TMT To Do List

Time Sensitive

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

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.
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.
3. Parameter sensitivities are not correct when the sequence section has a continue for 0 statement.
4. Jacobian greatly slows down after ~80 simulations are run from a single script.
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.