TMT To Do List

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(Experimental)
Current revision (18:39, 11 September 2007) (view source)
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==Jacobian Bugs==
 
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#Statistics from parameter estimation fails if there are more than 254 data points.
 
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#*john can't duplicate
 
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#When running estimation from script, you can't specify which parameter to estimate (parameter number can't be a variable), wheras when running estimation block directly, parameter number can be a variable.
 
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#*not a bug
 
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#Parameter sensitivities are not correct when the sequence section has a continue for 0 statement.
 
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#*problem identified - will fix it
 
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#Jacobian greatly slows down after ~80 simulations are run from a single script.
 
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#*John can't duplicate
 
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#Inconsistency with parameter variance in statistics of estimation report.
 
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==Experimental==
 
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*Get reporter working in glass bottom plate
 
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*Get reporter working in [[Stimulator]]
 
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*Check our microscope camera against molsci's (theirs is Micromax 512BFT)
 
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*Try using poly-Lys instead of ConA
 
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==Papers==
 
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Stimulator paper
 
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*Femlabs model of flow in chip.  Force on cells.
 
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*In Ste2 knockout and Ste2WT cells, see how long aF-fluorescein (David Drubin) takes to wash in and out of cell wall.
 
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*Use different pH to dissociate pheromone faster?
 
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*Hit cells with short (1-10s) dose of pheromone at different doses.  What fraction at what concentrations respond and shmoo or express Pprm1-YFP?
 
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*talk to Jeremy
 
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Time-Dependent Stimulation paper
 
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*Basis/core: identify time varying input timecourses that increase parameter sensitivity
 
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*Perform same number of expts with step inputs and with time-varying input -> fit model in each case and compare parameter uncertainty
 
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*Systematically look at different mutants (aF/Ste2, Sst2 deletion/overexpression, Ste2 overexpression, ...), and use of different potential outputs (if we could directly observe state of G protein then...., if we could measure nucleotide hydrolysis rate...).
 
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*Examine full pathway and other parts of pathway (MAPK cascade) using potential inputs (Ste11 kinase inhibitor, Fus3 kinase inhibitor), and outputs (Fus3 phosphorylation, Dig2/Ste12 FRET, gene expression).
 

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