10 A – 11:00 P
Transcription models
- Finished derivation from yesterday on multiple binding
- wrote up in Review, started extension to cooperativity
- Markov Chains in TeX
- write like chemical equations with mhchem package
- Use Tikz drawing package
- Named Graphs (Tikz + add-on packages)
Notebook updates
- SVG upload not supported
- can be overcome by changing mime perimssions: see discussion here
- PJW Mime Config
Chromatin — 405 validation
-
Samples:
- samples 1-2 are 2x Cy5 (back-to-back in the front of the Coplin Jar)
- samples 3-4 are 3x Cy5 (back-to-back in the middle of the Coplin Jar)
- samples 5-6 are 405-primary + 2x Cy5 (in positions 3 and 4 of Coplin Jar)
-
Other gift supplies
- requested emPCR libraries all at 1 ng/uL. Use 2 ng per 10 mL PCR.
- standard yield off a 10mL prep is ~1 nmol.
- Standard use per coverslip ~30-50 pmol. Large use would be 500 pmol.
STORM
- Imaging
Coding
- some updates to ImageShop
- need to remove DaoSTORM and Insight code from repository and re-initialize.
- First attempts following this using the folder name in place of the file name and leaving the folder intact did not work.
Worked
following dnasevic.
First physically removed the folder from the repository and committed the changes to master (locally).
$ git checkout branch master
$ git filter-branch --tree-filter 'rm -rf ./External' HEAD
$ rm - rf .git/refs/original/
$ git reflog expire --expire=now --all
$ git gc --prune=now
$ git gc --aggressive --prune=now
Now move to Alistair
$ git checkout branch Alistair
$ git filter-branch --tree-filter 'rm -rf ./External' HEAD
Gives error: cannot create a new backup. A previous backup already exists in refs/original/.
$ rm -rf .git/refs/original/
$ git reflog expire --expire=now --all
$ git gc --prune=now
$ git gc --aggressive --prune=now
$ git filter-branch --tree-filter 'rm -rf ./External' HEAD
Gives error: .git-rewrite already exists please remove it.
$ rm -rf .git-rewrite
$ git filter-branch --tree-filter 'rm -rf ./External' HEAD