MIBLab:Notebook/Systems and Synthetic Biology./Entry Base

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Project timeline

Jan 2010: -Began work on project

First deliverable: Gain a working understanding of the software tool GenoCAD.

Late Jan 2010: -Began examining IGEM team abstracts from 2009 competitions.

Deliverable: Recreate a single system design from these entries using GenoCAD Issues encountered: Significant number of the necessary parts for these designs were not included in the GenoCAD parts database at that point in time.

Possible workarounds: Creating a custom parts database containing the sequences of these more recent parts.

February 2010:

Shortlist 3 system designs from 2008& 2009 IGEM competitions.

Summarize systems' features and motifs.

Mid-February 2010: Reproduce designs using GenoCAD and available parts.

Issues: GenoCAD does not have any capabilities as a design modeling tool and/or allow for the creating of multi-module, multi-compartmental synthetic system designs.

March 2010: Performed a survey of the available software tools specifically suited to synthetic biology pursuits.

Mid-March 2010: Shortlisted the tools which best suited the following criteria

i) Extensibility

ii) Parts based design/construction

iii) BioBrick Standard compatibility or access

iv) Detailed User Documentation

v) Active maintenance by authors

April 2010:

Proceeded to acquire and become acclimatized with the following tools.

1. Clotho

2. SynbioSS

3. TinkerCell

These tools were subsequently used to recreate the design and/or model the behavior of the following synthetic system.


May-June 2010: Using the tools to recreate the design of and model the synthetic system chosen, the following criteria were used in order to establish the most suitable tool for our purposes.

i) Graphical interface for the construction of gene interaction networks and associated proteins and regulatory elements

ii) The ability to connect via the internet to standard parts repositories containing curated data on all parts within the repositories. This data should include but not be limited to the sequences and effects and controllers of regulatory elements.

iii) Extensibility via user generated algorithms and/or genetic parts.

iv) Parts-based design and modeling process.

v) Model analysis algorithms and/or capabilities to add such algorithms.

June-July 2010

Decided upon the use of TinkerCell as our primary tool based on our assessment criteria. Alb