Thursday, March 10, 2011

Converting models to English

The semantics used in TinkerCell allows conversion of a model into plain English. The Export menu has this feature. Below is an example:

Model:



English export:

transcription factor (repressor) LacI represses repressor binding site (target) lac_op
transcription factor (repressor) TetR represses repressor binding site (target) tet_op
coding (template) gfp_gene produces reporter (product) GFP
molecule (inhibitor) IPTG inhibits transcription factor (target) LacI
molecule (inhibitor) aTc inhibits transcription factor (target) TetR
coding (repressor) gene represses repressor binding site (target) op3

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