MIBLab:Notebook/Systems and Synthetic Biology./Entry Base
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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.
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
ii) Parts based design/construction
iii) BioBrick Standard compatibility or access
iv) Detailed User Documentation
v) Active maintenance by authors
Proceeded to acquire and become acclimatized with the following tools.
i) Graphical interface for the construction of gene interaction networks and associated proteins and regulatory elements
iv) Parts-based design and modeling process.
v) Model analysis algorithms and/or capabilities to add such algorithms.
Decided upon the use of TinkerCell as our primary tool based on our assessment criteria. Alb