Bismark and Primer databases

Spent the day working on a few projects, and documenting things I’d done previously.

Hollie’s bisulfite sequences continue to run on Emu, and should finish by tomorrow so another set of Oly reads can start.

Also began joining the Primer database and Primer location database. Currently have 839 of 1035 correctly labeled, the rest have issues. 81% isn’t bad, but we can make it better!

Oly Project

Moved all samples related to Katherine’s and Jake’s Oly projects from the -20˚ in Rm 209 to the -20˚ in Merlab.  Added the information of where samples can be found (boxes on top of fridge in Rm 213 and -20˚ in Merlab) to the Oly Schematic.

Emu re-resurrected and Shiny frustrations.

Emu lives once more, this time with Ubuntu installed.

Lab Enhancements/Organization

Uploaded the images and data sheets from yesterday’s Oly sampling at Manchester to the GitHub repo. Missing the images from samples 97 and 98 because they were taken on Steven’s phone.

Looked through the boxes in Room 213 that are on top of the refrigerator and attempted to the best of my current knowledge to identify their contents. A spreadsheet of what each box contains can be found here.

Lab enhancements

Working on finding homes for lab supplies and updating the google spreadsheet which details where everything is. I included the -80 room into the lab inventory spreadsheet as that is where the larger containers will be kept for now.

Manchester Oly collection

I labeled most of the collection tubes for the Manchester Oly sampling for Monday (will finish rest tomorrow).

There are five sets of tubes each numbered 97 through 192. In addition to the number, they are labeled with a letter that corresponds to the tissue that will be collected:

A –> adductor muscle

C –> ctenidia

E –> ctenidia in 1.0 ml ethanol

M –> mantle

WB –> whole body.

New computing resources

Spent the day getting two new Xserve blades online, as well as fixing the hard drive in roadrunner.

Shiny and computer frustrations.

Spent the day arguing with X-serve nodes and playing with Shiny for R. Don’t know if it was productive, but we’re a little bit closer to having Roadrunner up again, and a couple more standalone nodes to play with!

Proteomic paper and Oly Schematic

Continuing with citations and formatting of supporting information for the Geoduck proteomic paper.

Also, have a draft of the Oly schematic. There are a couple links in the schematic to other files. the title links to a data descriptor created by Katherine Silliman, and the “Oysters from Fidalgo Bay Outplant” links to a master data sheet from Katherine’s F2 generations.

Unsure of whereabouts for the oysters from Oyster Bay that were brought to UW in Autumn 2015. Also, will continue to modify schematic if any additional information is found to be useful/ links/ etc.

Computer fun

Spent the morning installing VMWare and Ubuntu on hummingbird. Had some issues with being able to rescale the hard drive, still working on a way to prevent that. Afternoon spent trying to get R to work with Jupyter and Docker. Not much luck there.