TMT To Do List: Difference between revisions
From OpenWetWare
Jump to navigationJump to search
(→Wiki) |
No edit summary |
||
Line 28: | Line 28: | ||
*Get reporter working in [[Stimulator]] | *Get reporter working in [[Stimulator]] | ||
*Check our microscope camera against molsci's (theirs is Micromax 512BFT) | *Check our microscope camera against molsci's (theirs is Micromax 512BFT) | ||
*Try using poly-Lys instead of ConA | |||
==Paper with Kirsten== | ==Paper with Kirsten== | ||
Line 42: | Line 43: | ||
*Email Roger re microfluidic flow cytometer. | *Email Roger re microfluidic flow cytometer. | ||
*talk to kirsten about thesis committee meeting | *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 well. | |||
*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? | |||
Time-Dependent Stimulation paper | |||
* |
Revision as of 12:51, 13 August 2006
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)
- 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 well.
- 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?
Time-Dependent Stimulation paper