
  • OptimalRBS.txt
  • P2.txt
  • P3.txt
  • PbofA.txt
  • PbofAmod.txt
  • PcotA.txt
  • PlcA.txt
  • PromoterToRBS.txt
  • Protein.txt
  • PspaS.txt
  • PspollQ.txt
  • Pxyl.txt
  • RBS.txt
  • RBSToCodingRegion.txt
  • RepressablePromoter.txt
  • ResponseRegulator.txt
  • Sensor.txt
  • Units.txt
  • veg.txt
  • XyloseIsomerase.txt
  • YFP.txt
  • YocF.txt
  • YocG.txt
  • zapA.txt

iGEM Java programme

The Java programme requires a level of communication to enable access of the PR to query information. JDBC(TM) was used to provide a connection between the Java code and the repository stored as a Microsoft Access database. Firstly a JDBC-ODBC bridge was installed, then using the ODBC data source administrator, a Microsoft Access driver was set up to access the PR. The sun JDBC driver was used (sun.jdbc.odbc.JdbcOdbcDriver). A Java programme was written to access data from the repository. Once an interface and its relative classes were created, a temporary interface was designed for the interaction of the parts repository and evolutionary algorithm.

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.

Further Reading

Contributors

Lead: Megan Aylward

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