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