Revision as of 14:54, 25 September 2008

Newcastle University

GOLD MEDAL WINNER 2008

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Workbench

Aims:

The proposed Synthetic Biology Workbench (cool name needed) will incorporate the functionality of a biological network modeling and simulation program along with spiffy new algorithms that can be used in modern synthetic biology. This will enable users to finetune the expression of models suitable for their purposes, particularly for such fun activities like iGEM competitions.

From a previously created repository of parts and devices, and using the (gentle) guidance of a set of assembly parameters, users will be able to create, edit and piece together biological networks at varying levels of complexity. Users will be able to piece together parts, adding ribosome binding sites, protein coding regions, terminators, etc. until they have exactly the device they desire.

Once the biological circuit is ready in principle, it can be put into practice. The user will be able to request the optimal biological circuit, composed from BioBricks from the repository.

Objectives:

get a model
- load from SBML and/or CellML
- create using parts and constraints
show the model
- network view
- basic parts view. Matt suggested being able to view both strands and flip them around.
take in conditions for synthetic evolution and send models to the evolutionary algorithm
output the sequence in a standard format

Contributors

Lead: Morgan Taschuk

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