8:40a – 6:20p, 11:30p – 12:55a
Goals
- Fix Ph model — neigbhors of neighbors
- in situs day 2
Cell Staining
- Hot washes (20 min, 2x 9 min in oven + 1 min switch)
- 1x SSCT cold wash
- PBT wash
- 45 min lamin-488 stain
- PBS wash
- back to SSC
Ph model
- Problems: Moving any attached molecules as a block doesn’t let flat sheets fold up.
- Aborted development of 131024b Neighbor’s neighbor’s all part of same sheet.
- New approach, single bond at a time
- speeding up simulation: sub2ind is slow, do this instead.
- Attempted merged approach, sometimes trying to move single molecules and sometimes moving all connected molecules. Groups still move slower than I think they should for realistic dynamics
- wrote again to author of “Strings and Binders” paper to ask about algorithm again.
- Contacted SD colleague and Berkeley colleague for suggestions on simulation.
- Need to be able to break bonds rarely (seems to be a fundamental part of the algorithm at least).
MultiStain bead correction
- no method aligns beads
- Try brightfield / phase contrast images.
Mentoring
- Need bench space and reagent space for Bogdan.