Grace’s Notebook: Tuesday, October 10, 2017

Today I added some hyperlinks to Capstone papers from previous students to the SAFS Capstone page. 

Then, I worked on some Skyline Daily things – working on going through Laura’s and Yaamini’s SRM protocols.


The new power connecter cord came and it’s amazing! I don’t understand why the other design exists.

Things are pretty much set-up now, but I’m unsure how it all works together. So I created some requests to seek out chemicals and supplies to run a test-run of the titrator.


Grace’s Notebook: Monday, October 9, 2017


Worked on the Titrator again… It was very frustrating because everything seemed right, except the Rondolino sample changer would not turn on!

Sam came over and checked it out. He moved the Rondolino to look at the back of it, and when he did that, it worked! The reason is because the power connection got pushed slightly by another cable, which put it in an angle that allowed for it to work! Kind of ridiculous, so Sam contacted Mettler Toledo and a new power connection cable will arrive tomorrow!

SRM Protocols

I continued testing Laura and Yaamini’s SRM protocols. Yaamini hasn’t had a chance to look at it since my last attempt, so I still had an issue with the first step of pasting the FASTA file into the lefthand window of Skyline Daily.

Laura’s is working great! I had a suggestion of perhaps adding some clarification at Step 5, Notebook 01 because I was a little confused when a window didn’t pop up in the order her protocol suggested it would. All the .raw files just downloaded, and I continued, but my final rearranged Skyline window doesn’t look like hers.

Grace’s Notebook: Wednesday, September 27, 2017

Today I tried really hard to get this titrator working. I still have some parts that I’m not sure how to fit together… Here’s what it looks like so far:


I just need to figure out how to get the probe set-up, and how to get the Rondolino to have power… I’ve followed the instructions over and over, but it still isn’t turning on.

Grace’s Notebook: Tuesday, September 26, 2017

The Traceable VWR Digital Thermometer needs a 9-volt battery in order for me to test if it works.

I am unsure how to test if the Accumet Eletrode (Fisher Scientific) pH probe works, because there is no manual, and there is nothing that I can see to plug it into.

Same as above with the Honeywell Probe Analyzer. No manual, no connecting cords…

I put the rest of the supplies from Manchester away, and updated the Roberts Lab Inventory. There are some things I’m not sure what to do with: some bottles of chemicals, a container of oyster shells, and all the empty storage bins.

I put purple tape on the handles of all the tools in the tool bag, and reorganized a little so that all the tools (wrenches, screwdrivers, hammer, etc.) are in the bag and all the smaller things, like the sealants, screws, tape, etc., is in the box.

Then, I unpacked more of the Titrator and read more of the manual. Having a hard time finding the connector cable for the terminal to the titrator…

Grace’s Notebook: Monday, September 25, 2017

Today I sorted through all of the things that Laura brought back from Manchester. When I placed things into new drawers/shelves, I updated the Roberts Lab Inventory . I will test all of the electrical equipment (probes) tomorrow before placing them in a storage location.

Tomorrow I will also work more on unpacking and potentially assembling the new Titrator, since we have a plethora of water quality samples to do!

Grace’s Notebook: Wednesday, September 20, 2017

I was only in today for a couple hours.

I went through this google drive folder (here) to see if any of the images match those in the O. lurida survey paper. They do, but only Figures 2, 3, 4, and 11-13. Figures 2-4 are missing the specifically labeled temperatures that are in the figures in the paper, and the site names are incorrect: they should be Southern, Northern, Hood Canal, and Central. I’m not sure what the resolution is on these images, but we’re trying to get figures that are 600 dpi.

Figures 1, 5-10, and 14 are still missing.

I then tried to work on the problem that occurred at the end of Monday with my blast to GOslim notebook: here. I really am not sure what’s going on, and Sam is trying to help me… but I don’t quite understand. It appears that the joining is working, but visualizing it isn’t working …? I don’t know.

Screen Shot 2017-09-20 at 3.24.52 PM.png

Grace’s Notebook: Monday, September 18, 2017

The Roberts Lab logo stickers arrived today! IMG_4324.JPG


Today, Steven and I checked on the BLAST of cgigas and swissprot that we started on Friday afternoon. It completed the process on Saturday 1:31 AM (took about 7 hrs).

Screen Shot 2017-09-18 at 1.56.48 PM

Next, we used this notebook template: here – to annotate the BLAST output with GOslim terms. I made a copy of the notebook and changed the working directory to my folder on the desktop of Genefish.

Link to my practice notebook: here. Things went well until the last step. Something isn’t allowing for the files to be joined. Created a GitHub issue for input.


Screen Shot 2017-09-18 at 3.01.15 PM

I also started a proteomic data inventory google spreadsheet. Link: Here.