TMT To Do List

Time Sensitive

• Summarize committee meeting and prepare for meeting with Drew on Tuesday (email him to set up a time)

Wiki

• add multiplier for membrane interactions
• Fus3 phosph/dephosph
• Kss1 phosph/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)

Jacobian Bugs

1. Statistics from parameter estimation fails if there are more than 254 data points.
   • john can't duplicate
2. 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
3. Parameter sensitivities are not correct when the sequence section has a continue for 0 statement.
   • problem identified - will fix it
4. Jacobian greatly slows down after ~80 simulations are run from a single script.
   • John can't duplicate
5. 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)

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)

Other

• Email Roger re microfluidic flow cytometer.
• talk to kirsten about thesis committee meeting