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| ==Time Sensitive==
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| ==Wiki==
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| *add multiplier for membrane interactions
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| *Fus3 phosph/dephosph
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| *Kss1 phosph/dephosph
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| *Kss1 phosph of Ste11, Sst2
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| *Scoring scheme for trust in given assumption
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| *means of attaching author to assumptions
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| *change naming from specific protein (Fus3, Ste7, etc) to protein family (MAPK, MAPKK, etc)
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| *Ideas on future management
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| *integration with BNG
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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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| ==Paper with Kirsten==
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| *Look over ultrasensitivity papers
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| **what are mechnisms that cause ultrasensitivity, and why isn't pheromone response ultrasensitive
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| *Yildirim model
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| *Kofahl model
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| *What tidbits have I uncovered in model building
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| **Ste5 dimerization is sufficient to help explain published data (more detail). Etc
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| *Email kirsten about Arkin paper. (model discrimination)
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| *mention idea of passing control of wiki to SGD
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| ==Other==
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| *Email Roger re microfluidic flow cytometer.
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| *talk to kirsten about thesis committee meeting
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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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