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Andrew's "ongoing work" record for the P2011 clock model. Many different versions, with annotations made during SBSI development in 2011-2013 - see version records.

Version Comments

Corrected m1 parameter and range, tested in SBSI

Andrew's "ongoing work" record for the P2011 clock model. Many different versions, with annotations made during SBSI development in 2011-2013 - see version records.Version Comments Derived from PLM_67v3 - LDLL transition at 314h, with wider parameter ranges, as used in LDLL_run2 - but with one modification in Copasi, to cL_m degradation to ensure light rate > dark rate. Value of m1 previously 0.54, now 0.3. Simulation in Copasi was identical.

Copasi file also attached. Originally submitted to ...

Andrew's "ongoing work" record for the P2011 clock model. Many different versions, with annotations made during SBSI development in 2011-2013 - see version records.Version Comments PLM_67v3 model, with TWO stepfunctions. Simulates fine but as of 21 March 2013 did not optimise.

Step2 is usually off because amplitude=0, but can produce LD-DD transition at 262h. To do so, initiate with amplitudeStep1=0 and amplitudeStep2=1.

NB the step1 will still go to LL at 314h, so need to stop DD costing before ...

Andrew's "ongoing work" record for the P2011 clock model. Many different versions, with annotations made during SBSI development in 2011-2013 - see version records.

Version Comments

PLM_67v2 set up for LDLL transition at 314h, with wider parameter ranges for most parameters. This is the model file used in LDLL_run2.

Andrew's "ongoing work" record for the P2011 clock model. Many different versions, with annotations made during SBSI development in 2011-2013 - see version records.Version Comments Version 2 is the 'public' version with the StepFunction, PLM_64v4. For some reason this was crashing SBSI, but was then cleaned up by passing through Copasi. Thus the file name of this version was Arabidopsis_clock_P2011_exCopasi.xml

This version should be suitable for SBSI optimisation to LD-LL data sets, because it ...

Andrew's "ongoing work" record for the P2011 clock model. Many different versions, with annotations made during SBSI development in 2011-2013 - see version records.

Originally submitted to PLaSMo on 2012-05-31 22:18:27