Difference between revisions of "TMT To Do List"

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==Jacobian Bugs==
#Statistics from parameter estimation fails if there are more than 254 data points.
#*john can't duplicate
#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.
#*not a bug
#Parameter sensitivities are not correct when the sequence section has a continue for 0 statement.
#*problem identified - will fix it
#Jacobian greatly slows down after ~80 simulations are run from a single script.
#*John can't duplicate
#Inconsistency with parameter variance in statistics of estimation report.
*Get reporter working in glass bottom plate
*Get reporter working in [[Stimulator]]
*Check our microscope camera against molsci's (theirs is Micromax 512BFT)
*Try using poly-Lys instead of ConA
Stimulator paper
*Femlabs model of flow in chip.  Force on cells.
*In Ste2 knockout and Ste2WT cells, see how long aF-fluorescein (David Drubin) takes to wash in and out of cell wall.
*Use different pH to dissociate pheromone faster?
*Hit cells with short (1-10s) dose of pheromone at different doses.  What fraction at what concentrations respond and shmoo or express Pprm1-YFP?
*talk to Jeremy
Time-Dependent Stimulation paper
*Basis/core: identify time varying input timecourses that increase parameter sensitivity
*Perform same number of expts with step inputs and with time-varying input -> fit model in each case and compare parameter uncertainty
*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...).
*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).

Latest revision as of 16:39, 11 September 2007