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Newcastle University

GOLD MEDAL WINNER 2008

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Parts Repository

Aims and Objectives

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.

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.

Progress towards defining Parts

The Entity Relationship Diagram for the parts repository database

A screen shot of the populated database

Showing relationships between the Parts and their IDs

Another view of the populated database, with defined functions for parts

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

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.

Contributors

Lead: Megan Aylward

</div>

@@ Line 4: / Line 4: @@
 <div id="maincol">
 ==Parts Repository==
+<html><a name="aims"></html>
-=== Aim: ===
+=== Aims and Objectives ===
 To develop a system that will define the kinds of parts that make up a biological circuit and their behaviour.
@@ Line 11: / Line 11: @@
 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.
 </div>
-=== Objectives: ===
-* to develop a database that stores clear definitions of the components of a genetic circuit, including:
+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
@@ Line 18: / Line 19: @@
 ** 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
+* To develop an API that will provide access to the repository in a standard, easily usable manner
-=== Contributors ===
+<html><a name="outcomes"></html>
-Lead: [[Team:Newcastle University/Megan Aylward|Megan Aylward]]
+== Outcomes ==
--------
-=== Outcomes ===
 The work for the Parts Repository (PR) was concluded on 1 Sept 2008.
+<html><a name="parts-repository"></html>
 ==== Parts Repository ====
 The database repository of genetic parts for bottom-up modelling of synthetic biology. Implemented as a Microsoft Access database.
@@ Line 44: / Line 41: @@
 </gallery>
+<html><a name="part-sequences"></html>
 ==== 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.
+<html><a name="cellml-models"></html>
 ==== CellML models ====
 The behaviour of each part was defined by a [http://www.cellml.org/ CellML model].
@@ Line 148: / Line 146: @@
 * zapA.txt
+<html><a name="java-programme"></html>
 ==== 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.
+<html><a name="further-reading"></html>
 ==== Further Reading ====
 * [[Image:Characterisation_of_the_comabcde_pathway_in_s.ppt]]
 * [[Image:Comd_noinducsynthwithcomep_.zip]]
+<html><a name="contributors"></html>
+=== Contributors ===
+Lead: [[Team:Newcastle University/Megan Aylward|Megan Aylward]]
+</div>
+<div id="sidebar">
+{{:Team:Newcastle University/Template:PostItBox
+|boxtype=bluebox
+|title=Parts Repository
+|detail-text=<ul>
+<li>[[Team:Newcastle University/Parts Repository#aims|Aims and Objectives]]
+<li>[[Team:Newcastle University/Parts Repository#outcomes|Outcomes]]
+<ul>
+<li>[[Team:Newcastle University/Parts Repository#parts-repository|Parts Repository]]
+<li>[[Team:Newcastle University/Parts Repository#part-sequences|Part Sequences]]
+<li>[[Team:Newcastle University/Parts Repository#cellml-models|CellML Models]]
+<li>[[Team:Newcastle University/Parts Repository#java-programme|Java Programme]]
+</ul>
+<li>[[Team:Newcastle University/Parts Repository#further-reading|Further Reading]]
+<li>[[Team:Newcastle University/Parts Repository#contributors|Contributors]]
+</ul>
+|link=}}
+</div>