Sunday 02/17/13


  • Finish O/N run of BXC + flank try2 (3D this time).
  • Did not lose TIRF. Did not overfill drive or crash computer (4GB left on hard-drive, 400 written). Copying to new Alistair10. (will move to the new Alistair9 when it gets formatted).
  • Setting up O/N of fab7 + ss
  • using previous run parameters.

System Maintenance

accelerating basic processing

  • Confirm clean finish O/N data analysis on Tuck
  • Try moving Alistair8 onto eSATA connection to Monet: success.
  • Try recording movies directly over the network to Monet: Does not work.

Shuffling files & Reformatting drives

  • Nearly out of data space.
  • Removing RAID from all backed up data to get more disk space.
  • Copying old RAID1 protected data from 4TB drive Alistair5 onto Fantom Green Drive Alistair9 (renamed the new Alistair5 to keep labels and data in order).
  • # Reformat Alistair5 as a 4 TB disk – rename as the new Alistair 9. Move Alistair 9 onto eSATA for analysis.
  • Deleted all windows backups from Buffalo Drive Station. (This is actually a rather nice, quick swappable-docking station for 4 drives. Currently all 1Tb, not sure if this unit will accept 2 Tb drives, but you can buy it that way today.
  • Reformatted as a single 4TB drive, RAID0, named Alistair10.
  • Reformat Alistair3 and 3b? (currently two separate drives on what I think is still a RAID5 formatted Buffalo Drive station).


  • Code is backed up to cloud (GitHub)
  • Lab notebook entries backed up to the cloud (My server)
  • Could do all word doc development in Dropbox, will be backed up to the cloud. Now this is partly true.
  • Could do all final version open-office/powerpoint in Dropbox. Partly true now.
  • Data is now not backed up at all. Could switch to all Buffalo Drive Stations, RAID 5 (with 4 disks allows 75% of total capacity, much better than 50% capacity achieved with RAID on dual drive units. The western digital dual drive units don’t make it easy to swap drives in the first place). Or if we ever get a backed up lab server. Buffalo Drive Station 12TB model is USB 3.0 at $845.00 is ~$70/TB + free shipping. Comparable to FantomGreen 2TB drives currently favored ($60/TB, no RAID options, USB2.0, but more portable).

Embryo Collections

  • Flipped collection cages at 10A: Scm shRNA, Scm, Pc, and Ph mutant, and Esc M/Z mutants.
  • Fixed all plates at 9:00 PM (should have done earlier).
  • Flip plates (11:15P)

Fly work

  • Collect esc virgins and males
  • Flipped Espl[D] and sim[D] into new bottles
  • Df/CyO-Esc and MAT bottle stocks should wait until we see whether we like these crosses
  • Flipped dl, twi and da bottles with fresh hydrated yeast. (original bottles from 2/11 are drying out. added water).
  • mBT x MAT at 29C = viable
  • Pc2 x MAT at 29C none yet
  • Pc3 x MAT at 29C none yet (few flies though)
  • Psc1 x MAT at 29C none yet (few flies)
  • Let’s give them a few more days to lay/hatch/grow
  • PM virgin collection

STORM Analysis

  • would like a better measure of compactness. Some spots have a pretty broad size in terms of all area which have localizations, but a very tight focused center still. Some loci have a much more diffuse structure:

    [portfolio_sideshow size=medium]

What’s a small decondensed arm of the region and what’s background? * should also write a new manual analysis script which shows the conventional, the STORM, the 3D, etc of every ‘candidate’ dot and has curation input to confirm whether it’s a good dot or not. There are still way fewer than the confocal localizations we were scoring (less than 200 in any category).

This entry was posted in Summaries and tagged , , , , , . Bookmark the permalink.